SARS-CoV-2 incidence, transmission, and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020–21
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SciScore for 10.1101/2021.07.20.21260855: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Study staff entered data in the field on tablets using REDCap (Research Electronic Data Capture)24 and had refresher training on specimen collection and the identification of respiratory signs and symptoms each week.
IRB: Ethics: The PHIRST protocol was approved by the University of Witwatersrand Human Research Ethics Committee (Reference 150808) and amended to include enrollment and testing for COVID-19 on 24 June 2020 and was registered on clinicaltrials.gov on 6 August 2015 and updated on 30 December 2020 (https://clinicaltrials.gov/ct2/show/NCT02519803).Sex as a biological variable not detected. Randomization Households were randomly selected, from the HDSS database in … SciScore for 10.1101/2021.07.20.21260855: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Study staff entered data in the field on tablets using REDCap (Research Electronic Data Capture)24 and had refresher training on specimen collection and the identification of respiratory signs and symptoms each week.
IRB: Ethics: The PHIRST protocol was approved by the University of Witwatersrand Human Research Ethics Committee (Reference 150808) and amended to include enrollment and testing for COVID-19 on 24 June 2020 and was registered on clinicaltrials.gov on 6 August 2015 and updated on 30 December 2020 (https://clinicaltrials.gov/ct2/show/NCT02519803).Sex as a biological variable not detected. Randomization Households were randomly selected, from the HDSS database in the rural site and using Global Positioning System (GPS) coordinates in the urban site. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Study staff entered data in the field on tablets using REDCap (Research Electronic Data Capture)24 and had refresher training on specimen collection and the identification of respiratory signs and symptoms each week. REDCapsuggested: (REDCap, RRID:SCR_003445)We conducted all statistical analyses using STATA version 14.1 STATAsuggested: (Stata, RRID:SCR_012763)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study had several limitations. We included two communities and households with >2 members, potentially limiting generalisability of study findings. The finding of very different attack rates in the two communities suggests substantial heterogeneity in disease transmission in different geographic areas. Participants were sampled using mid-turbinate nasal swabs because of potential SARS-CoV-2 transmission risk with a collection of more sensitive nasopharyngeal swab specimens. This could have led to some missed infections. However, the strong association between rRT-PCR- and serology-confirmed infection in individuals with both specimen types available suggests that the majority of infections were detected. Repeated questioning on symptoms twice weekly may be associated with participant fatigue and under-reporting. Participants may have been informed of their disease status before developing symptoms, potentially affecting reporting. We implemented several measures to reduce this potential bias including weekly retraining of field workers on symptom collection and regular field supervisory visits to evaluate data collection and symptom recording. A study of influenza infection in the same population with similar study design found that 56% of individuals infected with influenza were symptomatic, suggesting the robustness of our data.22 Our study covered a 9-month period, and we cannot speculate on the duration of natural immunity and risk of reinfection over longer timescale...
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT02519803 Unknown status A Prospective Household Observational Cohort Study of Influe… Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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