SciScore for 10.1101/2021.03.24.21253489: (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: The high rate of COVID-19 vaccine acceptance in our population may be the result of response bias, where healthcare workers with favorable vaccine attitudes were more likely to complete the survey. Our study may have some limits in generalizability given the setting in New York City and a substantial representation from an academic health system. Additionally, Black and Hispanic respondents were underrepresented in our survey, comprising 10% and 16% of our survey population respectively, whereas approximately 20% of the healthcare workers in our systems’ hospitals identify as Black and 18% identify as Hispanic. We chose explicitly to use receipt as the primary outcome, rather than intent. As such, participants who indicated they “planned” to receive the vaccine were categorized for the primary outcome along with those who stated that they did not plan to. We did review the differences between these two groups and assessed differences over time (see Supplementary Figure 5). Those who stated an intent may have had perceptual or belief reasons for delaying, as several participants expressed in their free text responses. Additionally, while the COVID-19 vaccines were made available to employees at the time of the survey, many may have had access issues, which our survey was not designed to assess. The 11% of respondents in our survey who reported they planned to get the vaccine but had not scheduled or gone for their vaccine yet may have experienced access issues. We...

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.

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 10.1101/2021.03.24.21252687: (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 observational study has several limitations. The sample size (959 patients) was small; our findings will need to be replicated in larger studies. We could not evaluate separately the effects of ACEI and ARB treatment, although investigators have reported greater effectiveness for ACEI compared with ARB treatment [94]. We did not correct for immortal time bias. We did not have access to information on outpatient treatments and thus could not evaluate whether outpatient statin treatment was continued in the hospital or initiated only after hospital admission. We could not evaluate deaths that occurred after 28 days or that might have occurred after hospital discharge. We also did not evaluate the effects of treatment on length of stay, ICU admissions or mechanical ventilation. We are currently expanding our study to include the second pandemic wave (1 August to 31 December 2020) and additional outcomes (e.g., ICU admissions, mechanical ventilation). We will also evaluate separately the contributions of ACEI and ARB treatments alone or in combination with statins to reducing in-hospital COVID-19 mortality and their effectiveness in treating asymptomatic (but PCR test-positive) patients. Observational studies and RCTs both have their places in the hierarchy of research designs [95]. However, if there are no RCTs [96], physicians and health officials will be forced to consider the trade-off between pandemic learning and doing [97]. In this circumstance, they might have to rely...

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.

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 10.1101/2021.03.24.21253576: (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 obviously several limitations in our study, such as the small size of our cohort. Thus, studies with higher number of patients could be of interest to clarify these results. Large-scale GWAS (Genome Wide Association Study) combined with WGS (whole genome sequencing) studies, such as the one being carried out by the SCOURGE consortium(26), will be very interesting to corroborate these results and to explore if they are extrapolable to the whole Spanish cohort or, in contrast, it is specific to our region. In conclusion, the G-containing genotypes of rs4341 and rs4343 confer an additional risk factor of developing severe forms of COVID-19 in patients with hypertension, dyslipidemia, or possibly with diabetes independently of gender. These genotypes are also associated with an increased risk of death, mainly in hypertensive patients. Thus, the genotyping of rs4341 and rs4343 in COVID-19 patients could facilitate a more appropriate clinical management at admission.

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.

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 10.1101/2021.03.25.21252280: (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 present here the results of a method evaluation study and not a seroprevalence study. Therefore, the PPV obtained here (based on a 33.3% proportion of cases defined as laboratory confirmed SARS-CoV-2 by RT-PCR) will probably be lower in a low prevalence setting. Another limitation of this validation study lies in its limited sample size leading to broad 95% confidence intervals, requiring confirmation of these data at a larger scale. Finally, our present conclusions only apply to this RDT, and must not be applied to any other RDTs currently available. In conclusion, this RDT is not meant to replace a SARS-CoV-2 RT-PCR but could be a reliable option for quickly assessing the presence of SARS-CoV-2 antigen in moderate to high COVID-19 prevalence settings and when high viral loads are expected, especially in situations where a rapid result is needed or where RT-PCR is not available. Further investigations in low prevalence situations and using capillary blood are necessary.

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.

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 10.1101/2021.03.24.21253992: (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 Study: As with all case studies, a limitation on the generalizability of our findings to wider patient populations is present. Also, while the lack of immunological responsiveness to vaccination or acute infection in immunosuppressed and solid organ transplant populations is well documented, there may be additional mechanisms contributing to these defects beyond those discussed in this manuscript - particularly with regards to SARS-CoV-2 infection. Our analysis of the immunophenotype of the patient was limited to surveys of circulating immune dynamics; however, numerous studies have also described perturbations in immunity at tissue sites not easily amenable to direct interrogation. We also did not directly analyze antigen specific T-cell responses during either infection, which may reveal additional dysfunction not discussed within this manuscript. Lastly, we also did not fully address every potential avenue of viral immune evasion to immune responses and accordingly suggest that a greater understanding of the virus-intrinsic and host-intrinsic features determining susceptibility to SARS-CoV-2 reinfections is required. Future studies should investigate not only the circulating and systemic adaptive immune responses during SARS-CoV-2 reinfections, but also the possibility that local defects in immune responsiveness among barrier tissue sites may also enable recurrent SARS-CoV-2 infection. Quantification and Statistical Analysis: All statistical analysis was per...

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.

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 10.1101/2021.03.24.21253923: (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.

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 10.1101/2021.03.23.21253873: (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.

There are three important limitations to our analysis: while we attribute improved outcomes in Canada to concrete public health actions, it is also possible that they reflect differences in structural, societal factors that have enhanced COVID-19 risk in the United States. Excess risk of COVID-19 and COVID-19 related death in the United States has been associated with lower income status and non-white ethnicity, but similar relationships have been observed in Canada as well (6, 7). A second key limitation of our analysis is our use of Ontario-specific case fatalities, and hospitalization and intensive care admission risks, to estimate outcomes averted at a national level; however, Ontario’s epidemiology is likely similar to that of Canada overall, both because of similarities in demographics and health systems across the country, and also because the population of Ontario represents approximately 40% of the Canadian population, and 35% of Canada’s COVID-19 case load, such that the Province’s epidemiology strongly influences that of Canada as a whole. Lastly, we assume that attribution of COVID-19 deaths in Canada and the United States occurs in a comparable manner; questions around over- and under-assignment of COVID-19 mortality have been raised in both countries (8).

