The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Collecter des données sur des expériences et attitudes sensibles : le cas du Mali

International audienceIn standard household surveys, the data collected are exposed to response bias, particularly for questions considered sensitive. The List Experiment method is an alternative survey technique for limiting these biases. This article presents the results of an experimental survey conducted using this method with 1,509 individuals throughout Mali. Individuals were surveyed by telephone during the summer of 2021 about their experiences and political attitudes related to insecurity. From a methodological point of view, we have drawn a number of lessons from the survey: among others, a very good understanding and acceptability of the method by the respondents, due in particular to the quality of the interviewers and supervisors; the need for a more complex sample design than for a standard questionnaire; and the importance of a short questionnaire when surveying by telephone. From an analytical point of view, the survey reveals the existence of significant social desirability biases - particularly for questions concerning political attitudes in relation to insecurity.Dans les enquêtes standards auprès des ménages, les données collectées sont exposées à des biais de réponses, particulièrement pour les questions considérées comme sensibles. La méthode par comptage de réponses est une technique d’enquête alternative permettant de limiter ces biais. Cet article présente les résultats d’une enquête expérimentale menée selon cette méthode auprès de 1 509 individus sur l’ensemble du territoire malien. Les personnes ont été sondées par téléphone durant l’été 2021 à propos d’expériences et d’attitudes politiques liées à l’insécurité. D’un point de vue méthodologique, nous en tirons plusieurs enseignements : entre autres, une très bonne compréhension et acceptabilité de la méthode par les enquêté·e·s, qui tient notamment à la qualité des enquêteur·trice·s et des superviseur·se·s ; la nécessité d’un plan de sondage plus complexe que pour un questionnaire standard ; et l’importance d’un questionnaire court lorsqu’on enquête par téléphone. Du point de vue analytique, l’enquête fait ressortir l’existence de biais déclaratifs significatifs – notamment pour les questions portant sur les préférences politiques en lien avec l’insécurité