SciScore for 10.1101/2021.11.03.21265876: (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).

When interpreting our results, the following limitations should be considered. Firstly, the analyzed sample is affected by a strong selection bias. Indeed, study participants were enrolled among individuals who voluntarily registered to undergo a serological test. In addition, the conducted survey was restricted to the population of the metropolitan city of Milan. Consequently, our sample is not representative of the age distribution and of the household composition of the Italian population and results may not reflect social behavior adopted in less urbanized areas. In particular, crude estimates retrieved from our sample suggest that, in August 2020 (i.e., before introducing the tiered restriction system), the daily mean number of contacts was 74.5% lower than that estimated for Italy by the POLYMOD study in 2008 [18]. Although it is likely that, even in the absence of strong restrictions, current social interactions could strongly differ from those adopted in the pre-pandemic period [25], these numbers should be considered in light of the sampling procedure we adopted for data collection. For this reason, instead of relying on absolute numbers, our analysis focuses on investigating the relative changes in the contact patterns observed across different time periods and at different ages. To minimize potential biases, the potential impact of tier restrictions on the number of reported contacts was assessed by adopting a regression model, where a variety of potential confound...

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.

• 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 10.1101/2021.11.02.21265778: (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).

Our analysis has several important limitations. First, while recruitment was agnostic to the presence of persistent symptoms, the cohort is not representative of the general population with PASC. Second, we relied on self-report to ascertain the presence of symptoms. This risks misattribution of symptoms to neurologic causes and therefore misclassification of individuals as having CNS PASC. In addition, it is difficult to disentangle neurologic symptoms from non-neurologic symptoms which might co-occur and it is possible that differences are driven by more severe PASC in general rather than neurologic symptoms specifically. Affective symptoms may also co-occur and be inter-related. Third, we did not include any objective neurologic measurements, and studies that do include such measurements (which may include detailed neurological history and examination, neurocognitive and neuropsychiatric testing, and/or neuroimaging) are likely to be more informative. Fourth, we measured a limited set of biomarkers. Our measurements were all taken in blood, and while there are established relationships between blood and CSF measurements in other disease conditions,62,63 these have yet to be established for COVID-19.28 For this reason, more detailed studies that include CSF analyses will be critical. Finally, paired pre-pandemic specimens were not available, and it is possible that elevations in these markers among those with CNS PASC preceded SARS-CoV-2 infection. Regardless, we believe th...

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">NCT04362150</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">Long-term Impact of Infection With Novel Coronavirus (COVID-…</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.

• 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 10.1101/2021.11.02.21265668: (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 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.

• 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 10.1101/2021.11.03.21265685: (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).

Study limitations include its retrospective design, with data being collected by chart review only, and the fact that thyroid disease status was based on patients information given at hospital admission, so it was not possible to know if the hypothyroidism was compensated or not. Nevertheless, to the best of our knowledge, the study has the largest sample of COVID-19 patients with hypothyroidism published so far. TSH and thyroid hormone (T4 and T3) levels were not evaluated during the time of hospitalization and time in the ICU, as this is not recommended during hospitalization due to Covid-19 or other acute diseases is by the health organizations, and it was not our aim to access the effects of NTIS. The assessment of thyroid hormone levels throughout the course of Covid-19 is still challenging due to the possibility of overdiagnosis due to abnormal hormone levels during acute systemic disease. It is important to emphasize that these hormonal changes are adaptive processes and cannot be defined as a disease itself.

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.

• 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 10.1101/2021.11.03.21265478: (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).

The present work possesses several limitations, including bias in sample collection due to daytime recruitment of participants, thereby excluding most emergency cases. The period of sample collection differed among groups, as the Israeli vaccination campaign started after the commencement of the study. Additionally, antibody levels were quantified using antigens of the original virus, and may thus show reduced affinity to antibodies induced by the alpha variant. Pregnancy induces particular changes in a women’s immune system placing them at a vulnerable position when it comes to infections. Therefore, general population immunity dynamics are not always applicable to pregnant women. This is the first study to compare the evolution and dynamics of the maternal-fetal humoral response between Alpha variant and Wildtype SARS-CoV-2 infections, demonstrating that pregnant women response is variant dependent. Additionally, this work enhances the important role of active transport and placental regulation for fetal immunity supporting vaccination during pregnancy.

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.

• 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 10.1101/2021.11.03.21265819: (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).

Despite the important results found out on the effectiveness of COVID-19 vaccines against the incidence of infection, hospitalization, and mortality after vaccination, the present study had a number of limitations, including the possibility of vaccination of specific age or occupational groups (health care worker) associated with an increase or decrease in the chance of contracting SARS-COV2 infection. However, the confounding effect of the background variables was somewhat controlled through the use of HR adjusted studies. Herd immunity was another issue that could distort the overall results; i.e. with increasing follow-ups, the risk of infection in the community and non-vaccinated people would gradually decrease, and this would overestimate the effectiveness of various COVID-19 vaccines.

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.

• 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 10.1101/2021.11.03.21265877: (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.

As with any study, the REACT-1 study has limitations. We cannot meaningfully calculate a response rate for round 15 since it is not yet complete, but between rounds 1 (May 2020) and 14 (September 2021) the response rate declined from approximately 30% to approximately 12%. Although we used rim weighting to adjust our prevalence estimates for differential response by age, sex, deprivation, LTLA counts and ethnicity, it remains possible that our estimates are not fully representative of the population as a whole. The data on participants who consented for their REACT-1 data to be linked to their NHS records which include data from the COVID-19 immunisation programme are not yet available for round 15. Surveillance in England indicates that influenza incidence was low up to 26 October 2021 (the most recent data reported by UKHSA [19]), although it will almost certainly increase in coming weeks unless strict social distancing were to be reinstated. For viral infections, co-infections with other bacterial and viral pathogens can increase the risks of complications and mortality. The combined effects of SARS-CoV-2 and influenza co-infections are not well understood [20]. Even if co-infected individuals do not experience increased risks of serious disease, the dual demands on the NHS of caring for COVID-19 and influenza patients is likely to put its resources under pressure. It is therefore essential to monitor ongoing infection risks of both SARS-CoV-2 and influenza so that appropr...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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

• 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 10.1101/2021.11.02.21265826: (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 and data.