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.

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 10.1101/2021.03.24.20208835: (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).

Thus, the most practical and representative material would be the nasal swab for both mild and severe cases, but with the caveat that its sensitivity is around 70%. A systematic review of the literature showed that the rate of false-negative results from RT-PCR is 29% (6). Out of the patients evaluated, 96% were positive for IgA (24/25) and 100% were positive for IgG (26/26), both of which were collected after 14 days. K Imai et al., using the immunochromatography technique, found IgM and IgG sensitivity for symptomatic patients with more than 14 days of symptoms of 95.8% and 65.2%, respectively. When the serological test is combined with chest tomography in symptomatic patients, sensitivity after two weeks reaches 100% (17). As the molecular analysis through RT-PCR can be falsely negative, the erroneous investigative conduct of the case would lead to misdiagnosis with new exams and unnecessary treatments, thus postponing fundamental interventions to prevent the patient from evolving with pulmonary fibrosis and permanent functional alteration. Patients confirmed for COVID 19 who presented pneumonia maintained presented pneumonia maintained evaluated around 30 days after the onset of symptoms, reaching 84.2% of DLCO in the pulmonary function test. (18) Previous studies with SARS showed that 52.4% of the patients who were hospitalized maintained abnormalities in the DLCO after 2 years (19). However, in other analysis, the improvement of this parameter occurred in 80.4% in 3 mon...

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.

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 10.1101/2021.03.23.21254146: (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).

[17] This rapid-reaction pilot study has a number of limitations. First, the sample size was small and addressed patients only in one portion of West Los Angeles. Nevertheless, the results have been received as valuable to public health officials who are supporting additional enrollments across all service areas to increase the sample. Second, while all homeless-flagged patients with phones had the opportunity to answer the survey and response rates were considerably higher than most online or phone-based polls, we know that those who answered the survey were more likely to be female (59% vs. 35%) and less likely to be African-American (9% vs. 24%) than that clinic’s homeless patient base as a whole. Given the lack of differences in hesitancy across any demographic groups and the small sample size, we did not report weighted results. Finally, we note that these interviews were conducted prior to PEH receiving universal vaccine eligibility on March 15, 2021, and that some hesitancy may more accurately reflect indifference or frustration at the difficulty of obtaining the vaccine. In spite of these limitations, our findings point to challenges in widespread vaccine scaleup that are not so different than those faced in the general population. It is important to know that those people who need the vaccine most - those who fear COVID-19 but are less likely to protect themselves through social distancing measures - are those most highly willing to be vaccinated. But achieving wides...

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.

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 10.1101/2021.03.24.21254124: (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.

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 10.1101/2021.03.23.21253730: (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: The strengths of our study include the random sample, population-based study design, high completion rate of DBS samples (88%), and the low risk of overestimation of seroprevalence. There are no stability issues related to the time elapsed from DBS sampling to time of arrival at the laboratory. However, this study also has limitations. The response rate was 30%; but the age and sex distributions were similar to that of the Norwegian general population, so the overall results may still be representative of the population. However, even though we oversampled, the results from some subgroups may be more uncertain and not representative of the Norwegian population. Studies involving personal information linked to risk behavior tend to have a lower response from high-risk groups [21]. However, having antibodies is not necessarily linked to a stigma or viewed as high risk. Because of the low response rate in the youngest age group and because this group had the highest seroprevalence, the estimates could be too low. On the other hand, weighting and adjustments for sensitivity and specificity of results reduced underreporting to a minimum. There are several reasons why seroprevalence may be underestimated in our study. First, those who were very recently infected, were less likely to have detectable antibody levels at the time of sampling [22]. Second, because of the sensitivity of the two tests (94% and 84%), some false negative results were expected, but...

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.

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 10.1101/2021.03.24.21253599: (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.

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 10.1101/2021.03.23.21253520: (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, a limitation of this approach is that emergence of variants devoid of N501Y mutation such as the recently-recognized B.1.525, reported here, may be underestimated due to failure of detection by qPCR targets employed, and requires alternative qPCR assays for identification (9, 10). In summary, this study demonstrated the feasibility of a combined targeted and WGS testing strategy for VoC prevalence assessment in one Canadian province, which will be instrumental for continued VoC surveillance, and to inform public health efforts.

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.

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 10.1101/2021.03.23.21254054: (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).

One of the limitations of the meta-analysis is integral to the methodology. The summarization of information may ignore the important difference between studies. Secondly, the number of patients in the RECOVERY trial was much higher than other RCTs (study weight 77%) [33]. There were differences in enrollment criteria, the time at which anti–interleukin-6 therapy was initiated, the primary outcome, and background care. Also, five of the included studies had an open label design, implying high risk of performance and selection bias due to lack of blinding of participants and personnel to intervention, limiting our ability to interpret results. Lastly, we included one trial from the preprint databases, which has not been peer-reviewed [33]. Preprint articles possibly indicate the undetermined quality of available literature. One of the trials also ended early due to safety concerns, although mortality in the control arm was extremely low [29]. In conclusion, our meta-analysis suggests tocilizumab, when used along with dexamethasone, could be an effective therapeutic option with promising evidence on reduced mortality, progression to mechanical ventilation, and discharge from hospital. Limitations may exist in terms of obtaining tocilizumab as it is an expensive monoclonal antibody. Supplies may be limited, and many hospitals may not necessarily have adequate quantities. Clinical judgement is also necessary as some patients may not require the use of tocilizumab. Future studies ...

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.

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 10.1101/2021.03.23.21253460: (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.

