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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.

Published onAug 30, 2021
Review 2: "A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa"
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key-enterThis Pub is a Review of
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

AbstractThe progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.

RR:C19 Evidence Scale rating by reviewer:

  • Strong. The main study claims are very well-justified by the data and analytic methods used. There is little room for doubt that the study produced has very similar results and conclusions as compared with the hypothetical ideal study. The study’s main claims should be considered conclusive and actionable without reservation.



By RR:C19’s strength of evidence scale, the claims are reliable and supported by the data and methods used. Decision-makers should consider the claims in this study actionable with limitations based on the methods and data. This well-written manuscript represents an impressive genomic surveillance effort of African SARS-CoV-2 sequences by a multinational set of researchers, labs, and centers spanning several continents. Even though it is understood that this represents a low sampling level given the true number of COVID-19 infections and the severity of the second wave of infections, the number of sequences analyzed in this study is close to 9000 (one in 300 officially reported cases) and this is a reasonably decent number to draw conclusions from regarding the variants of concern and variants of interest circulating in the continent and the dynamics of emergence and spread of these variants.

The phylogenetic and phylogeographic analyses are state-of-the-art in terms of the methodology used. The data shows a high number of early introductions from Europe in a manner similar to other places, like New York City, where the virus was also seeded multiple times—mainly from Europe. This early phase was followed by introductions from within African countries, with one of the major drivers being South Africa towards other African countries. The Beta variant, B.1.351, which was first detected in South Africa, is the variant present in the highest proportion as of May when this paper was uploaded to medRxiv. The manuscript emphasizes the importance of genomic surveillance to monitor the evolutionary dynamics of SARS-CoV-2 in the African continent, and this is an important endeavor that is highlighted right now by the rapid worldwide spread of the Delta variant. These efforts are important to determine future vaccination strategies and the composition of vaccines. The authors state that if the pandemic is not controlled in Africa, we may see the emergence of other variants that may escape at least part of the protection offered by vaccines—and this can affect not just Africa, but the entire world.


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