Another limitation of this work includes not accounting for under-reporting. Due to the highly contagious nature of SARS-CoV-2, many countries advised individuals with COVID-19-like symptoms to self-isolate at home instead of going to the hospital, except they have a severe case of the disease. As a result, these individuals may not get a test to confirm if they had the disease, and therefore, they may not be captured in the reported cases. This may lead to under-reporting. The availability and consistency of data is also another limitation of this work. Data collection during the COVID-19 pandemic has been very tedious worldwide, especially during the early stage of the disease when non-pharmaceutical interventions that impede movement and access to resources were imposed. Particularly, data collection in many developing countries across Africa is challenging due to the lack of adequate infrastructure, leading to inadequate data. The framework presented in this paper requires knowing the transition rates of infected individuals between the different compartments of the model. These parameters may not be immediately available for a novel disease like SARS-CoV-2 during the early stage of the disease. Another limitation of our model includes not explicitly modeling the dynamics of asymptomatic individuals. An interesting extension of the work presented in this paper includes incorporating a parameter for the ascertainment fraction of the reported cases of COVID-19 in each count...

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.

• 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 10.1101/2021.11.03.21265861: (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).

Strengths and limitations: Strength’s worth highlighting, is the tandem use of longitudinal data on individuals aged 18-24 and repeated samples of individuals aged 18 years originating from the same baseline population. Moreover, our data collection during the initial lockdown included up to 7 measurements spanning the reopening phases, as well as one measurement subsequent to a second and more prolonged lockdown. The repeated cross-sections allow us to quantify seasonal variations and is only vulnerable to attrition if the participation in DNBC-18 systematically changed over year of birth or season, as opposed to the longitudinal setup which is more vulnerable to attrition due to loss to follow-up. We attempted to reduce bias from differential attrition by inverse probability weighting. The validity of this method relies on a correctly specified model including all relevant predictors for loss to follow-up, which cannot be assumed. Interpretation of our findings likewise deserves consideration of a few limitations. In the longitudinal setup, the baseline data was collected at age 18 years and three months for all participants, whereas the participants’ ages during lockdown was 18-24 years. Thus, the timespan between the before and during lockdown measurement was greater for the older participants. For older participants, changes in mental health may be underestimated, since the pre-lockdown measurement represent a younger age than the follow-up measures, and on average repor...

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.

• 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 10.1101/2021.11.01.21265729: (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).

There are several limitations of this research. First, the contact pattern in the matrices was already affected by NPIs and might be not identical to the contact pattern before COVID-19, necessitating the normalization done on the matrices. For example, transmission rate among those age 0-17 might be underestimated because of restricted attendance in schools. Second, vaccine waning is not considered. However, booster shots are administered and vaccine hesitancy remains low in Korea, which mean that the effect of administered vaccines might be maintained [22]. Third, our age-age matrix focused on the Delta variant, and we were not able to examine transmission of other previous variants. The coverage of genomic surveillance among COVID-19 cases in Korea has steadily increased, and it covers about 30% of all confirmed cases. Therefore, the number of cases with genomic results before the occurrence of the Delta variant was small to be analyzed separately by variant types. Our result highlighted the transmission pattern of Delta, which is currently the dominant variant in most countries.

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.

• 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 10.1101/2021.11.01.21265527: (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).

This is an intrinsic limitation of regression models, and the variable may be seen as non-significant due to the fact that it is a non-linear association. As previously mentioned, an important limitation of regression models is collinearity. When exploiting LASSO regression in our previous work (4), we had to exclude some features which had shown to be important in the boosting model due to high collinearity. This may explain the difference in the features included in both models, despite the fact that all features included in both had previous evidence of association with COVID-19 prognosis. Another interesting remark is shown in Fig 4, in which we can see the relative importance of each feature. Here, again, age is the most important single feature (due to higher mean SHAP value), which is in line with previous studies (3,31,32). In an American study in intensive care units, age has shown higher discriminatory capacity when used in isolation (AUC 0.66) than the Sequential Organ Failure Assessment (SOFA) score (0.55) for mortality prediction, in a cohort study of adult patients from 18 ICUs in the US, with COVID-19 pneumonia. This score is widely used at emergency departments and ICUs worldwide to determine the extent of a person’s organ function or rate of failure (42). In the present study, the remaining features, when combined, yield higher predictive value in this task than just age. Reliability: Finally, we investigate issues related to the reliability of the models. Ne...

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.

• 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 10.1101/2021.11.01.21265660: (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 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.

• 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 10.1101/2021.10.30.21265680: (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).

This evaluation was subject to limitations. First, while Fulton County Board of Health offered testing to individuals of all ages beginning in May, 2020, not all testing facilities in and around Fulton County made COVID-19 testing readily available to children. This is an important factor that likely contributed substantially to the number of pediatric tests being far fewer than the number of adult tests. Second, data available from case investigations of young children depend entirely on interviews with proxies, which do not always result in the most accurate data on symptomaticity or source of infection. It is also important to acknowledge we did not have data on whether children were attending school in-person during this time frame, limiting an ability to make inferences about the role schools may have played in pediatric COVID-19 transmission; however, studies have revealed low rates of COVID-19 transmission within schools when mitigation strategies are in place.22,23 Strengths of this study include our data sources. In Georgia, SendSS is the most comprehensive surveillance data source for COVID-19 cases and includes data on cases tested across the majority of testing sites in Fulton County. This allowed us to observe pediatrics trends using the most data possible for cases diagnosed among Fulton County residents, regardless of testing location. Because our datasets included case age, we could also examine COVID-19 trends among smaller, informative pediatric age groups.