This limitation is highlighted in the apparent 50% IgM seropositivity for MERS-CoV in the Control Group. While there was a MERS outbreak in South Korea in 2015, there were only 186 confirmed cases in that outbreak [21] and a more likely explanation is that this reflects a cross-reactivity from immunity to a related beta coronavirus. On a similar note, we were surprised to find 25% IgG seropositivity for SARS-CoV-2 in the Control group. Given that they were all seronegative to SARS-CoV-2 by IgM, this suggests the possibility of either a prior asymptomatic SARS-CoV-2 infection or cross-reactivity from immunity to another coronavirus. Assessing the serological landscape of CoV-specific IgM and IgG responses resulted in several key observations: 1) IgG seropositivity to seasonal OC43 and HKU1 as well as influenza H3 was high, while IgM seropositivity to these antigens was low; 2) IgM seropositivity to SARS-CoV-2 was highly specific, with 90% seropositivity in COVID-19 samples and 0% seropositivity in Control or Pre-COVID samples; 3) SARS-CoV-2 IgG responses were highly cross-reactive with almost 60% of SARS-CoV-2 IgG seropositive samples being seropositive for all five CoV spike antigens; and 4) IgM and IgG SARS-CoV-2 spike responses appear to show different fine specificities, with IgM spike responses being largely recapitulated by the SARS-CoV-2 RBD antigen, while IgG spike responses were not. Taken together these observations suggest a few explanations. First, that the IgM res...

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.

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 10.1101/2021.03.24.21253807: (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).

Several survey limitations should be considered. Although these results provide a useful initial global snapshot of the impacts of COVID-19 on AMR, they could also be considered an oversimplification of complex and varying experiences across national and facility levels. Heterogeneity between countries in the robustness of their existing AMR surveillance systems and activities (i.e. capacity, experience, resources) may have affected survey interpretation. If national focal points did not coordinate their responses with other experts or did not have sufficient knowledge of the data or dynamics in their country, the validity and reliability of some responses may have been affected. Furthermore, self-reported perceptions of national focal points on the impacts of COVID-19 on AMR could have also been affected by self-desirability bias. This survey was the first concerted effort to explore the global impact of COVID-19 on AMR surveillance, prevention and control among GLASS countries. Although much focus is understandably placed on COVID-19 at present, we believe that AMR must remain high on the global health agenda. This survey included a wide range of country settings and responses which highlighted both the universal effects of COVID-19 on AMR as well as the heterogeneity of impacts across countries. The results underscore the importance of finding ways to leverage the COVID-19 response activities to also support routine AMR prevention and control, where possible, and advocate ...

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.

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 10.1101/2021.03.23.21253748: (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">NCT04327570</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">In-depth Immunological Investigation of COVID-19.</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.

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 10.1101/2021.03.23.21253727: (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.

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 10.1101/2021.03.22.21254125: (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.

Strengths and Limitations: We calibrated our model to a real-world nursing home. The basal transmission model, in which no agents were vaccinated, generated plausible attack rates when compared to California nursing homes of a similar size. This, plus incorporating parameters from real-world data, provides external validity to the changes observed in our model. A particular strength of ABM is to show how complex outcomes can emerge from simple sets of rules; our model took advantage of this approach to show how interactions between staff and residents manifest the outbreak patterns observed in vivo. However, this model is primarily useful as an exploration of the impact of multiple interventions and introduction probabilities on an outbreak once introduction has occurred, and is therefore not meant to model the processes that lead to an introduction in the first place. Simulations were run for 150 days or until the facility was disease-free for up to 7 days; thus, it is also not able examine the impact of multiple introductions over longer periods of time or waning immunity from recovery or vaccination in its current form. Not all data-derived parameters were made equally. The estimated effect of PPE use on transmission varied widely, thus making a reliable parameter difficult to define and the model sensitive to changes. Testing was also oversimplified in our model, as we assumed instantaneous results and all tests were equally sensitive. Additionally, we assumed that the ef...

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.

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 10.1101/2021.03.22.21254140: (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.

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 10.1101/2021.03.23.21254060: (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.

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 10.1101/2021.03.22.21254127: (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).

Finally, given the concentration of transmissions in the context of workplaces and their overlap with household density (3), vaccination at workplace and among subgroups with high rates of contact (i.e. essential workers) represents a potential prioritization strategy to mitigate transmissions, severe outcomes and VOC growth (9, 10) The limitations of these analyses include the use of ecological data, rather than individual-level data on income and occupation for this analysis; and the potential for differential SARS-CoV-2 testing across tertiles. Proportionally there has been less testing in lower-income neighbourhoods (3) resulting in the potential for underestimating both wild-type in VOC cases in economically marginalized communities. Restrictive intervention strategies have represented the foundation of most COVID-19 public health interventions. Given that VOCs rapidly spread in the same transmission networks as wild-type SARS-CoV-2, and their emergence during a period of intensive societal restrictions, suggests supportive measures in these communities are needed. Moving forward necessitates ensuring that public health measures avoid reinforcing underlying inequities by leveraging resource and service-based strategies to minimize the future spread of novel VOC and associated morbidity and mortality.

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.

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 10.1101/2021.03.23.21254092: (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.

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 10.1101/2021.03.22.21254139: (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).

A limitation of our study is the lack of identification of the responsible pathogens. This is a common limitation to pneumonia studies 101. When pathogens are identified, they are viral more often than bacterial, with the top three in US hospitalized patients being human rhinovirus, influenza A and B, and Streptococcus pneumoniae 102. Although we did not attempt to determine, from clinical records or postmortem culture, the presence of associated pathogens, the confluent intra-alveolar accumulation of neutrophils is generally regarded as indicative of a bacterial cause 103 and therefore this study is likely to have been biased towards the inclusion of bacterial pneumonia and against the inclusion of purely viral pneumonia, although mixed bacterial and viral causes were very likely to have been common 101,102,103.

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.

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 10.1101/2021.03.22.21253831: (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.

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 10.1101/2021.03.21.21254061: (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 the use of a single assay to quantify post-vaccine anti-spike antibody levels, however as it is commercially-available and well calibrated (Figure S1), results should be generalisable. Our focus on a defined group, i.e. HCWs, is both a strength and a weakness, and we are not able to assess variations in vaccine response in children or those >65 years. Additional data on post-vaccine antibody responses in older individuals, at highest risk of adverse outcomes from SARS-CoV-2 infection, is particularly important. Our cohort was also 76% female and predominantly of white ethnicity. We did not assess neutralising antibodies or T cell responses, both of which reflect vaccine response and may vary by vaccine. Further work will be required to determine the duration of antibody responses. In summary, vaccination leads to detectable anti-spike antibodies in nearly all healthy adult HCWs. Markedly higher responses to vaccine are seen after previous infection; single dose or delayed vaccination could be considered where vaccine sparing is needed in healthy individuals with robust evidence of previous infection. Some caution is required with antibody result interpretation and any subsequent behaviour change, as despite good protection from vaccination, seroconversion with high antibody levels still does not afford absolute protection from infection. Large-scale studies will be required to assess how protection from infection varies by antibody titre.

