SciScore for 10.1101/2022.03.11.22272259: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Our study has some limitations. Firstly, the study was single-centred which limits the extent of our results. Secondly, being a retrospective study, procedures and therapeutic strategies may have changed during the study period. Nonetheless, we feel we have provided a generalizable pipeline that may be applied to various datasets to identify patients with different outcomes and therapeutic sensitivity.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.12.22271872: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

There are several caveats to our model predictions. First, we use an age-contact structure derived from European data in our model; although some local data exist from South Africa, the fit of the model using these data was not as good (not shown). This study uses a short duration of RSV immunity (150 days), on the basis of it producing an optimal model fit to pre-pandemic data, as information on this parameter is scarce. In order to test the validity of this parameter, immunity was varied between 2-24 months (Appendix II). For immunity lasting beyond 150 days, the model overestimated the length of the typical RSV season in South Africa. Further, the model used does not distinguish between primary and secondary infections in relation to transmissibility and severity. We assume instead that age is the primary predictor of whether an infection will result in hospitalization. By fitting the age-structured model to age-structured observations, we show that the model predicts the distribution of hospitalizations among the studied age groups with confidence. We additionally conduct a sensitivity analysis by fitting a time-series SIR (TSIR) model which assumes a fully immunizing infection (lifelong immunity) to observed data [24]. Using the TSIR model we predict that the outbreak will occur earlier than typical and be about 3 times larger than average at the peak of infection [Appendix III]. Comparison between the two models suggest that the age-structured short-term immunity SEIRS ...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22272276: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

This study also has some limitations. First, we were unable to identify the strain of the infections, meaning that we could not dissect differences between the delta and omicron variants that were both dominant at different points in our study; however, more than 90% of the breakthrough infections in our post-booster analysis occurred after omicron became dominant in the UK, suggesting it largely captures the effects of that variant. Second, with very few hospitalisations, we did not have the power to assess risk factors for different levels of disease severity in vaccinated individuals. Third, as a self-selected cohort, several groups—including people younger than 30 years, people of lower socioeconomic status, and non-White ethnic groups—are under-represented in COVIDENCE UK. Lack of representativeness is not necessarily a barrier to valid scientific inference, however.37 Fourth, as with any observational study, it is possible that some of the associations we report can be explained by residual or unmeasured confounding; we have attempted to minimise this by adjusting for a comprehensive range of potential risk factors for infection, made possible by the large number of breakthrough infections recorded in our study (ie, >30 events per variable in each fully adjusted model). Finally, we explored several potential associations and cannot exclude the possibility that some achieved statistical significance as a result of type 1 error; however, by including the same predictors i...

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04330599</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Longitudinal Population-based Observational Study of COVID-1…</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.13.22272311: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: Thank you for sharing your code.

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22271912: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

(as this was not possible) Limitations: It has been suggested that the minimum sample size for external validation should be at least 100 events and 100 non-events. [35] The Leiden cohort had 41 deaths, falling below the number suggested by this rule of thumb. The sample size of the Lombardy cohort was acceptable for external validation. However, the Lombardy cohort consisted of patients that were enrolled in the first months of 2020. After this period, the incidence COVID-19 related mortality has changed a lot due to many treatment changes. This limits the applicability of the recalibrated 4C risk score as the population in which the scores were recalibrated may not be representative of the current patient population in 2022. Furthermore, some patients who were already very ill before being hospitalized for COVID-19 would have chosen to receive end-of-life care at home. Despite not dying in the hospital (in-hospital mortality was the study outcome), the 4C mortality score would have assigned these patients a very high predicted in-hospital mortality risk. This will have reduced the model performance (especially model discrimination), depending on the proportion of patients that received end-of-life care at home. Lastly, missing data may have influenced model performance. For example, the oxygen saturation on room air (a predictor in the 4C mortality score) was missing in more than half of all patients in both the Lombardy cohort and the Leiden cohort. This is most likely bec...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22272264: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Limitations: Symptom status only captures self-reported symptoms before or at diagnosis and may not always be related to the subsequent SARS-CoV-2 diagnosis. Three persons reported a symptom onset > 10 days before diagnosis. Some asymptomatic persons may have later become symptomatic. Prior infections > 90 days only included confirmed infections reported in the medical records. There likely are missed prior infections that occurred during breaks or before routine screening was implemented at the university in Fall 2021. The PCR CT value was only measured at diagnosis. Some CT values were missing due to external tests or RAT. Our study population, primarily 18-22 year old students, may not be representative of the general population due to their youth and likely lower rate of comorbidities. However, it is unlikely that older age groups or those with higher comorbidity rates would experience shorter isolation durations. We do not have a full medical history for our study population, and it is possible that some persons may experience longer isolations due to medical conditions. There could be changes in staff accuracy over time in reading RAT results, which are qualitative in nature, although their training procedures render this less likely. We do not have RAT data for days 1-4 and accounted for this interval-censoring in our analysis. RATs have a lower sensitivity than PCR, reducing the risk that a non-infectious person would remain in isolation but increasing the risk of a f...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.13.22272176: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

However, we also acknowledge the weaknesses of our study. Our data are generated by a volunteer citizen-science initiative delivered through an app, with the CSS cohort more likely to be of White Caucasian ethnicity and higher family socioeconomical status than the overall UK population 14. By virtue of UK government policy timing and age-tiered approach, our study was restricted to considering single-dose vaccination with BNT162b2 in CYP aged 12-17 years; our results may not apply to other vaccines or in younger age- groups. Our study was conducted with the prevailing SARS-CoV-2 variants Delta and Omicron; the impact of vaccination (both effectiveness and durability) and the profile of post-vaccination COVID-19 might differ with other variants. Indeed, the durability of vaccine protection against Omicron beyond 3 months in our cohort remains to be determined, due to insufficient data, noting here the ability to assess vaccination effectiveness in CYP naïve to SARS-CoV-2 is dwindling rapidly, given widespread infection in the community, particularly CYP. Vaccinated CYP were also much more likely to be tested for SARS-CoV-2 than unvaccinated CYP, for reasons that we are unable to determine. Our data do not allow determination of causal variants for CYP testing positive either post- or prior to vaccination: we can only infer likely variant based on population prevalences at time of testing. Vaccination can attenuate viral RNA shedding 29; this might result in the overestimation...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22272185: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