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.

• 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 10.1101/2021.11.01.21265742: (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).

This study’s limitation is that the study relied on expenditure plans rather than actual expenditures. However, this was mitigated by augmenting this data with structured interviews with vaccine deployment implementors. The strength of this paper is that the assumptions, unit prices, and vaccination scenarios used in the cost analysis are country-specific and therefore can be used to inform local policy and may further inform parameters used in cost-effectiveness models. However, although the results are less generalizable to other similar low-and middle-income settings in the current format, they could potentially be adapted and adjusted to country-specific assumptions.

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.

• 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 10.1101/2021.11.01.21265775: (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 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.

• 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 10.1101/2021.11.02.21265755: (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 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.

• 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 10.1101/2021.11.01.21265766: (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).

Our study has limitations, as the large COVID-19 wave in New York City in 2020 occurred, many subjects were recruited but we have not been able to assemble a large replication cohort as case numbers in New York City have remained low after the severe first wave. A replication cohort would be ideal, and we will await with interest future studies of these loci from data sets at other centers. This is a candidate gene study, which allows us to benefit from prior knowledge and rationale, and we maintain an appropriate type I error correction. Despite this, replication in future studies will be important. In summary, we document a number of IFN pathway lupus risk alleles that significantly impact mortality following COVID-19 infection, and these alleles provide some clues about key points in our viral defense against COVID-19. The study also supports the idea that type I IFN pathway risk alleles for autoimmune disease may persist in high frequency in modern human populations due to a benefit in our defense against viral infections.

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.

• 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 10.1101/2021.11.02.21265789: (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 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.

• 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 10.1101/2021.11.01.21265731: (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 and data.

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.

• 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 10.1101/2021.10.28.21265593: (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).

While combining analyses from several UK prospective studies represents a clear contribution to understanding the potential impact of furlough, there are limitations that should be taken into account. Firstly, we were not able to achieve full harmonisation of measures across studies, for example, a number of studies had only asked questions on recent pre-pandemic smoking of those who were smoking during the pandemic, meaning smoking cessation during the pandemic was unobserved in those studies. This means the analyses of change in smoking for these studies focused only on reductions in cigarettes smoked, rather than outright cessation. The main analyses will be less affected, though there may have been some residual confounding from participants who had smoked but given up before being surveyed during the pandemic. Focusing on maximising comparability of measures across studies also limited our scope to explore more varied definitions with respect to frequency, quantity or other aspects of use, such as binge drinking, or concurrence of smoking and vaping behaviour. Our findings focus on the initial stages of the pandemic (April-July 2020) and observed relationships could change with the duration of lockdown or furlough, and subsequent changes to restrictions and the furlough scheme. Further research is needed to explore potential heterogeneity over the course of the pandemic, within workers who retained employment, and between different measurement definitions/thresholds. As ...

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.

• 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 10.1101/2021.10.31.21265676: (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 data.

Our findings must be considered in light of some limitations, which we address here. First, we captured different degrees of confidence through an ordinal scale with 4 values, while the variability of confidence may be higher. Second, although we approached different sociodemographic characteristics, it is necessary to consider additional aspects such as cultural, ethnic, rurality and income, among others. Third, given the context of physical distance, the application of the online survey mostly reached those who have constant access to the internet and technological resources, thus excluding people with lower accessibility or knowledge about the internet and technology. Although in these limitations we highlight aspects that must be considered and remedied in future studies, it is necessary to clarify that the present study is consistent and clearly underlined the conditions that propitiate the willingness to accept an annual vaccination, booster doses and the vaccination of children. In conclusion, our study reports a high intention of the Chilean population to receive a booster dose of the COVID-19 vaccine, annual vaccination and vaccination in children under 16 years of age. Vaccine acceptance is associated with trust in scientists, medical teams and in different media such as television and radio. Perception of risk is a factor that determines in adults the acceptances of vaccination or children vaccination or booster doses. This study provides the foundations on aspects...

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.

• 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 10.1101/2021.10.31.21265718: (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).

However, our study has some limitations. It includes a small sample size of patients, so it was not powered to assess differences across medication subgroups. Furthermore, only humoral serological responses were assessed, it is likely that T cell-mediated immunity plays a possible protective role. Finally, given the observational nature of the study, possible confounders may exist, such as difference in biologic dosing and serum drug concentrations were not accounted for. A follow up larger studies needed to evaluate if decay of antibodies occurs over time and if a possible third booster vaccine dose may be needed. To conclude, this study showed that most patients with IBD on infliximab, adalimumab, and vedolizumab seroconverted after two doses of SARS-CoV-2 vaccination. All patients on ustekinumab seroconverted after two doses of SARS-CoV-2 vaccine. BNT162b2 and ChAdOx1 nCoV-19 SARS-CoV-2 are both likely to be effective after two doses in patients with IBD on biologics. A follow up larger studies are needed to evaluate if decay of antibodies occurs over time and if a third booster vaccine dose may be needed.

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.

• 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 10.1101/2021.10.30.21265662: (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).