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.

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 10.1101/2021.03.17.21253847: (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.

Another limitation of the study is that the data of days-since-symptom-onset came from limited documentation in the medical records based on patient self-reporting. These data may not always be accurate or complete. Ct values were not available from some rRT-PCR methods used in this study, and are in general not well-standardized across platforms 19. This may lead to heterogeneity in the nucleic acid data presented. We had access to a relatively small number of serial samples from immunocompromised patients. Finally, due to the poor culturability of most clinical specimens, we did not use viral culture to assess the infectivity of antigen positive samples. In future studies, the Microbubbling SARS-CoV-2 Antigen Assay can be automated and multiplexed with other infectious disease antigens, and applied to other sample types. With the convenient computer vision and ML based algorithms on smartphone for automated bubble recognition, quantitation and result classification, this assay also has the potential to be used at the point-of-care for frequent and repeated testing. Our relatively simple computer vision and ML pipeline produced accurate automatic classification results, which we expect will be further improved through training more sophisticated deep learning-based systems on larger datasets. In particular, a common failure mode in our current visual bubble detection system is when bubbles appear blurry because they are not on the focal plane, or are inconsistently lit in di...

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.

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 10.1101/2021.03.22.21254006: (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.

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 10.1101/2021.03.22.21254032: (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">NCT04370808</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Not yet recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">VITACOV: Vitamin D Polymorphisms and Severity of COVID-19 In…</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.

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 10.1101/2021.03.22.21253818: (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).

Above all, as some individuals reportedly remain PCR positive weeks after SARS-CoV-2 infection recovery, knowing whether viral RNA in these persistent carriers is contagious provides key insights for quarantine policy, to safely discontinue self-isolation and contact tracing as essential public health measures to definitively prevent transmission.(6,26,32) Besides some limitations, the proposed viability RT-qPCR effectively reduced the amplification signals of non-infectious and free RNA of SARS-CoV-2 in complex matrices finally providing a better estimation of the infectiousness of samples. Thus, mathematical models derived from laboratory scale experiments comparing viability RT-qPCR and viral replication could correlate viral load and infectivity, finally providing relevant tools of interest based on rapid molecular assay for prevention strategies and risk assessment.

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.

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 10.1101/2021.03.25.436907: (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">NCT04315948</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Trial of Treatments for COVID-19 in Hospitalized Adults</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04385095</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Trial of Inhaled Anti-viral (SNG001) for SARS-CoV-2 (COVID-1…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04492475</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Adaptive COVID-19 Treatment Trial 3 (ACTT-3)</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.

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 10.1101/2021.03.22.21251380: (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: There are several limitations to our study. First, survey respondents were recruited using MTurk, an online platform that—while as effective as traditional survey sampling methods— skews towards younger, more well-educated individuals [29]. Thus, our participant cohort cannot be interpreted as a nationally representative sample. Nonetheless, given the current pandemic and the need to minimize viral exposure for both researchers and participants, surveying study participants remotely using a well-established, online platform seemed the most reasonable and ethical means to conduct our study. Study findings may also be limited by the hypothetical nature of the survey design, where we asked participants to imagine how they would react in such a scenario. However, survey scenarios were designed to be easily readable and were repeated on several pages in order to facilitate participant comprehension and immersion (Supplement eFigure 4). To further reduce the number of participants who did not take an appropriate amount of time to imagine the scenario, we restricted analysis to participants who spent at least 2 minutes on the survey and passed all attention checks. External validity of this study is limited by the fact that the study only evaluated behavioral intentions. A large body of prior research has noted that behavioral intentions do not immediately translate to behavioral engagement but are rather attenuated or enhanced by other factors. Nevertheless, behavioral...

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">NCT04459520</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Effect of Availability of COVID-19 Testing on Choice to Isol…</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.

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 10.1101/2021.03.22.21254090: (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).

A limitation of registry studies is that health definitions rely on registrations from contact with healthcare. Test capacity for SARS-CoV-2 and healthcare availability for those with milder COVID-19 symptoms have varied through the pandemic. In the initial phase, testing was limited, and healthcare was restricted to those with more severe symptoms or underlying risk conditions. We found that pregnant women were slightly more likely to be tested in the initial phase than non-pregnant women, but after the initial months when testing capacity increased, pregnant women were slightly less likely to be tested. Asymptomatic women and women with milder symptoms were not captured and classified as infected in our data. However, results for the two waves of the pandemic in Norway yielded similar estimates, supporting that test-or healthcare availability was unlikely to explain our findings. Identifying ongoing pregnancies and early terminations through healthcare contacts is also prone to misclassification. Towards the end of the follow up period we were less likely to capture ongoing pregnancies that will end in miscarriage or induced abortions. Only 44.2% of miscarriages and induced abortions had a prior antenatal code. This could have resulted in underestimation of the number of pregnant women and attenuation of associations. Since antenatal visits are without information on gestational length information, we defined pregnancy start date and durations for ongoing pregnancies and ea...

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.

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 10.1101/2021.03.22.21254057: (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 a number of limitations. The patients represent a small sample of the total number of patients discharged from hospital following COVID-19 infection in the UK. The study population is younger than the whole population in the UK that survived hospitalisation for COVID-19 infection40 and only included those able to attend clinic visits and undertake the study procedures. This acquisition bias might under-represent the most severely affected patients but conversely those patients with ongoing symptoms might have been more willing to participate. The patient-reported outcomes, physical and biological tests assessed cross-sectionally does not allow for the clear differentiation between the contribution from premorbid disease versus emergent impaired health status and symptoms. Further analysis of the trajectory of recovery and linkage to primary and secondary health records within PHOSP-COVID will enable further discrimination. Notwithstanding this limitation, the magnitude of burden of physical and mental health is substantial in this group. Our definition for recovery in this report is a subjective definition based on patient perception and will fail to identify pathological changes that have not yet led to clinical expression, but might become overt in later follow-up. However, patient-perceived recovery did correspond well to the overall burden of disease identified in the recovery phenotypes. Further comparisons are also required with recovery following acute r...