However, it is also well recognised that blood donors are a selected population, a limitation of using these samples. Blood donors tend to be healthier, may generally have a higher average income and education, and may also be at lower risk of COVID-19 infection than the general population [18, 19]. To help address this bias, we collected residual specimens using a sampling approach that stratified based on case notification data to provide broad representation across the metropolitan Melbourne populations at risk of COVID-19. While our seroprevalence estimates were broadly consistent with corresponding relationships observed for notified cases, the patterns were not as pronounced. Of note, the ratio between the high and low incidence strata was 5.9-fold based on notified cases but only 1.5-fold based on seroprevalence. Similarly, the ratio between the lowest and highest socioeconomic quintiles was 3.4-fold based on notified cases, but only 1.6-fold based on seroprevalence. A previous study that used routine notification data to inform sampling to estimate seroprevalence in a single urban area in Houston, Texas, found a much greater divergence in seroprevalence between areas with high (18%) and low (10%) case notifications and between demographic groups known to be disproportionately affected by the pandemic. Overall seroprevalence in the city was 14%, suggesting extensive community transmission. The Houston study employed a random sampling approach of the general population ...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22272269: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Our study had several strengths and limitations. Some of the sex-specific effects observed were differences among males that were absent among females, without statistical evidence of a sex difference (i.e., non-significant sex interaction terms) [45]. It is important to note that our findings were generated from post-hoc analyses that were not necessarily powered to investigate sex differences, and conclusions are limited by small samples sizes in certain sub-groups. Given the small sample sizes, it is not surprising that statistically significant sex differences were not consistently observed. Particularly for age-based analyses, however, the consistency of trends between assays and timepoints, coupled with statistically significant sex differences in the effect of aging at 3M_PD2, lend credibility to the conclusion that the effects of age on antiviral antibody responses are driven by males. Further supporting these findings are similar sex-specific effects of age observed following seasonal influenza vaccination in both younger and older adults [17, 46]. While it is important to not over-interpret ‘within-sex’ differences as ‘between-sex’ differences [47], there is considerable value in studying differences within males or feamles [48, 49]. This is particularly true given the uniqueness of the community-dwelling older adult cohort, which represent the ‘oldest’ old subset, and are distinct from the population of long-term care facility residents that has been the focus of m...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22272140: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Another limitation is that the data do not allow estimation of variant-specific VE. As a surrogate we stratified the analysis by calendar time and used sequencing data to show which variant dominated each quarter. Due to the recent emergence of Omicron, its effect on VE in Finland can only be studied in the latest quarter. However, to provide timely estimates supporting policy makers, we ended the study prematurely before the end of the quarter reducing the statistical power of this particular analysis.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.12.22272300: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.13.22271253: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.12.22272083: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: Thank you for sharing your data.

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22272153: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

As a limitation of our study, we recognize that we had a small sample size in some vaccine groups such as Ad5-nCoV; however, to the best of our knowledge, there is no other study where this type of vaccine has been compared to other types of vaccines in a real-world setting. It will be of interest to follow the IgG titers for a longer period and to evaluate the effect of heterologous combinations of these vaccines. This comparative study of vaccine types shows positive immunogenicity and seroconversion of BNT162b2 mRNA, mRNA-1273, Gam-COVID-Vac, Coronavac, ChAdOx1-S, Ad5-nCoV, and Ad26.COV2. The highest IgG response was for the mRNA vector vaccines and the lower for the inactivated vaccine. Women and young individuals developed more AEs. In the naïve SARS-CoV-2 cohort, the vaccines Gam-COVID-Vac, Coronavac, and ChAdOx1-S were related to fewer AEs after the second dose of BNT162b mRNA. For patients who received Gam-COVID-Vac, higher antibody levels after the second dose were related to a greater number of AEs. In people previously exposed to SARS-CoV-2, those receiving Gam-COVID-Vac showed a greater number of AEs than BNT162b mRNA, while subjects receiving Coronavac showed significantly fewer events when compared to BNT162b mRNA. In general, an increase in antibody levels was related to AEs.

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT05228912</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Immunization of 7 Different Vaccines Against SARS-COV-2 Acro…</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272177: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

No key resources detected.

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Our study has limitations. We have observed a slow decline in response rates since the beginning of the study, from approximately 30% returning swabs with valid RT-PCR test results in round 1 (1 May to 1 June 2020) to 12.2% in round 17 (5 to 20 January 2022). To improve response rates and make the study more representative we included a small monetary incentive in round 18 among those aged 13 to 44 years, following a successful pilot. This had the result of more than doubling response rates at these ages, giving an overall response rate of 15.0%. We used rim weighting to correct the sample to the characteristics of the base population16. Unlike in previous rounds, the rim weighting correction led to only small changes in round 18 between the unweighted and weighted prevalence, reflecting the improved representativeness of the obtained sample. In conclusion, we report continued high prevalence of SARS-CoV-2 infections during February 2022 as the Omicron wave in England has persisted. The ongoing replacement by BA.2 of other Omicron sublineages demonstrates a transmission advantage for BA.2 which may be contributing to the high rates of infection, alongside the opening up of society as all domestic legal restrictions related to COVID-19 in England were lifted. Of some concern is the recent uptick in hospitalisations in England which may reflect the level or increasing rates of infection in older people in the most recent data. Continued surveillance of infection and hospitalisa...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22272263: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Limitations include the fact that genome sequencing was not employed in contact tracing for any of these cases. Cases that did not engage with the national contact tracing system and those that did not report an interaction with a dental setting will not have been picked up. Contact tracing also relies on recall of individuals and for cases to be well enough to take part. Some cases experiencing the worst symptoms and morbidity associated with COVID-19 will not have been able to partake fully or at all in contact tracing reducing ability to break chains of transmission. Cluster and outbreak locations were not visited by DPH to assess the measures in place but instead relied upon what was reported by local management teams. The DPH team took the opportunity to constantly reflect using regular team huddles to debrief, share learning and ask questions. Reactive trouble shooting huddles took place via MS TEAMS daily. Use of a shared folder for documenting actions on cases and maintaining case notes provided ease of handover between staff working remotely. The DPH team were well place due to existing networks that straddle both public health and dentistry. The findings from this paper would likely be comparable with other areas of Scotland or the UK where similar contact tracing processes were in place.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.13.22272304: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