This study has several limitations related with small patients’ group and lack of mechanistic investigations. Noteworthy, our study group is well-defined and limited to the ARDS and sepsis forms of COVID-19. Although we analyzed several proteins related with activation of the inflammasome we did not measure other relevant mediators that can interact with this pathway (e.g. interferons). The present study would also benefit from the flow cytometry data of the inflammasome activation in circulating blood cells. Moreover, we analyzed only plasma proteins and it should be noted that they may not fully reflect the tissue response. Finally, we were not able to explain the heterogenic pattern of the inflammasome activity in these patients.

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.

• 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 10.1101/2021.10.31.21265714: (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).

Our study has limitations. The data on individual patients were not available and we could not follow up dispensed azithromycin from pharmacies to patients. However, it is quite certain that all quantities of distributed azithromycin have been dispensed to patients. We were also not able to report more standard measures of antibiotic usage such as defined daily dose or DOT per 1000 patient-days. Nevertheless, we did provide data on azithromycin overuse during the COVID-19 epidemic in Croatia. Even though an increase of 8.1% of total azithromycin DOT from the average of 2017– 2019 compared to 2020 seems modest, we should highlight the fact that Croatia is already one of the countries with highest percentage of macrolide resistant isolates among EU/EEA countries [20]. Macrolides were the second most common used antibiotics with azithromycin accounting for most of the use in Croatia in 2014 – 2019 with daily defined doses (DDD)/1000 inhabitants per day of 2.58, 2.82, 2.55, 2.56, 2.73, 2.72, respectively, after penicillins including beta-lactamase inhibitors [21,22]. Sample of Streptococcus pneumoniae with estimated national population coverage of 80% showed increasing trend in macrolides resistance in the period 2015 – 2018 (19, 34, 36, 32%, respectively) [20]. Resistance data collected from 38 centers in Croatia in 2019 showed 31% resistant S. pneumoniae to macrolides with a range of local results from 0 to 53% and 9% of macrolide resistant Streptococcus pyogenes with a range o...

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.

• 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 10.1101/2021.10.30.21265430: (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.

Limitations: As with all analyses of observational data, this approach has several limitations. Firstly, while the machine learning optimization seeks to allocate effect sizes to most statistically reliable indicators, we do not use any side information (such as treatment mechanism of action or time-series data) to perform causal inference. In addition, in this study we have considered only binary indicators for each treatment, choosing to assume that providers are following dosage protocols to standardize care. Finally, while additive models are interpretable and accurate, they are still susceptible to statistical biases [21] which may cause different model classes to recover different effects from a single dataset. Further works should investigate the potential for other classes of additive models to corroborate or dispute these findings.

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.

• 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 10.1101/2021.10.31.21265672: (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).

There are several limitations associated with our study. The time-frame during which the study was performed did not allow for adjustment for anti-viral treatments (such as dexamethasone and remdesivir) which have been shown to decrease severity of radiographic edema (26) as these were introduced later during the study period within the healthcare system (late August-September). We were also not able to adjust for any variables other than those obtained at baseline when performing the longitudinal analyses, raising the question of whether other organ failure outside of the pulmonary system (renal) and fluid status have contributed to radiographic deterioration that is not directly associated with COVID-19 pulmonary disease. Lastly, while the study is a multi-center study across multiple hospitals and states in the United States, practices and procedures early in the pandemic were often institution-based and not necessarily guided by the Centers for Disease Control and Prevention and/or the World Health Organization. As such, institutional standards of treatment may not have been reflective of other healthcare systems around the same time period. Despite these limitations, we excluded patients for which there was incomplete data that would otherwise require imputation and potentially affect our analyses. Instead, the study protocol structured the CXR sampling periods to provide early, standardized meaningful clinical data that may assist clinicians in prognostication and decis...

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.

• 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 10.1101/2021.10.31.21265711: (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 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.

• 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 10.1101/2021.11.01.21265737: (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 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.

• 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 10.1101/2021.10.29.21265555: (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.

The present study has several limitations. Firstly, the prospective validation cohort was relatively limited in size. Secondly, patient cohorts were recruited prior to the availability of vaccination. Accordingly, our findings do not apply to vaccinated individuals experiencing ‘breakthrough’ infections. Finally, we could not correlate the changes in IFI27 expression levels between the peripheral blood and the infected lung. Future studies (e.g., in animal models) are needed to unravel the coupled dynamics of IFI27 expression between these tissue compartments. In conclusion, the findings provided herein represent the first evidence that IFI27 expression has a potential as a severity biomarker for risk stratification in COVID-19 patients.

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.

• 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 10.1101/2021.11.01.21265764: (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).

SHINEv2 addresses these limitations. Lyophilization considerably simplifies the assay and facilitates its transportation and storage. SHINEv2 can be distributed overseas without a loss in performance. Moreover, the use of an equipment-free and ambient-temperature sample lysis method further increases the user-friendliness of the assay. SHINEv2 involves as few steps from the user as antigen-capture tests, while providing a 50-fold boost in sensitivity7,42,43. Importantly, SHINEv2 demonstrates perfect (100%) concordance with RT-qPCR, the gold standard for SARS-CoV-2 diagnosis, in samples with RNA levels above our analytical LoD of 200 copies/μL. This level of sensitivity could enable the detection of every potentially infectious individual, including those missed by antigen-capture tests10,46. SHINEv2 can accurately identify several clade-specific mutations in the Alpha, Beta, Gamma and Delta SARS-CoV-2 VOCs, and it can be rapidly adapted to respond to emerging viral variants as well as other viruses in current and future outbreaks. Thus, SHINEv2 can provide critical information to inform public health responses, and it fills a major gap in point-of-need diagnostics. At the population level, SHINEv2 could be used to prioritize testing and vaccine rollout in highly-affected communities or to select subsets of samples for further viral sequencing. SHINEv2 could also assist clinicians in selecting the right treatment (e.g. monoclonal antibody cocktails) for patients with severe 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.