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">ISRCTN10980107</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td></tr></table>

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

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

• 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.

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 10.1101/2021.03.20.21253990: (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).

A key limitation of this study is that the released provisional data from 2020 did not allow us to examine other outcomes, particular subgroups, or severely affected geographies. Future detailed data will allow researchers to study the patterns we identify here in greater detail, including changes in fertility decisions and other proposed mechanisms (e.g., elevated selection in utero, reduced air pollution, and changes in clinical practice) that may have caused the observed outcomes.

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.

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 10.1101/2021.03.16.21253634: (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 strengths and weaknesses: While the present study has its strengths, including its size, national representativeness, and timing, there are also some weaknesses. First, we used vaccine intentionality as an indicator vaccine uptake but the correlation is imperfect. In a small scale longitudinal study conducted during the period of the 2009 H1N1 pandemic in Hong Kong, less than 10% of people who expressed a commitment to being inoculated reported that they had received a vaccination two months later.50 Elsewhere, in a US adult population at high risk of seasonal influenza, around half of those intending to be vaccinated had received the inoculation within the following 5 months.51 Second, there was inevitably some loss to follow-up (figure 1). While this attrition may have impacted upon the estimation of the prevalence vaccine hesitancy which is likely to be lower in our select sample relative to the general population,52 it is unlikely to have influenced our estimation of its relationship with cognitive function. Thus, in other contexts, we have shown that highly select cohorts reveal very similar risk factor–disease associations to those seen in studies with conventionally high response.53 In conclusion, people with lower scores on standard tests of cognitive function reported being less willing to take up the future offer of vaccination for COVID-19. It is possible that erroneous social media news reports have complicated decision-making. Special efforts should be made...

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.

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 10.1101/2021.03.25.21253802: (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).

Unfortunately, the nature of the B cell epitope recognized by the antibody utilised in the Abbott test is not known but apparently other SARS-CoV-2 antigen tests, COVID-19 Ag Respi-Strip and LumiraDX SARS-CoV-2, seem to suffer of the same limitation as supernatant of cultured cells infected with virus isolates D1_7_B.1.1.119, D1_8_B.1.177.7, D2_1_B.1.160, and D2_3_B.1.177.4 carrying respectively mutations R209I, P365S, M234I-A376T, and D348Y failed to generate a positive signal thus suggesting that these assays use antibodies with similar specificities. The fact that some virus variants are “undetectable” irrespectively of the Ct value combined with a lower sensitivity of antigen tests may have accounted for the partial and disappointing results obtained when antigen tests were utilised in large population screens. It should also be considered that the massive use of antigen tests could exert a positive selection for undetectable virus variants and thereby causing their relative increase in frequency over time. Our results would support this notion: The DNCOV+/ANCOV- A376T-M241I virus variant accounted for 42% of all mutation found in the N-antigen B cell epitope 337-422. Analysis of virus sequences isolated from January 2020 to December 2020 indicated that in Veneto the A376T-M241I variant progressively increased in frequency from the beginning of October 2020 to 20% by the end of December 2020 while in Europe and the rest of Italy, after a small peak in October 2020, it fol...

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.

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 10.1101/2021.03.25.21253694: (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).

Aside from our findings and risk assessments, some limitations of our study have to be taken into account. First, the study was conducted with highly professional singers, and the results can therefore not automatically be transferred to other settings or amateur singers. Second, the test results are rather specific. We took into account different singing styles and three different singers from two different musical backgrounds. Therefore, the findings are very representative for professional classical singers as well as modern rock/pop singers, with restricted transferability to the amateur music sector and large choir groups. Since the test singers have been part of the study and know their voices very well, relevant lung capacity or ways of singing were identified for every test person. This seems to be one of the strengths of our study. Further limitations concern the fact that the measurements were conducted with three singers only, while being sensitive to individual differences of singing, lung volume, etc. They were also performed only once for every singer, whereas more repetitions of the same sequence or analyzing more persons would have given more information on reproducibility of the test setting. Another limitation of the measurements is the fact that air velocity measurements are very sensitive to surrounding movements, with the waving of a hand already influencing the measurements at the sensor.

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.

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 10.1101/2021.03.23.21253487: (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.

Sample size is a limitation of this study; however, the reproducibility of our observations across both bulk and scRNA-seq analyses and the significant number of differentially expressed genes among the comparator groups support the validity of our conclusions. Because this study was limited to critically ill, intubated patients, we were unable to assess early stages of COVID-19, which may provide additional insight regarding determinants of secondary bacterial infection. Additionally, we were unable to assess whether epithelial cells contributed to VAP risk due to enrichment for immune cells prior to scRNA-seq. With larger cohorts, the early detection of specific immune pathway suppression and microbiome collapse could be leveraged to develop clinically useful models for identifying COVID-19 patients with increased susceptibility to secondary bacterial pneumonia.

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.

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 10.1101/2021.03.24.21253517: (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.

As with any modelling study, the various assumptions and simplifications can contribute to a number of limitations. With no reneging or balking or priority-based service order, the vaccination pathway actually represents a straightforward queueing network. Given also the evidence that arrivals are random (Poisson distributed) and that activity-level service times are adequately represented by the considered 2-parameter distributions, the limitations of this study relate mainly to application as opposed to conceptual or methodological appropriateness. Specifically, the conditions surrounding data collection should be carefully considered. First, vaccinees were typically over 70, since vaccination priority in the UK was based primarily upon decreasing age [10]. Second, vaccinations took place over winter, when additional clothing was being worn. Third, data was collected within four to six weeks of each site opening, when staff would not yet be fully familiarised to their new roles. Therefore, in the months following this study it would reasonably be expected that service times would reduce, which, in turn, would allow greater throughput than that deduced here. However, it is important to note that these three factors are not wholly explanative of service time variation, given the substantial differences in Combined duration between Vaccination Centres A and B (Section 3.3). This would therefore suggest caution in seeking to extend the specific results of this study to other si...

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.

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 10.1101/2021.03.21.21254065: (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.
• Thank you for including a protocol registration statement.

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 10.1101/2021.03.26.437153: (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.

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 10.1101/2021.03.24.21253587: (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.