The goal is to better understand the scope and limitations associated with the QTA process when considering a single sewershed under different normalization modes, parameters and metrics. Note that the detailed analysis of Lv and Lvb normalizations are provided in the Supplement but summarized and discussed here. Figure 3 shows the Ashbridges Bay WWTP sewershed, overlay plot of the wastewater virus signal (WVS) for PMMoV normalized N1 viral viral concentration (Cvb) (upper right panel) and the cases by reported date (lower right panel) as demonstrated on the Ontario Dashboard. The corresponding aggregated data sets were used to generate trends as part of the QTA under the different normalizing conditions (unnormalized, Cvb, Lv, Lvb), respectively. 3.1.1. PMMoV Normalization (Cvb) and Cases by Reported Date: Figure 4 provides the longer-term QTA of clinical cases by reported date and the PMMoV-normalized wastewater viral concentration from March 21/21 to August 22/21. Table 4 summarizes the trend results with the 95% confidence interval (CI) and Table 5 provides the interpretations based on the PHAC interpretations given in Table 2. The standard errors (SE) associated with the estimated breakpoint and trend slopes for both the CCC and WVS, for each time interval, are provided in Tables 6 and 7, respectively. This is an example of the complete QTA 2-page model report for the WVS metric that may be used directly to inform public health decisions. 3.1.2. PMMoV Normalization (Cvb)...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.13.22272308: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

This study has limitations. With the lower severity of Omicron infections20 and the young population of Qatar15,21, case numbers were insufficient to estimate the duration of protection against COVID-19 hospitalization and death for each subvariant separately. BA.1 and BA.2 ascertainment was based on proxy criteria, presence or absence of an S-gene “target failure” using the TaqPath PCR assay (Methods), but this method of ascertainment is well established not only for Omicron subvariants, but also for other variants such as Alpha22-24. Some Omicron infections may have been misclassified Delta infections, but this is not likely, as Delta incidence was limited during the study duration (Methods). Vaccine protection was assessed for only several months after the second dose, and only several weeks after the booster dose. Longer-term protection against symptomatic infection and COVID-19 hospitalization and death remain uncertain. Vaccine effectiveness reached small but statistically significant negative values at 7 months or more after the second dose. Negative estimated effectiveness likely reflects an effect of bias and not true negative biological effectiveness. This bias may have risen from vaccinated persons having a higher social contact rate or adhering less to safety measures than unvaccinated persons25-27. With the high vaccine coverage among adults in Qatar (>85%)13, this bias may have also risen because the reference group of unvaccinated individuals included mainly ch...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22272282: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272081: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Strengths and Limitations: This interim analysis of the UKILD Post-COVID study is the largest assessment of ILDam in patients hospitalised for COVID-19 to date, and the findings are consistent with findings from a number of smaller studies that demonstrate persistent radiological patterns and impaired gas transfer during extended follow-up of patients with COVID-19.[20-24] For participants in receipt of a clinically indicated but unscored CT, we observed that 67/335 (20.0%) people were in moderate to very-high risk strata (sensitivity 57/238, 24.0%), which was similar to the percentage of CT scans with radiological patterns suggestive of fibrosis within the first year post-hospitalisation estimated in meta-analysis (29%; 95%CI 22% to 37%).[25] The UKILD long-COVID cohort excluded participants with any evidence of ILD prior to hospitalisation, and we used informative sceptical priors and power priors for more conservative estimates, which continued to suggest a substantial burden of Post-COVID ILDam. The approach we report can be reasonably applied to later follow-up, with current findings used as informative priors for updating Bayesian inference. Whilst included CTs were assumed to be representative of clinically indicated radiology, this is limited by local management protocols and timing of services, which increases chances of selection and ascertainment bias. Furthermore, individuals with linked CT may have unrecorded pre-existing disease or present with radiological patt...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22270766: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Despite the many compelling and significant findings of our work, there are still a few limitations to be noted. First, the sample size we used is relatively small, and the limited sample size limits the statistical power for identifying rare variants. More studies with large sample sizes are demanded to validate our results and uncover more candidate variants. Second, even though our work has suggested several candidate genes and pathways potentially related to Covid-19 severity, the true underlying genetic mechanisms of how they affect disease progression need to be explored by more persuasive experimental designs. Covid-19 is assessed as a complex infectious disease and affected many risk factors. Symptoms of Covid-19 are highly variable, ranging from unnoticeable to severe and even death. The host genetic background is only partly responsible for the phenotypic heterogeneity. In recent years, multi-omics studies have proven a powerful and successful strategy to provide a broader perspective in understanding disease development and biological phenomena. Several multi-omics analyses of Covid-19 have been proposed to integrate multiple “omes” data to unravel disease mechanisms at multiple omics levels (Overmyer et al. 2021; Su et al. 2020; Montaldo et al. 2021; P. Wu, Chen, et al. 2021; Stephenson et al. 2021). The integrative analyses of rare genome and other “omes” data (e.g., proteome, transcriptome, epigenome, metabolome, and microbiome) may inspire us to discover new ri...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22271805: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22271815: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272204: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Limitation: Despite the fact this study benefits from its real-life data in an important group of health-care workers, and a relatively large number of participants, it comes with some limitations. This study is limited by its single-center design. The inclusion of health-care workers led to the overrepresentation of women and younger people, whereas groups with a higher risk for low immune response to vaccination, such as elderly and participants with an immunomodulatory treatment, are underrepresented. Unfortunately, the number of individuals in each group of vaccination protocols were unequally distributed, as there was no individual choice regarding the vaccine received.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22271297: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