• 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 10.1101/2021.11.01.21265761: (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).

Completing cognitive testing remotely can be done but has limitations, particularly for young children and youth with attentional or social difficulties. Solely completing ASD-specific testing does not give a full diagnostic picture and could cause a clinician to misinterpret difficulties or delays related to other factors of development (e.g., when social skills are immature for chronological age, but may be consistent with developmental level). For this reason, understanding an individual’s cognitive functioning is an important factor in putting their social skills and behaviors into context. Some widely used cognitive measures (e.g., Wechsler series) have been made available online, though there are limitations to which tasks can be administered remotely or without using shared materials and manipulatives. Caregivers may be able to act as facilitators in testing cognitive abilities or developmental level for children, though caution should be used in interpretation of results, as parents could unknowingly provide prompting, making it more difficult to determine the child’s true ability level. Interviews, such as the Vineland Adaptive Behavior Scales, Third Edition (Vineland-3; Sparrow et al., 2016), can be conducted over telehealth to aid in obtaining a thorough report on adaptive functioning. With these considerations and limitations in mind, obtaining comprehensive information should be prioritized to get a full and accurate diagnostic picture as assessment services cont...

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.

• 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 10.1101/2021.10.31.21265627: (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 data.

Another limitation may be the difficulty in comparing these findings to other countries, for example, Australia’s COVID testing rate is much higher than many other countries; 2.7 per day per 1,000 people55 compared to the US (1.9 per 1,000), the UK (1.3 per 1,000) and India (0.654 per 1,000).56 This may be due to Australia’s relatively high national wealth (and lower inequality compared to US), as well as finanical support for individuals and businesses afflicted by the pandemic.57

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.

• 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 10.1101/2021.11.01.21265653: (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 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.

• 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 10.1101/2021.10.31.21265703: (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).

The main limitation of this study— as of most phase 3, COVID19 VE studies— is the narrow time window for VE evaluation. The waning of immunity over time and its impact on efficacy are key aspects that deserve the highest attention. At present, we are following time evolution of protection as well as its behavior towards new circulating variants; these aspects will be addressed in other communications. In conclusion, the conjugate vaccine SOBERANA 02 was efficacious and induced cross-protection during a dominant circulation of the VOC β and VOC δ. The third heterologous dose of SOBERANA Plus increase efficacy up to an outstanding 92.4 % preventing severe disease and death. Taken together, our findings indicate that SOBERANA 02 is a promising vaccine that can be used in a two-dose regime or in heterologous three dose combination with SOBERANA plus to fight COVID19 pandemic in adults population. According to the safety profile and efficacy, it is a potential vaccine for pediatric age.

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.

• 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 10.1101/2021.11.01.21265384: (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 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">NCT02735707</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">Randomized, Embedded, Multifactorial Adaptive Platform Trial…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04536051</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">A Study of a Candidate COVID-19 Vaccine (COV003)</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.

• 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 10.1101/2021.11.01.21265749: (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 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.

• 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 10.1101/2021.10.30.21265694: (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).

Considering the limitations related to a subsampled global phylogeny analysis, it is not possible to know if the absence of well-supported monophyletic groups is due to the missing branches and nodes representing the most related sequences and their ancestors or some technical limitation inherent to the application of the branch support statistical tests to the SARS-CoV-2 genomic sequences, since bootstrapping approaches require multiple sites supporting a clade to infer strong support value in near-perfect trees (57). In fact, SARS-CoV-2 genomes present a low number of informative sites, which may generate topology with low statistical support and ambiguous clustering of large data sets (58). Additionally, both SH-aLRT and ultrafast bootstrap methods rely on bootstrap resampling (57). Considering all aspects discussed above and the divergence among sequences, it is expected that the P.1 genomes (specially in the spike sequence analysis) cluster together and phylogenetic trees including multiple lineages present better statistical support values inter-lineages in comparison with intra-lineages. In summary, the association of diversification of P.1 sequences, the known phenotypic consequences of some signature mutations, the confirmation of positive selection acting on some sites and the absence of evidence for recombinations, all suggest that the main driving force in the evolution of P.1 viruses was selective pressure.

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.

• 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 10.1101/2021.10.30.21265449: (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).

It is essential to thus engage various level of health care providers and strategize vaccine messages to parents especially from lower education status Limitations of this study that should be considered include the sampling strategy adopted by the study which may not be representative of all parents in the country, hence limits the generalizability of our finding. The cross-sectional design of the study should be interpretated carefully when accessing overall prevalence of vaccine hesitancy among parents in India. Our sample represented individuals with internet access and having mobile literacy. This does not necessarily reflect the country wide perception of parents towards vaccine and their intention to get children vaccinated. Despite the above limitations, our study assessed nationally representative sample of parents regarding their perceptions and intentions to vaccinate their children at a critical time, just as adult COVID-19 vaccination programs was initiated in India. Our findings reminiscent of recent research suggesting that there is a low demand for COVID-19 vaccine among parents, and highlights the need for longitudinal studies to measure the acceptability of a COVID-19 vaccine at different intervals. Future studies are thus required to supplement our current findings to enhance vaccine uptake among children in India. Nevertheless, our study establishes evidence regarding parent’s hesitancy towards getting their children vaccinated and their concerns in coming...

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.

• 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 10.1101/2021.10.30.21265699: (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 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.

• 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 10.1101/2021.10.29.21265683: (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).