A limitation of the study is the sequences available for analysis; accurate estimation of the likely source of infection depends on having sufficient sequences available from the community of affected patients and of cases from the hospital setting. Here, we obtained sequences from two-thirds of the lab-detected SARS-CoV-2 cases from RDU1-RDU5, and 44% for RDU6. We also compared data from the RDUs with 944 other cases in the community, 700 inpatients and 546 samples taken from patients presenting in emergency departments in the same health boards as provide care for dialysis patients. Additionally, COVID-19 is asymptomatic in up to 20% of patients, which may have reduced the number of infections captured.26 Further, early in the pandemic, HCWs were ineligible for testing. Frequent, regular testing of all HCWs and all patients, regardless of symptoms is warranted. There is also mounting evidence that HCWs have a higher seroprevalence for SARS-CoV-2 antibodies than the general population, with a high proportion being asymptomatic.27,28 The low substitution rate of SARS-CoV-2 limits the granularity of outbreak analysis; as demonstrated in this study, indistinguishable sequences may not be part of a transmission cluster if there is widespread circulation in the patients’ home communities. To address this limitation, we employed the SRT, which combines sequence data with both temporal and geographic data to improve estimates of within-unit and within-hospital versus community tran...

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">NCT04405934</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Not yet recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">COG-UK Project Hospital-Onset COVID-19 Infections Study</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.

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 10.1101/2021.03.24.21252635: (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">NCT04812496</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Tenofovir-DF Versus Hydroxychloroquine in the Treatment of H…</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.

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 10.1101/2021.03.22.21254121: (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).

Strengths and Limitations: A strength of this study was the variety of perspectives that were obtained on routine immunization programs during the COVID-19 pandemic from most P/Ts. As well, the use of key informant interviews rather than survey methods allowed us to gather in-depth perspectives on routine immunization programs in each P/T. However, as only a few select individuals were interviewed from each P/T, the perspectives gathered are not representative of entire P/Ts. Furthermore, there may be variation in individual perspectives across a single P/T, although the perspectives shared were very consistent within a given P/T. At the time the interviews were conducted, most P/Ts did not have up-to-date information on routine immunization coverage rates during the pandemic. Similarly, given that the COVID-19 pandemic is ongoing and there is a lack of available information on immunization coverage rates, we do not know which P/T strategies were the most effective in ensuring continuity of routine immunization programs. Implications: This study adds to existing literature by identifying and synthesizing pan-national public health approaches to the continuity of routine immunization programs during the pandemic. Results can inform policymakers and program planners and can assist in future development of national guidelines. As well, we anticipate that the information in this study will enable P/Ts to learn from one another by comparing their approach to maintaining routine im...

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.

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 10.1101/2021.03.22.21254120: (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).

A study limitation was that seropositivity thresholds could not be estimated with pre-pandemic saliva samples due to lack of access to them, and thus sensitivity and specificity could not be established for the saliva assays by standard methods. Using RT-PCR negative pandemic samples was somewhat useful for serum/plasma samples, but with saliva there was substantial overlap between antibody levels in infected and non-infected individuals. In addition, being pandemic samples, we cannot ascertain that they were not previously exposed at low levels and therefore this approach is not optimal. This constraint could be overcome in follow up studies by assessing seroconversion in consecutive samples calculating the fold change increase in levels (e.g. ≥4) over a given study period16 and, in future, access to pre-pandemic samples in international biobanks will be sought. Finally, there could be some imbalance between age and infection that could affect the antibody results. However, we analyzed the effect of age stratifying by infection status to take that into account. In conclusion, antibody levels in saliva measured with our high-throughput qSAT assay largely correlated with those in serum/plasma from individuals with confirmed RT-PCR diagnosis of SARS-CoV-2 infection, depending on the antigen. Higher antibody levels found in asymptomatic individuals and in children, particularly among males, could indicate protection against disease and stronger immunity. This non-invasive field ...

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.

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 10.1101/2021.03.22.21254130: (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).

Another important limitation is that only households with a lead householder able to speak English were able to take part in the study and that all participants must have access to the internet. Guided by the advice from our community advisory board, the study surveys have since been translated into 9 languages to allow non-English speakers to participate. The increase in intention to accept a COVID-19 vaccine when offered observed in this study is encouraging. It is possible that public health communications to promote vaccination uptake have contributed to this shift; it is also possible that growing numbers of people being vaccinated during the period of this study has contributed to the change in intention. It is particularly encouraging that the intention to accept a COVID-19 vaccine has increased consistently across ethnic and social groups. Our findings show the importance of making repeated offers of a COVID-19 vaccine because many people have changed their mind over the course of a few months. Our findings also suggest that communications focussing on COVID-19 vaccine safety and effectiveness may be more effective than those focussing on COVID-19 illness risk and perception. Disparities in vaccination coverage should not be conflated with disparities in vaccination intention. If differences in vaccination coverage persist between ethnic groups and areas of social deprivation, our findings suggest they may not be fully explained by differences in vaccination intention...

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.
• No funding statement was detected.
• No protocol registration statement was detected.

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 10.1101/2021.03.21.21253498: (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).

Another limitation is the small number of positive cases for the 501Y.V2 compared to the two other strains. This number was principally due to the only few positive cases in Paris area at that time. Our data observed a gradient in Ct values. Indeed, the two new variants seem to present a higher viral load compared to the historical SARS-CoV-2 which might arise from the fact that they share the same N501Y mutation probably leading to a better infectivity [2,3,10]. When we compared these two variants, we observed that the 501Y.V2 seems to be associated with lower viral load compared to the 501Y.V1 for the N target gene, a difference which fades for the ORF1ab target gene. The difference of Ct values that we have observed could be due to their other specific mutations. Considering the 501Y.V2, it does not seem that the Spike RBD has higher affinity for ACE2 as compared to the reference Spike. If indeed the transmission is enhanced, this could be due to mutation outside the direct ACE2–Spike interface[11]. Moreover, it has been shown that an active viral replication was associated with the transcription of subgenomic viral RNA and that this active replication occurs during the first days after the onset of symptoms[12]. As we collected only the first presentation test sample, which suggest the presence of an active viral replication, the difference between the N and the ORF1ab genes for these two new variants could be explained by the presence of these subgenomic viral RNA. Our s...