The limitation of this discussion is that the possibility of leukocyte-platelet aggregates co-purifying during i-WBC isolation cannot be completely ruled out. It remains uncertain whether SARS-CoV-2 is capable of established a persistent and stable chronic infection in human tissues like other SARS coronaviruses [54]. Nevertheless, viral RNA is known to persist in human body well past the resolution of the active infection [3] and SARS-CoV-2 RNA had been identified in samples from patients long time after the resolution of the active infection [55-57]. Considering that SARS-CoV-2 RNA present in the blood stream was associated with platelet hyperactivity [58, 59], a similar mechanism for platelet activation can be suggested for Long-COVID case. The key limitation of such a hypothesis would derive from the fact that the above studies observed SARS-CoV-2 RNA up to a maximum of 3 months after the infection, while in the presented case, the Long-COVID patient (LC) presented platelet hyperactivity at 20 weeks and experienced severe Long-COVID symptoms even at 28 weeks after the resolution of active COVID-19 disease. In that regard, the potential for persistent SARS-CoV-2 or presence of active viral RNA in patient body more than half a year post resolution had not been fully assessed. The uncertain potential for disease resurgence and/or spread gives this question extra importance and urgency. The clear limitation of this work is the observation of a single Long-COVID patient, even ...

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04435184</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Crizanlizumab for Treating COVID-19 Vasculopathy</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272024: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272221: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272236: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

During the early era of the COVID-19 pandemic, it may have been difficult to participate in field experience opportunities due to facility policy limitations designed to reduce transmission. Grawey et. al examined an alternative model to the traditional ambulance “ride along” by providing a field-like experience in an emergency department setting. Grawey and colleagues report that this alternative experience was likely as effective as traditional prehospital clinical internships. Additionally, they found university medical students to have increased knowledge regarding EMS roles and responsibilities, which may have beneficial implications for transfer of care (23). With regard to continuing education, the Commission on Accreditation for Prehospital Continuing Education (CAPCE) saw a 179% increase in EMS refresher courses during 2018 to 2020, with a 185% increase in asynchronous online learning (54). This may suggest that distance learning as a method for recertifying provider credentials may increase rates of recertification, in contrast with in-person continuing education programs. Vaccine Perspectives and Prevalence: US EMS clinicians have also assumed nontraditional healthcare roles during the COVID-19 pandemic, such as in the case of a scope of practice expansion which allowed EMS clinicians to administer the COVID-19 to patients in states like New York, Massachusetts, and Vermont. Because EMS clinicians are highly trained in specific psychomotor clinical skills and knowl...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22271220: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

A limitation of this study was the ability to associate clinical or virologic outcomes with FPV drug exposure. Overall, this study provides novel data on the pharmacokinetics of FPV and its metabolite in adults with symptomatic SARS-CoV-2 infection without pneumonia and can help to guide dosing recommendations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272160: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

These findings should be viewed in the context of several limitations. While we were intentional in ensuring diverse representation of interviewees across sectors, organization type, and geography (across North Carolina), the sample does not represent an exhaustive list of organization types involved in the COVID-19 response. The snowball sampling technique employed increases the potential that the opinions uncovered were more homogenous than they would be otherwise. However, we were explicit when asking for recommendations that we were interested in uncovering a more complete and broader perspective on the subject. Thematic saturation was based on generalizable themes that emerged across sectors. Future research should investigate specific instances of cross-sector collaboration, interviewing more stakeholders involved, to gain a more detailed understanding. The timing of interviews with respect to official guidance, transmission rates, and vaccination rollout undoubtedly influenced participant responses. We incorporated timing into interviews and analysis. Additionally, participant responses may be subject to self-report bias, given limitations of recall and the potential for selective reporting. Lastly, decision-makers willing to participate in public health research may have differed from those who refused in the extent to which they valued and trusted scientific information. However, participants described a range of perspectives on how they incorporated scientific infor...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272097: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Some caveats should be discussed. Our data pertain to fatalities during the first wave of COVID-19 and until the fall of 2020. The first wave was the most devastating in most high-income countries, with a few exceptions (e.g. Australia).15,16 The relatively lower proportion of fatalities in LTC residents in subsequent waves may reflect a combination of multiple factors: high levels of prior infection (seroprevalence studies have found 5-10 times higher infection rates in LTC facilities than in the general population in the first wave),17-19 better protection of nursing homes, more extensive testing, widespread use of vaccination in 2021,16 and the possibility that the sickest individuals were the first to succumb.20 Moreover, the significantly lower risk of death after the first month post-infection versus the uninfected controls should not be interpreted as a sign that SARS-CoV-2 infection causally decreases the risk of death during long-term follow-up, as it probably reflects mostly a selection process (residents who died in the first month were probably more sick and debilitated before infection, while those surviving probably had better life expectancy). Allowing for these caveats, the major strength of our study is that it uses on large databases with nationwide coverage. Even so, similar analyses should also be performed in other countries because the health status of LTC residents may be different. This will allow to obtain more solid evidence on both the years-of-life...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272171: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Our study had several limitations. First, we could not exclude the effects of previous or current infections on antibody levels. However, none of the participants had a previous infection, although it relied on self-reporting. Furthermore, our findings were robust in a sensitivity analysis involving patients who tested antibody levels within 3 or 5 days of symptom onset or diagnosis. Second, since our study hospital has specific criteria for admission, which allowed only patients with mild to moderate severity to be admitted, we could not investigate the effects of antibody levels on outcomes such as moving to the severe phase (n=2) or death (n=0). Therefore, further studies involving a larger number of patients with a wide range of disease severity are warranted. Third, the diagnosis of pneumonia in this study was based on chest radiographic findings. Chest radiography is limited in its ability to detect subtle pneumonia. Furthermore, we did not routinely perform follow-up chest radiography if the initial test did not report abnormal findings and if the patient’s condition did not change. Therefore, the results associated with pneumonia should be cautiously interpreted. Fourth, we did not consider the type of vaccine (e.g. adenoviral vector-based, mRNA-based) when analysing antibody levels. Most previous studies have demonstrated the effectiveness of vaccines based on homologous vaccination data. However, the real-world population receives heterologous vaccines from differen...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272197: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