With the limitations of the current widely used methods, there is a constant need for techniques that are rapid, easy to operate, inexpensive and can be applied to any kind of viruses with no/minimal modifications. The sensing platform we report here has the capability to be built into an inexpensive mass testing technology with a positive result in less than 25 minutes. Although rapid antigen testing can provide marginally faster results (15 mins), the accuracy is lower (44). The large area nano manufactured flexible sensor surface can be mounted on any surface like doorknobs, cylinders, building entrance etc. to enable on-site rapid testing with a handheld Raman setup. The capability of having the entire sensing area on a flexible substrate enables the fabrication of sensor patches that can be placed on face masks or skin for continuous surveillance. Our choice of nanostructure encompasses an architecture with realistic design parameters to enable one-step lithography-free fabrication while ensuring enough interaction between the nanostructures for increasing the detected signal. It is well known that Raman scattering is a weak phenomenon and signals from biological material are even weaker. Thus, to have a sufficient signal-to-noise ratio, we have used silver nanostructures with resonance matched to the excitation laser frequency for maximizing the Raman scattering signal. A less noisy spectrum enables more accurate use of machine learning algorithms for successfully class...

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: Please consider improving the rainbow (“jet”) colormap(s) used on page 6. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

• 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 10.1101/2021.10.29.21265687: (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 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.

• 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 10.1101/2021.10.29.21265628: (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).

This study has several limitations. First, we may underestimate the relevance of education and occupation because we used indirect measures of risk that were indexed by codes for primary occupation in life rather than direct measures of occupational exposure. Second, we did not account for within-household transmission initiated by an occupational exposure. We may underestimate the importance of occupation since household members with different occupation codes share COVID-19 risk associated with each other’s work. Third, we only included confirmed COVID-19 deaths, conceivably leading to an underestimate of true inequities: some racial/ethnic groups may be more likely to die at home without COVID-19 testing and therefore not be counted as a COVID-19-confirmed death.(36) Fourth, we could only control for potential confounders measured in both the death and ACS records. Absent further covariate adjustment, education and occupation may proxy for other factors such as social class, intergenerational wealth/debt, parental education, and non-citizen legal status.(37) Unmeasured potential confounders of particular concern are comorbidities, housing composition and density (including housing instability, homelessness, and incarceration), access to high-quality healthcare, and undocumented legal status. However, these factors may also be part of the causal pathway from structural racism, education, and occupation to COVID-19 death.

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.

• 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 10.1101/2021.10.29.21265691: (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 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.

• 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 10.1101/2021.10.28.21263107: (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 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.

• 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 10.1101/2021.10.28.21265635: (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).

There were some limitations in our study. The choice of vaccine was not randomized and there might be a selection bias in those opting for each vaccine. Our study only focused on investigating the immunogenicity at 1 month after two doses of vaccination. The durability of immune responses needs to be monitored; and indeed, this cohort will be followed up to address this question in the coming years. Our estimates to adjust for antibody waning was based on reports on CoronaVac, comparable to data for BioNTech was lacking. Thus our assumption of comparable rates of antibody waning for the two vaccines may not be correct. We did not collect plasma prior to the second dose of vaccine to assess the effect of the first dose of the vaccine, or acute phase responses, where earlier responses may account for the final post vaccine differences as our primary study endpoint was neuralization titers after vaccination. Similar comparisons between vaccines in teenagers and older adults will be needed.

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.

• 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 10.1101/2021.10.28.21265629: (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 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.

• 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 10.1101/2021.10.29.21265669: (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).

Limitations of this study include the cross-sectional nature of the analysis, which precludes our ability to determine causal associations. Although this was a binational study, sampling was non-random and results may not generalize to other samples of PWID. We also relied on self-report and recall for many behaviors, which may have been subject to socially desirable responding. Although the COVID-19 disinformation scale we utilized had good internal consistency, other COVID-19 related knowledge measures have only been recently developed and, to our knowledge, have not been validated in this or other populations impacted by substance use. Our analysis excluded participants who were recruited before survey items on COVID-19 knowledge and vaccine hesitancy were developed. Since attitudes to COVID-19 vaccines may have changed over time, we controlled for time in our analysis. Future longitudinal, qualitative, and intervention-development studies are needed to better understand contextual factors influencing vaccine hesitancy in this population to identify strategies to best address these intervention targets. In conclusion, we identified a concerning level of COVID-19 vaccine hesitancy among community-recruited PWID in the San Diego-Tijuana border region, which was associated with COVID-19 related disinformation, reliance on social media as a source health information, younger age and co-morbidities. Interventions that increase accurate COVID-19 vaccine knowledge, trust and moti...

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.

• 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 10.1101/2021.10.28.21265601: (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).

There are several limitations to this study. First, we recruited participants who were registered with an internet research company. Therefore, we may have selected people who actively used the internet, smartphones, and apps. However, we consider this potential selection bias to be negligible because the COCOA downloading rate announced by the Ministry of Health, Labour and Welfare in December 2020 was 20.8%,23 and thus close to the rate in the present study (25.1%). Second, the present study used cross-sectional data for a single period of time. Therefore, the findings can only suggest associations between factors for this given period of time, and cannot capture changes over time within individuals. Third, in the multivariate logistic regression analyses, there was a possibility of unmeasured confounding. Unmeasured personal habits and behavioral patterns may have influenced the adoption of the DCT app.

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.

• 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 10.1101/2021.10.22.21265385: (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).