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.

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 10.1101/2021.03.20.21253896: (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.
• No funding statement was detected.
• No protocol registration statement was detected.

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 10.1101/2021.03.25.437060: (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).

While the K18-hACE2 mouse model has been previously used to recapitulate features of COVID-19 in humans 12, our study has several limitations. The expression of the hACE2 transgene is non-physiological, resulting in tissue expression levels that are distinct from endogenously expressed ACE2. Sex differences, which are known to occur with SARS-CoV-2 infection, could not be assessed since we only used male animals in these experiments. Finally, the absorption of SFN after oral administration can be modified by the intestinal microbiome 1, leading to potentially variable drug exposures between animals. Our results demonstrate that pharmacologically relevant micromolar concentrations of SFN inhibited viral replication and virus-induced cell death. The bioavailability of SFN in humans is dependent on dosage and dietary form 1. Safety studies using SFN-rich broccoli sprouts corresponding to 50 to 400 μM SFN daily have shown that SFN is well tolerated without clinically significant adverse effects 1,21,49,50. After intake, the plasma concentration of SFN is rapidly eliminated but SFN exerts a sustained effect on gene expression 51. Consumption of SFN-rich broccoli sprouts (single oral daily dose equivalent to 200μM of SFN) reportedly results in a peak plasma concentration (Cmax) of 1.9 μM at 2-3h 52,53. By comparison, SFN inhibited in vitro SARS-CoV-2 replication in human cells with an IC50 of 2.4μM. Doses of 100μM of SFN administered twice daily led to higher steady-state concentra...

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.

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 10.1101/2021.03.22.21253577: (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.

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 10.1101/2021.03.20.21253956: (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.

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 10.1101/2021.03.20.21254035: (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.

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 10.1101/2021.03.20.21253835: (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.

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 10.1101/2021.03.16.21253669: (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.
• No funding statement was detected.
• No protocol registration statement was detected.

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 10.1101/2021.03.18.21253604: (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.

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 10.1101/2021.03.21.21253418: (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.

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 10.1101/2021.03.20.21253819: (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 also has a few limitations. First, as our participants were from the anaesthesia department of hospital settings, thus it may not speculate the exact association of immune response among the whole HCW community. Second, underestimation during reporting of the symptoms might be happened due to the immense workload of health workers which force them to neglect mild symptoms and timely diagnosis. In conclusion, health workers are the most susceptible group to get COVID infection. Conditions like asymptomatic or pre-symptomatic make the scenario complicated due to the non-occurrence of routine diagnosis. Although our study has few limitations, there is no such study with health workers only from the anaesthesia department of hospital settings to demonstrate the seroprevalence and its association with symptoms, RT-PCR test, age and gender to our best knowledge. Our result concludes that HCWs should routinely get tested for COVID-19 as most of them may be asymptomatic or pre-symptomatic which indeed a much more concerning situation when it comes to patients’ safety.

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.

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 10.1101/2021.03.18.21253888: (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 our study. First, we were not able to follow all the cases that were discharged from hospital, either because they did not give permission or because they did not respond to repeated requests for information. We attempted to reach non-responders to the survey via telephone follow-up to limit potential for selection bias, but not all could be reached. It is possible that those who did not respond might have been well and therefore uninterested in responding, but it could also be that some were too unwell to respond, had died or moved away. Our results may therefore not be fully representative of with the entire population of those hospitalised with Covid-19. Secondly, we did not include patients hospitalised with other non-Covid-19 illness or a contemporaneous control group, therefore it is unknown if the changes in our outcomes e.g. quality of life, are specific to recovery from Covid-19 or may be linked to other aspects of life during the pandemic. Thirdly, patients only completed the survey at one timepoint, limiting comparison across repeat measures. This also meant retrospective measures asking patients to rate outcomes before their Covid-19 illness were included, which are open to recall bias. Finally, as our study focussed on hospitalised patients primarily from the first wave of infection in the UK, our data cannot be generalised to those with disease managed in the community who comprise the majority of individuals affected by Covid-19...

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.

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 10.1101/2021.03.25.437083: (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.

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 10.1101/2021.03.25.437035: (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.

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 10.1101/2021.03.25.436930: (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.

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 10.1101/2021.03.24.436885: (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.

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 10.1101/2021.03.24.436523: (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).

We have made attempts to overcome this limitation by analyzing specimens with orthogonal assays harmonized to consensus platforms. Additionally, our pseudovirus neutralization assay demonstrated equivalence to others in a multi-site concordance survey of reference laboratories. Potent neutralizing antibody responses may offer advantages for both vaccine efficacy and durability. Thus far, neutralizing activity has been predictive of efficacy in human trials, as vaccines that generate lower antibody titers have diminished efficacy (34). An open question remains, however, regarding the length of immunity conferred by SARS-CoV-2 vaccines. For those infectious diseases that are contained by neutralizing antibodies, peak titers have been shown to predict durability (43-45). As such, SpFN may offer longer protection than counterparts; though this requires empirical confirmation. Cross-neutralizing activity against SARS-CoV-2 VOCs is largely diminished for other vaccines at an approximately ten-fold reduction. SpFN induced serum cross-neutralizing responses, however, that were not significantly reduced. Additionally, we found serum binding to mutated SARS-CoV-2 RBD was either unaffected or mildly diminished. Cross-neutralizing activity against SARS-CoV-1 has not been reported yet for other vaccines in advanced development. Some early reports of nanoparticle vaccine approaches presenting RBD have begun to show breadth of neutralizing but these studies either have been limited murine i...

Results from TrialIdentifier: No clinical trial numbers were referenced.

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

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

• 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.

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 10.1101/2021.03.20.21253892: (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 is not without limitations. There is a risk of selection bias and this would limit the generalizability of our findings to all the healthcare professionals in EMRO. Additionally, our study only included nurses, physicians, and pharmacists. Despite these limitations, these findings are not inconsistent with the findings from previous studies about vaccine hesitancy among healthcare workers. The survey questionnaire was available in English and distributed in an online format, which can further introduce selection bias favoring English-literate HCWs and those with access to the Internet. Social desirability bias may also affect the interpretation of our study results. Most importantly, the survey was conducted in January 2021 when information regarding COVID-19 vaccines may have not circulated widely. Therefore, it possible that intention to be vaccinated would have changed.