PCS is a challenge for clinicians, as there are no well-defined criteria to define this condition, patient-reported symptoms can be complex, changing and fluctuating, and complementary tests may be of little diagnostic value [59] This study has some limitations. Firstly, its design allows defining associations, but it does not establish causality. Secondly, it is a single-center study, on a Caucasian population, and the results may not be extrapolated to other populations. The frequencies of the ABO groups in the studied population are a confounding factor since geographical variations constitute potential bias [6]. In our case, the blood group proportions have been very similar to those in Spain (43.3% group A, 43.3% group O, and 13.4% groups B+AB). The main strength in this study is the well-characterized sample and the control group with subjects that came from the same population as the cases, and did not differ from them in any characteristics except for the PCS. Biomarkers have shown slight elevations, without exceeding the upper limit of normality (Figure 2), in a similar way to our previous study [19]. Besides, the use of composite indices of inflammation has increased the ability to detect parameters with values in the upper ranges of their distribution.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272123: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT00789685</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Safety, Tolerability and Preliminary Efficacy of FP-1201 in …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT02622724</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Terminated</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Efficacy and Safety of FP-1201-lyo (Interferon Beta-1a) in P…</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272113: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272100: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: Thank you for sharing your data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

There are several limitations to this study. The study limited recruitment exclusively to the United States. As noted previously, placebo-controlled data was limited to patients at Low risk for severe disease. Thus, we could not demonstrate statistically significant differences in viral clearance or rapid resolution of symptoms in patients at increased risk for severe disease between two active therapies at a time when circulating variants largely remained susceptible to BAM+ETE. This proof-of-concept study was also not powered to examine improvements in clinical outcomes in those with active treatment; however, the proportion of patients with COVID-19 related hospitalization and all cause mortality are in line with similar observations with other mAbs to SARS-CoV-2. Finally, this study was conducted over the spring and summer of 2021, prior to the emergence of omicron in November 2021. There are no clinical data evaluating the clinical efficacy of BEB in patients infected with omicron; however, non-clinical pseudovirus data with all sublineages of omicron (including BA.2 ) and confirmatory authentic omicron SARS-CoV-2 virus neutralization assays presented here indicate that BEB is effective in neutralizing omicron20. Moreover, this same limitation would be applicable to any EUA product studied at an earlier phase of the pandemic, and for which surrogates of antiviral efficacy would also be required. The BLAZE-4 study enrolled its last patient in July 2021. At that time, the ...

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04634409</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Study of Immune System Proteins in Participants With Mild …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT03383419</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Transplant of Redeemed Organs by Judicious Administration of…</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272237: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Further, there were some limitations to our meta-analyses. The quality of the meta-analyses results depends on the quality of the studies included. Table 3 contains a list of all the methodological aspects that future studies need to consider. We can observe that all studies had a high probability of bias, including lack of standardized definitions recall, selection, misclassification, nonresponse, and/or loss of follow-up. Additionally, the included studies have the limitations inherited in all observational studies, including bias due to residual and unmeasured confounding. Another limitation relates to the high level of heterogeneity. To account for heterogeneity, we used a random-effects model 41. However, ideally one should stratify the meta-analysis to identify what is causing the heterogeneity. This was not possible because most studies did not include data on different groups. The differences between studies were likely due to differences in study designs, settings, populations, follow-up time, symptom ascertainment methods, inconsistent terminology, little details on stratification on pre-existing comorbidities, and prior receipt of COVID-19 therapeutics and vaccines. Only four studies mentioned what percentage of the population was already vaccinated 14,15,23,28 (Table 3). It has been shown that vaccines reduce the risk of long COVID. A study in Israel compared the prevalence of symptoms of long COVID and found that fully vaccinated participants who had COVID-19 wer...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272222: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

3.1 Limitations of the study: Our modeling makes many assumptions that may limit the generalizability of our findings. We do not explicitly characterize co-morbidities or other factors such as immuno-suppression at the individual-level in the model. For these populations who are at highest risk of severe outcomes if infected with SARS-CoV-2, ongoing boosters remain a highly relevant and valuable strategy. We are also not capturing new birth cohorts into the model with near complete susceptibilty and no prior immunity to COVID beyond mother-to-child immune transference, for whom any vaccination strategy would be better than risking infection (30; 31). While our model has a robust mechanistic representation of immune dynamics, we do not capture the process of affinity maturation that antibodies go through over time and after repeated exposures to an antigen that increase the breadth of the immune response even in the face of waning (32). As a result, we may at times be under-estimating the protection retained over time against infection.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272155: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Due to the limitations of the instrument and limited availability of chemical references standards, fourteen compounds out of thirty were detected and quantified (Table 4) and (Table 5). Table 4 summarizes the molecular ions, product ions, retention times, and ionization modes for targeted LC-MSMS analysis of these compounds. The results showed that most of the bioactive compounds had higher concentrations in the wastewater of facilities exhibiting SARS-CoV-2 signal suppression than the control facilities. Four compounds had much higher concentrations in the suppression facilities than the control facilities. In particular, 4-nonylphenol, palmitelaidic acid, sodium oleate, and polyethyleneglycol dioleate exhibited concentrations that were 73.3%, 35.3%, 54%, and 58.8% higher in the suppression facilities than the control facilities, respectively (Figure 6). These compounds are mainly used in the production of surfactants and detergents in various industries [53, 54] The concentrations of 4-nonylphenol in the urban wastewaters were determined in Japan, China, and USA. The concentrations were about 190 µg/L [55], 2 µg/L [56], and 400 µg/L [57], respectively. In this study, average concentrations of 4-nonylphenol were 1169 ± 13.3 µg/L and 2025.7 ± 247 µg/L in the control and suppression facilities, respectively. No information was found regarding the concentrations of the other three compounds in wastewater. Palmitelaidic acid was reported to be used to produce cosmetics, soaps, ...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272098: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Limitations included the inability to distinguish hospitalisations and deaths that occurred ‘with’ rather than ‘from’ COVID-19, particularly for frail and comorbid residents, which is likely to underestimate VE; the probable significant under-ascertainment of prior exposure, particularly amongst staff, which is also likely to underestimate VE; and the possible under-ascertainment of infection events detected on LFDs without PCR confirmation, particularly amongst staff, which may overestimate VE against infection. Based on these data, and what is already known about immunity waning, we expect the reported trends to be generalisable over future rounds of vaccinations and variants. The available evidence suggests that while vaccines can induce powerful short-term immunity, this protection may quickly fade. While the risk of severe outcomes currently appears lower for the Omicron variant,31, 32 this risk is likely to increase with waning immunity, particularly for the frail LTCF resident cohort. Our data suggest that regular boosting may be required to maintain protective effects over a longer term; however, given the complex economic and political backdrop to vaccine procurement and distribution, it will be important to consider how vulnerable groups can continue to be protected against COVID-19 whilst ensuring global vaccine equity. Our findings also highlight the critical importance of ongoing surveillance in LTCF residents, to provide early warning of surges in infection asso...