There are two additional limitations worth noting. First, these results primarily reflect nurses as only three doctors participated. While the backbone of clinical care is nurses and nurses are key to patient monitoring during advanced respiratory care, this training may be more suitable for doctors than nurses. Given the very limited doctor participation we were unable to stratify our analysis by cadre as initially planned. For advanced respiratory care to be successful it will be important for doctors to participate in future trainings and reasons for their lack of attendance need clarification. In addition, given the severe human resource constraints in the health sector of Lesotho, nurses need to function independently when providing advanced respiratory care since doctors are few and unable to be continuously available for all patients. Second, to deploy the training quickly we made assumptions about the baseline educational background and working medical knowledge of providers. Before revising and redeploying this training a deeper understanding of healthcare worker educational backgrounds is needed. In sum, this study illustrates the challenges and lessons learned in designing and administering an advanced respiratory care educational training program in Lesotho during the COVID-19 pandemic. If a LDHF approach is not feasible then future renditions of this training will need to be lengthened to at least two days and better incorporate case based and simulation training...

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.

• 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 10.1101/2021.10.14.21264837: (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).

There are a number of limitations that need to be considered when interpreting our findings. First, we were not able to have representation from the A5 priority group (indigent population). While we initially were able to get a participant from this group based on the survey response, we later found during the interview that this individual belonged to a different vaccination priority classification. This may point to issues with online data collection where researchers are unable to reach individuals from low-resource households. Second, there may be social desirability bias because we were unable to ensure if the respondent had other people with them that may have caused a change in their responses. Additionally, we did not disclose any political affiliations and interests, but participants may have been cautious in mentioning negative experiences related to vaccination. Third, there may also have been Hawthorne effect with participants choosing more positive responses considering our background as health researchers. However, we emphasised that they will remain anonymous and their data treated with utmost confidentiality. Lastly, factors influencing COVID-19 vaccination uptake is context-specific, and this paper does not aim to represent all situations and circumstances.

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.

• 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 10.1101/2021.10.30.21265693: (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).

This study has several limitations. For instance, the data on SP-specific T-cell response immediately after the vaccination was lacking and the sample size of the cohort was small. In addition, generally, cellular immunity is weakened in elderly and immunosuppressed individuals. However, our study demonstrated that antibody titers do not necessarily correlate well with cellular immunity, indicating that the dynamics of cellular immunity are different from those of humoral immunity and suggesting that the evaluation of cellular immunity is warranted for long-term evaluation of the efficacy of SARS-CoV-2 vaccines.

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.

• 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 10.1101/2021.10.29.21265678: (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.

Our findings are subject to at least several limitations and biases. As noted, selection bias could arise because fundamental risk differences between pregnant women and the general population are not accounted for in our statistical model. The direction and causes of this potential bias vary: pregnant women could have less exposure to SARS-CoV-2 due to behavioral choices, depending on sociodemographic characteristics, but increased biological susceptibility to infection due to immune weakening. Nonetheless, estimates from cohorts with clear selection biases, such as blood donors or healthy volunteers, can still meaningfully inform seroprevalence estimates in the general population [18, 24-26]. Second, misclassification bias can occur due to imperfect test sensitivity and specificity. We have estimated specificity using a pre-pandemic sample of DBS and have incorporated it into the statistical model; however, we do not have an estimate for sensitivity. Accounting for imperfect test sensitivity would be expected to shift the seroprevalence estimates higher and widen the credible intervals (Supplementary Figure 7), due in part to the uncertainty involved in measuring sensitivity itself. By assessing the distribution of maternal antibodies to SARS-CoV-2 statewide and over time, our study provides a strategy for the systematic evaluation and estimation of population-wide cumulative incidence of SARS-CoV-2. Prospective use of NBS-based cumulative incidence estimates of exposure fo...

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.

• 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 10.1101/2021.10.28.21265549: (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 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.

• 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 10.1101/2021.10.28.21265622: (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 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.

• 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 10.1101/2021.10.28.21265624: (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 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.

• 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 10.1101/2021.10.18.21264530: (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 data.

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.

• 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 10.1101/2021.10.28.21265616: (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).

Our study has limitations. First, reporting may not have been uniform across centers despite the use of a study protocol and a standardized data capture tool. This includes but is not limited to the interpretation of chest radiographs, definition of obesity, and the severity of comorbidities. Also, the respective comorbidities can represent a heterogeneous group of diseases with different etiologies. Second, despite being one of the largest pediatric cohort studies with more than 100 severe cases, the numbers of some individual comorbidities are small. This might overestimate or underestimate the impact of infrequent comorbidities such as anemia and/or hemoglobinopathy, chromosomal, or cardiac disorders. Third, laboratory investigations were not systematically performed. Complete blood counts, CRP, and albumin values were missing in 4.2%, 15%, and 67%, respectively. We therefore could not assess the latter in multivariable models. Moreover, laboratory investigations were done at the clinicians’ discretion, not at set time points during the illness. Other parameters previously described as risk factors could not be evaluated. This includes ethnicity4,7,9,12 which was not readily accessible from hospital records. In addition, viral sequencing data was not available, accordingly we cannot evaluate the impact of different SARS-CoV-2 variants. Fourth, indications for testing for SARS-CoV-2 likely varied by center and over time, which might have affected the clinical spectrum of in...

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.

• 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 10.1101/2021.10.29.21265511: (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).

As limitations, this study is a case-control study and prospective data collection especially for patients who were not positive for SARS-CoV-2 was not possible. Secondly, although older healthy controls were enrolled for this study, this group remained younger and had fewer co-morbidities compared to the cancer groups. And lastly, as the study was conducted in an oncology unit setting, cancer patients that were immediately transferred to the COVID-19 wards and had succumbed to the infection, were not included.

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.

• 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 10.1101/2021.10.28.21265615: (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 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.

• 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 10.1101/2021.10.28.21265608: (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 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.

• 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 10.1101/2021.10.28.21265596: (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).

Study limitations: The study restricts the analysis to only five countries and hence future studies using ICTR can check its validity and implications for larger set of countries.