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.

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 10.1101/2021.03.18.21253862: (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 data form the present study should be taken cautiously owing to several study limitations. Symptoms were self-reported, based on cross-sectional surveys, and may therefore contain suboptimal sensitivity. Subjective evaluation of the olfactory function was observed, indeed, to be inadequate to fully evaluate olfactory recovery with several authors having underlined that subjectivity of self-reporting may lead to underestimation of the prevalence of olfactory dysfunction. It is clear that patients’ rating of whether smell and or taste are impacted differentially is very difficult to interpret, due to impact of loss perception of flavour through retronasal olfaction, and little can be inferred from this aspect of the study. Moreover, the study cohort was relatively small and patients with more severe COVID-19 were excluded. In conclusion, a substantial proportion of patients with previous mild-to-moderate symptomatic COVID-19 characterized by new onset of chemosensory dysfunction still complained on altered sense of smell or taste one-year after the onset. As recovery from post-viral loss may continue beyond this period [6,15], further assessments will be necessary to conclude whether smell and taste dysfunction is permanent. Moreover, there is urgent need for more efforts and research on treatment strategies for post-COVID-19 chemosensory dysfunction.

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.

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 10.1101/2021.03.16.21253662: (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).

Additionally, depending on campus priorities and resource limitations, different campuses can use this same data to model policies differently. The effectiveness of reopening policies is expected to be sensitive to a campus’ specific context that includes physical infrastructure, overarching guidelines, and human compliance [5]. For certain campuses policies might not need to be constrained by exposure risk as testing might be frequent, ubiquitous, and voluminous. Other campuses could have limits on quarantining capacity. Policymakers might even consider the cost tradeoffs by actually forecasting actual financial losses incurred by reduction in mobility [6], or valuate loss of services based on community needs [53]. We elaborate on these considerations in the SI Implications for Policy Design. Operational Considerations: Beyond assessing cost-benefits, universities also need to consider practical methods of obtaining, storing, and processing mobility of the community as WiMob. University can access logs from the managed network internally as it is passively collected. Moreover, it does not require any new form of surveillance sensing but universities must revise terms of use and stay sensitive to community perspectives. While aggregate data on population mobility is valuable for many applications [64], which includes informing pandemic response [8], the major privacy challenge with localization data is to avoid accumulation [56]. Instead, operational applications need to conc...

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.

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 10.1101/2021.03.24.436812: (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.

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 10.1101/2021.03.19.21253675: (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.

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 10.1101/2021.03.17.21253849: (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.

Study limitation: The authors suggested that relatively young age of patients and absence of cases with severe illness were restricted the chance to find enough significant differences in hematological and immunological features according to disease course of SARS-CoV-2 infected patients in this study.

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.

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 10.1101/2021.03.21.21253984: (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.

These limitations are not minute, and caution should be employed in reporting any results based on this widely cited and publicly available dataset. While informative conclusions can be reached, they must be followed by proper disclosure about issues surrounding how representative or small the filtered, high quality data actually is, even if the parent dataset spans millions of entries.

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.

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 10.1101/2021.03.17.21253760: (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 some limitations. Adherence to or support for NPIs are self-reported. Social pressure on respondents to report greater affinity toward mask wearing, or support for school closures for example, may be higher given the state of the ongoing pandemic. We note however that the measurement of relative difference between groups was highly significant across a variety of NPIs. It is difficult to imagine why these pressures would differ between groups; further, it is unlikely that social pressures would be greater on individuals reporting chronic diseases than those without to the point that they confound otherwise insignificant results. Additionally, our sample may not be representative of the US public as this study utilized a convenience sample using quotas based on reported disease state. We have controlled for multiple demographic factors, and note that it would be extremely difficult to recruit sufficient populations that satisfied quotas for disease state while maintaining representative sampling. This limitation thus represents a necessary trade-off between our ability to test our key hypotheses about chronic respiratory and autoimmune diseases, and our ability to make statements about the general population. Samples also reflect the real-world social dimensions of these diseases, such as the disproportionate recruitment of women in the autoimmune quota being indicative of the higher prevalence of those diseases among women. This research provides a timely first...

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.

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 10.1101/2021.03.17.21253791: (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 of the study: The study employed a systematic and rigorous approach to source for the information relevant to these research objectives. This research summarizes global distributions and quantitative impacts of COVID-19 on global health. This will stimulate the research community, stakeholders in the government and non-governmental organizations, and healthcare professionals to optimize strategies to mitigate the impact of the ongoing pandemic and strengthening preparedness for any future outbreaks. Also, it will inform the entire public to emulate compliance towards personal protective measures against the future outbreak. Our study only focuses on the top 20 countries with the highest confirmed cases in the COVID-19 global timeline. Although, it failed to reflect the entire COVID-19 cases worldwide due to redundancy in some countries’ figures.

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.

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 10.1101/2021.03.16.21253632: (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).

In interpreting the above results, it is important to acknowledge some limitations. Our analyses do not formally establish causation, which would be very challenging in the context where this study is conducted and the research questions we attempt to answer. Yet, the consistent patterns of findings across multiple outcomes and specifications is suggestive of potential underlying causal path-ways. Moreover, all our outcomes, including Covid-19 knowledge and prevention behavior, are necessarily self-reported, and therefore subject to “social desirability” bias. This limitation is inherent as in-person surveys and direct observation were not feasible during the time-period of this study, and indirect measures (e.g., based on cell phone mobility data) are not viable in a rural Malawi context where cell phone ownership continues to be uncommon (albeit growing). Also, notwithstanding the “success” that we highlight in terms of curtailing Covid-19 infections and mortality in Malawi, the social and economic impacts of the pandemic are severe and possibly lasting. For example, a substantial fraction of the MLSFH respondents reduced non-food consumption as a result from Covid-19, and about 61% reported worries about having enough food to eat. For more than half of the interviewed respondents (55%), the economic situation deteriorated compared to the previous year. Worries about access to health care for NCDs and other medical needs such as malaria treatment or HIV/AIDS care were also ...

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.

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 10.1101/2021.03.17.21253626: (What is this?)

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

Table 1: Rigor

Table 2: Resources

No key resources detected.