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">ISRCTN14447421</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272066: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Our study has limitations. The relatively low number of individuals analyzed did not allow evaluating the clinical efficacy of Evusheld against BA.2. We did not have access to nasopharyngeal samples of the patients. Measuring antibody levels and neutralization in these swabs will help providing insights into the capacity of mAbs to neutralize Omicron sub-lineages at the infection site. We did not test BA.1.1 and BA.3 sub-lineages of Omicron. Future experiments with these viruses are needed to determine the antiviral activity of mAbs against the full landscape of the Omicron clade, which we recently proposed to be considered as a distinct SARS-CoV-2 serotype from ancestral strains and previous variants (Simon-Loriere and Schwartz, 2022). Based on our observation of breakthrough infections and awaiting clinical trials which will provide a complete evaluation of the impact of BA.2 on the treatment efficacy of mAbs, we expect more frequent treatment failures. It is also possible that the progressive accumulation of further mutations will increase the level of resistance of BA.1 or BA.2 to mAbs during prolonged infection. The low or intermediate sensitivity to Ronapreve and Evusheld, when used as a pre-exposure prophylaxis in immunocompromised persons at risk for severe disease is of potential concern. The risk that further escape mutations will arise in these patients is higher compared to Delta. We therefore recommend a close follow-up of these patients, particularly in case of ...

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04750720</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Study of the Kinetics of COVID-19 Antibodies for 24 Months i…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04870411</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Immunological Response to COVID-19 Vaccine in Patients With …</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272165: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.22272196: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

One limitation with our study is that a higher proportion of patients admitted to ICU had known variant (see supplement A, part 3). Given the increased risk of ICU admission for Delta patients, we may have oversampled severely ill Delta patients, which may cause us to slightly overestimate the reduction in our outcomes for Omicron patients. Another important limitation is that we could not distinguish sublineage BA.1 and BA.2 for all Omicron patients. In Norway BA.2 has gradually begun to outcompete BA.1 (16). However, up to the end of the study period, BA.1 was still the dominant circulating Omicron sublineage, and our results were robust when we excluded 57 patients known to be infected with BA.2 (see supplement A, part 2.4). Further studies are needed to investigate whether disease severity differs between Omicron sublineages. Evidence of lower disease severity among hospitalised Omicron patients in Norway and elsewhere is encouraging in the ongoing response to the COVID-19 pandemic. Analyses of circulating variants in a local context are important for informing decision-making on control measures and hospital capacity planning in different settings.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.04.22271934: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.22271887: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

This important limitation should be taken in account when interpreting these findings, given the high frequency of comorbidities among patients with systemic rheumatic disease[6–12] and the strong influence that comorbidities and disease activity exert on Covid-19 associated outcomes in this patient population[16, 17]. Regarding the risk of Covid-19 infection, with the exception of AS patients, all other patient subgroups were at higher risk, in agreement also with a general population-based cohort study[18]and two recent-metanalyses[4, 5]. However, the possibility that these patients were more susceptible to increased rates of testing cannot be excluded. Therefore, whether a tendency to contract the infection more easily, together with the increased comorbidity burden, can explain the higher Covid-19 associated death risk found collectively in systemic rheumatic disease patients compared to the general population needs further study[19]. As regards to hospitalization rates, there are three nation-wide studies from Sweden[14], Denmark[20] and Iceland[21], in line with our findings, while two meta-analyses[4, 5] report different results on this matter. This could be interpreted in light of several differences between countries, such as local guidelines, intensity of pandemic wave, saturation level of health care system, access to healthcare facilities and other confounders[22]. Increased hospitalization rates could be possibly also due, at least in part, to lower threshold for...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272168: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

While interpreting the results, there are some limitations that need to be addressed. First, this is a cross sectional study where respondents were asked to recall their symptoms and duration of experience. This may subject to recall bias and it is impossible to retrospectively confirm the length of COVID-19 related symptoms. In order to overcome these issues, a prospective cohort study may be a better study design. We also did not assess whether the symptoms reported were intermittent or continuous for the entire three or six months. Next, selection bias cannot be avoided in an online study as younger, more highly educated and tech-savvy individuals were more likely to respond. Therefore, our respondents may not be fully representative of the general population. We could not ascertain the effect of vaccination on Long COVID. Some studies suggested that vaccination may lead to potentially lower prevalence of Long Covid (36). This should be explored in future studies. The definition of Long COVID used in the current study may be different from the latest definition proposed by WHO on the 6 October 2021 (37). The latest definition defines Long COVID or Post COVID-19 condition as condition that occurs in individuals with a history of probable or confirmed SARS-CoV-2 infection, usually 3 months from the onset of COVID-19 with symptoms that last for at least 2 months and cannot be explained by an alternative diagnosis. The difference between the two definitions is that the symptom...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.483948: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.483930: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.483934: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• No funding statement was detected.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.08.22272020: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22272125: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.01.22271507: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

