A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
- Evaluated articles (Rapid Reviews Infectious Diseases)
Abstract
The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA
Article activity feed
-
-
Adriana Heguy
Review 2: "A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa"
This preprint explores the genetic changes of SARS-CoV-2 in Africa by offering an in-depth epidemiological analysis of virus introduction, circulation, and evolution over a year. Reviewers agree that the claims are reliable and supported by the data.
-
M Hossain
Review 1: "A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa"
This preprint explores the genetic changes of SARS-CoV-2 in Africa by offering an in-depth epidemiological analysis of virus introduction, circulation, and evolution over a year. Reviewers agree that the claims are reliable and supported by the data.
-
Strength of evidence
Reviewers: M Hossain (University of Dhaka) | 📘📘📘📘📘
Adriana Heguy (NYU Langone Medical Center) | 📘📘📘📘📘 -
SciScore for 10.1101/2021.05.12.21257080: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Phylogenetic reconstruction: The African sequences were aligned against the reference panel using MAFFT v7.471 (23). MAFFTsuggested: (MAFFT, RRID:SCR_011811)Prior to phylogeographic reconstruction each cluster/lineage was assessed for molecular clock signal in TempEst v1.5.3 (30) following the removal of potential outliers that may violate the molecular clock assumption. TempEstsuggested: (TempEst, RRID:SCR_017304)Markov Chain Monte Carlo (MCMC) analyses were set up in BEAST v1.10.4 in duplicate for 100 million interactions and sampling every 10,000 steps in the chain. BEASTsuggested: …SciScore for 10.1101/2021.05.12.21257080: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Phylogenetic reconstruction: The African sequences were aligned against the reference panel using MAFFT v7.471 (23). MAFFTsuggested: (MAFFT, RRID:SCR_011811)Prior to phylogeographic reconstruction each cluster/lineage was assessed for molecular clock signal in TempEst v1.5.3 (30) following the removal of potential outliers that may violate the molecular clock assumption. TempEstsuggested: (TempEst, RRID:SCR_017304)Markov Chain Monte Carlo (MCMC) analyses were set up in BEAST v1.10.4 in duplicate for 100 million interactions and sampling every 10,000 steps in the chain. BEASTsuggested: (BEAST, RRID:SCR_010228)Convergence for each run was assessed in Tracer v1.7.1 (ESS for all relevant model parameters >200). Tracersuggested: (Tracer, RRID:SCR_019121)Country level maps of each variable were created using ArcGIS® by ESRI version 10.5 (http://www.esri.com). ArcGIS®suggested: (ArcGIS for Desktop Basic, RRID:SCR_011081)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a protocol registration statement.
Results from scite Reference Check: We found no unreliable references.
-