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.

• 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 10.1101/2021.10.28.21265604: (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).

However, strengths and limitations of our approach need to be considered. A checklist was used in this derived from the “PIET-T Process model” which was designed specifically to examine the scope for the potential transferability of healthcare interventions from one context to another. While it is a strength to have a theoretically informed approach, there are no established cut-offs for transferability. We chose to focus on those interventions that were amongst the most highly rated and tried to minimise subjectivity by using multiple scorers. The limited research in the area meant we had to broaden our scope to all workers and not just healthcare workers. Extracting intervention information from a previous systematic review6 allowed for a more thorough search of the literature to be conducted. Studies not written in English were excluded from the search and this may have led to important studies being left out of the review. Only one database was searched for updated relevant literature from 2015 onwards. Only one study gave any information about how the intervention could be transferred to a different context. The target context of this study included frontline HCWs in a hospital setting in Ireland due to the analysts involved being more familiar with this healthcare system, this may limit the generalisability of our findings. Interventions were generally poorly described and therefore replication of the original intervention may be difficult. A thorough examination of rob...

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.

• 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 10.1101/2021.10.28.21265578: (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 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.

• 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 10.1101/2021.10.28.21265610: (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 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.

• 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 10.1101/2021.10.28.21265544: (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 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.

• 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 10.1101/2021.10.28.21265499: (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 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.

• 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 10.1101/2021.10.28.21265588: (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 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.

• 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 10.1101/2021.10.28.21265598: (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.

To overcome some of these previous limitations, we used electronic health records (EHR) from eastern Denmark, identifying 33,938 patients who had at least one positive SARS-CoV-2 RT-PCR test. To enable ML algorithms, clinical data need to be encoded into features that can be computed. Multiple approaches have been suggested for encoding EHR into computationally meaningful representations30,31. We opted for a simple feature engineering approach by considering the latest values or counts in clinically relevant time windows prior to FPT depending on the type of variable. Additionally, instead of characterizing patients’ relevant history using a limited set of pre-selected variables, the set of 22 features in the final model were derived using a data-driven approach from an initial set of 2,723 features that encoded available demographics, laboratory test results, hospitalizations, vital parameters, diagnoses and medicines. This approach enabled us to reduce model complexity to a smaller feature set while avoiding potential bias introduced by pre-selecting variables. While EHR are more representative of patient populations in terms of real-world data (RWD)32, some challenges arise when processing EHR for clinical research. Data collected from routine care may present inconsistencies33 that cannot be appropriately curated for in such big data sets, especially for information regarding clinical interventions or hospitalization status. We thus selected SARS-CoV-2 positive status and...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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

• 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 10.1101/2021.10.29.21265248: (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 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">NCT04969276</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 a Quadrivalent High-Dose Influenza Vaccine and a Mo…</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.

• 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 10.1101/2021.10.27.21265591: (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.

Limitations: Our study was limited in that it focused on the population of individuals over 70 years old. The number of deaths in this age group was 61% of total deaths before mass vaccination of the older population, i.e., before the study period. During the study period the percentage of deaths in this group was 40%. The study period after vaccinations was limited due to uncertainties related to the Delta variant and the temporal period of vaccine efficacy in individuals. Therefore we limited the study period to the end of June before the Delta variant created new patterns of rising cases. Thus, the precise results relate to conditions in which the Alpha variant was predominant, and the vaccine efficacy was presumed to be high. Many questions about the effects of vaccination on the Delta variant remain unanswered with real world data as it is presently in clear how much of the rise in deaths may be due to vaccines wearing off. Calculating the precise number of saved lives by any vaccine is an impossible task. The counterfactual number of deaths if the public had never been vaccinated depends upon many variables that change because of the patient’s vaccine uptake. For example, we might assume that due to the high uptake of the COVID-19 vaccine in Israel, the government became less strict in terms of closures, but how strict exactly it might have been in the counterfactual world is a mystery and only one of many variables affecting transmissions and deaths. After a steep rise...

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.

• 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 10.1101/2021.10.26.21265497: (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 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">NCT04318314</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">COVID-19: Healthcare Worker Bioresource: Immune Protection a…</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.

• 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 10.1101/2021.10.26.21265146: (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).

Lack of information regarding population and COVID-19 infection dynamics in each sewershed is one of the limitations of this study, preventing us from doing a sewershed-based analysis. Peak concentrations of SARS-CoV-2 were observed on the day when critical-level restrictions were enforced and the following 4th and 6th day (Fig. 4). Other observed concentrations after the first detection were generally in close proximity with the modeled concentrations for at least one genomic target. Different decay rates for N1 and N2 resulted in higher concentrations of N1 for back-trajectory modeled samples collected between November 16th and December 15th, while the difference between N1 and N2 concentrations for the rest of the samples was smaller than 0.35 on log10 scale (Fig. 4). The decay rate of N1 was calculated based on the degradation of genomic signals of gamma-irradiated SARS-CoV-2 by Ahmed et al. (2020b) and had a higher standard deviation of 15% and lower R2 of 0.79 compared to those values of N2, which were based on degradation of active SARS-CoV-2 (Hokajärvi et al., 2021a) (Table 2). Gamma irradiation of SARS-CoV-2 and relatively higher variations in the decay rate of N1 might result in significant biases in such a back-trajectory modeling approach. Therefore, we mostly consider N2 concentrations for back-trajectory modeled samples in the discussion. The critical level restrictions in Manitoba were applied when extensive community transmission of COVID-19 occurred, outbreak...

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.

• 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 10.1101/2021.10.26.21265261: (What is this?)

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

Table 1: Rigor

Table 2: Resources

No key resources detected.