This study has several limitations. First, the participants included in this study were all white, although conversely, this also provided the first data in a non-Chinese, European population. Second, this trial did not include children or pregnant women, and there were only a small number of older adults (35 were ≥60 years in the Ad5-nCoV group). An ideal candidate vaccine for COVID-19 should cover vulnerable populations of all ages. Anti-S protein-specific antibodies have been reported to decline rapidly in individuals who have recovered from COVID-19, especially those who were asymptomatic or had mild symptoms [23]. Third, the sample size was relatively small and some of the calculated 95% CIs were wide. Finally, virus mutation, an emerging problem, may reduce the effectiveness of current vaccines [24]. It is not known whether participants of this study were exposed to any COVID-19 variants. Further study is underway to determine neutralising antibodies to the widely circulating variants following vaccination with Ad5-nCoV, which include but are not limited to the Alpha (B.1.1.7), Beta (B.1.351) and Gamma (P.1 ) variants. Conclusions: Analysis of data from this phase 3 trial demonstrated the immunogenicity and safety of this Ad5-vector based COVID-19 vaccine. More data are required to determine whether this vaccine reduces infections and transmission. Overall, this stable, single-dose vaccine could contribute to the global fight against the evolving SARS-CoV-2 virus.

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04540419</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Clinical Trial of Recombinant Novel Coronavirus Vaccine (Ade…</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.01.22271679: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

The study design has some limitations. The discovery and the replication samples were run on two different microarrays. The discovery set used Illumina H-6 with six blood samples on the chip, compared to the 12 blood samples on the Illumina Hu-12 in the replication. The shift was due to the sudden stop in the production of Illumina Hu-6. Hu-6 had approximately twice as many probes per gene as Hu-12 (Appendix Figure A). It might be that the reduction in probe numbers per gene reduced the sensibility of the microarray. Still a reasonable test-retest result was obtained. The original NOWAC study invited only women since it was based on hypotheses related to female reproduction, oral contraception, and hormonal replacement therapy. The age span included mainly women in their middle age. Due to the original design of building a biobank for functional genomics the study covered only four years. On the other hand, the sampling was independent of any knowledge of seasonal influenza. A major issue in the interpretation of the findings is the lack of knowledge about many basic aspects of the antibody response to the influenza A virus (15). This makes it difficult to test specific hypotheses. Preliminary analyses of the gene expression did not support any specific hypothesis. This could be due to lack of knowledge of the biological relationship between host and viruses. A major strength of this study was the completely random assignment for blood sampling regardless of place of living i...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.483772: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.11.483836: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: Thank you for sharing your data.

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.483704: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: Thank you for sharing your data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

The current study has several limitations. First, although we included a large number of shotgun metagenomic sequencing samples from the COVID-19 related human microbiome study (publicly available as of August 2021), most of the microbiome samples came from China. This limitation could be addressed by following this work with collection of more human microbiome samples from different populations and body sites to construct a more comprehensive genome catalog to reveal the full landscape of the human microbiome in COVID-19. Second, even though we adjusted for some potential confounders in our statistical models, we were unable to assess some covariates such as: medication, diet, and psychological stress that are not publicly available. Third, consistent with multiple MAG-related WMS studies25,65,66, we only recovered MAGs from bacteria and archaea. Given the fact that de novo discovery of non-bacterial genomes is quite challenging67, future study targets for other domains, including fungi and viruses, will give a more comprehensive view in the context of host-specific microbiotas and COVID-19. Although the majority of MAGs we reconstructed in this study have high quality, future investigations aiming for recovering the complete genome of microbes will further enhance our understanding of the interaction between human microbiome and SARS-CoV-2 infection68,69. Finally, additional experiments are needed to assess the casual role of candidate permissive and protective nrMAGs in CO...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• No funding statement was detected.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.07.483402: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• No funding statement was detected.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.08.22271905: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

No key resources detected.

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Our study has several limitations. Only five modeling groups were able to provide age-resolved projections and the exact age groups differed between models due to different model structures and data inputs. Additionally, our results only considered health outcomes (cases, hospitalizations, and deaths) and did not consider other important outcomes such as missed days of work or school, or the cost of medical care. Accounting for these considerations would tend to increase the benefits of vaccination. Additionally, we projected the benefits of vaccinating 5-11 year-olds on a relatively short time scale of a few months. Longer-term benefits are difficult to estimate as they depend on the balance between duration of immunity and viral evolution in different age groups. As we move into the next stages of the pandemic, with immunity increasing in all age groups through natural infection and vaccination, a shift to endemic dynamics with annual wintertime outbreaks is expected33[Antia-Halloran]. Incidence would also be projected to shift towards younger and immunologically naive individuals34,35 [Lavine-Bjornstad-Antia,, Li-Metcalf-Bjornstad-Antia], as is observed across a range of pathogens [e.g., Bansal et al.]. Based on observations of other pathogens36,37 [e.g., Olson et al., Arinaminpathy et al.], as the age distribution of disease becomes more concentrated in children, we expect direct and indirect vaccine benefits to increase in this age group. Finally, the results in this pap...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.08.22272082: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

While caution on their conduct needs to be applied, especially on issues of data management and reporting, our review protocol has attempted to control for such potential limitations and learn from previous reviews. Specifically, we have included a preprint search and citizen searching, and will leverage social media via Twitter and GoogleDocs for identification of articles and feedback from the global community on the process and findings. There are, however, recognized potential limitations of this review. Firstly, there are no specific systematic review software programmes that support monthly iterative searching, resulting in foreseeable challenges in data management. To limit any effects of this, all searches and their results will be saved and catalogued prior to uploading into Covidence. It is also anticipated that multiple data management systems may need to be used, and/or that flexibility across time will be required. Secondly, conceptualizations of ‘community engagement’ will likely vary across settings. Such terminology is regular vernacular within some contexts, specifically the implementation of health programmes within low- and middle-income countries. Yet, even within this work, how community engagement is defined and what it encompasses is varied and often unclear (50,51). Moreover, the use of ‘community engagement’ as a term may be limited in contexts that implement fewer activities at the community level, for instance in high-income contexts or contexts wit...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.07.22272026: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Strengths and weaknesses: The key strengths of this study are the scale, detail and completeness of the underlying raw electronic health record data. The OpenSAFELY-TPP platform runs analyses across the full dataset of all raw, pseudonymised, single-event-level clinical events for all 23.4 million current patients at all 2,545 general practices in England using TPP software; whereas the GPES dataset available in NHS Digital is a subset of this raw data created through a series of processing rules for specific aspects of GP records applied at source before extraction. OpenSAFELY-TPP also provides data in near-real time, providing unprecedented opportunities for audit and feedback to rapidly identify and resolve concerns around health service activity and clinical outcomes related to the COVID-19 pandemic. The delay from entry of a clinical event into the EHR to its appearing in the OpenSAFELY-TPP platform varies from two to nine days. This is substantially faster than any other source of comprehensive GP data. Additionally OpenSAFELY now contains linked COVID-19 therapeutics data which is collected from CMDUs with typically only 2-3 days delay between form submission and data being available for analysis. This can support timely monitoring of treatments administered through CMDUs as well as safety and efficacy studies of these treatments and other COVID-19 analyses. We recognise some limitations to our analysis. Our population, although extremely large, may not be fully repres...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.483600: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

The basic concept of utilizing a high-quality reference to improve lower quality data might be applied to many other research areas where technological limitations restrict biological insights. The usage of deep generative networks and other artificial intelligence methodology to infer information beyond what is technically measurable could be transformative in future biomedical research.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.483790: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: Thank you for sharing your code.

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• No funding statement was detected.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22271973: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

The present study had some limitations, including its self-reported and retrospective nature, which may have introduced recall bias. In addition, the survey may not be fully representative of the Vietnamese population living in Japan since some older adults, refugees, and subsequent generations of Vietnamese people may not have been able to participate using the online format. Therefore, further studies involving in-person surveys and Japanese forms of the questionnaire are warranted. Nonetheless, we attempted to reduce the risk of bias by controlling for potential confounders using multivariable logistic regression analysis.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.483652: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• No funding statement was detected.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.10.483726: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• No funding statement was detected.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.08.22272057: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

As may be expected in the evaluation of a novel and heterogeneous condition, our study has several limitations. Using CDC and WHO case definitions for PCC based on 4-week or 12-week duration may have overestimated the prevalence of clinically-significant PCC. Clinical significance may be improved by requiring longer duration, but remains suboptimal in allowing any symptom of any intensity. Temporal patterns were identified using a single-time survey completed at different moments since illness onset and asking only about ongoing symptoms. This may have underestimated the prevalence of symptoms for shorter intervals but avoided recall bias and the selective attrition of less symptomatic patients in follow-up studies.3,15 We did not collect information on some potentially relevant risk factors, such as comorbidity or initial COVID-19 symptoms and their severity.14,15,25,32,34 Our questionnaire, designed in the fall 2020, did not collect data on insomnia or post-exertional malaise later also considered to be PCC-qualifying symptoms.21 Cognitive functions were not formally measured with the validated instruments neurologists use to investigate patients, and self-reporting might have over-estimated their prevalence. Physical symptoms among non-COVID-19 controls were not collected. Comparing the prevalence but also the severity of symptoms among cases and controls would have allowed better characterization of PCC and should be considered in future research. Our participants were mo...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.22271788: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Several limitations should be considered. First, children meeting COVID-NET and FluSurv-NET criteria may have been hospitalized for reasons other than COVID-19 [2] or influenza. This may have been more common for COVID-19 compared with influenza due to SARS-CoV-2 screening practices, which were universal among hospitalized patients at some facilities during certain time periods. While COVID-19 or influenza may not have been the primary reason for admission for all hospitalizations, such cases were included in rate calculations because use of a standard and consistent surveillance case definition allows for robust monitoring of trends over time. Among cases with influenza or SARS-CoV-2 incidentally identified, it is unclear what impact the infection ultimately had on the decision to hospitalize a patient, the hospitalization course, or in-hospital outcomes. In sensitivity analyses limited to hospitalizations where children had ≥ 1 symptom at admission or COVID-19 as the primary reason for admission, the proportions of children with severe outcomes were similar to proportions with severe outcomes when all hospitalizations were included. Second, COVID-19- and influenza-associated hospitalizations might have been missed because case identification was reliant on clinician-directed or facility-based testing practices and test availability, which varied across time and facilities. Under-detection of influenza was likely greater than for COVID-19 due to under-utilization of seasonal...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.01.22271693: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Results from OddPub: Thank you for sharing your data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Limitations: The classification performance reported in our study needs to be interpreted in the light of the well-known challenges of data collection via crowdsourcing, including data validity, data quality, and participant selection bias (Afshinnekoo et al., 2016; Khare et al., 2015; Porter et al., 2020). The COUGHVID database does not allow to verify the COVID-19 status of the participants, as the participants were not asked to provide a copy or confirmation of their positive or negative COVID-19 test. Another limitation is that the participants have not been instructed to record the data during a defined time window after the positive or negative COVID-19 test. Therefore, it is possible that some participants recorded their cough at the beginning of their infection, whereas others did the recording towards the end of their infection. Interestingly, the disease stage of COVID-19 was found to influence the nature of the cough (shifting from dry at an early disease stage to more wet at a later disease stage), concomitantly affecting acoustic parameters of the cough (Cohen-McFarlane et al., 2020). Moreover, the participants were asked to answer whether they had respiratory and/or muscle/pain symptoms, but no information on the severity of their symptoms is available. Although the safe recording instructions provided on the web page are reasonable with regard to the transmission of the virus, the suggestion to put the smartphone into a plastic zip bag while recording is subopt...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.08.22270920: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.03.09.483635: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).