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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

Strong breeding colony fidelity in northern gannets following high pathogenicity avian influenza virus (HPAIV) outbreak

High pathogenicity avian influenza virus (HPAIV) caused the worst seabird mass-mortalities in Europe across 2021–2022. The northern gannet (Morus bassanus) was one of the most affected species, with tens of thousands of casualties in the northeast Atlantic between April–September 2022. Disease outbreaks can modify the movement ecology of animals by diminishing spatial consistency, thereby increasing the potential for disease transmission. To detect potential changes in movement behaviour, we GPS-tracked breeding adults following the initial HPAIV outbreak, at three of the largest northern gannet breeding colonies where major mortality of adults and chicks occurred (Bass Rock, Scotland, UK; Grassholm, Wales, UK; Rouzic, Brittany, France). We also gathered background epidemiological information and northern gannet colony dynamics during the outbreak. Our data indicate that HPAIV killed at least 50 % of northern gannets, and suggest the presence of HPAIV H5N1 antibodies in juveniles. GPS-tracked adult northern gannets remained faithful to their breeding sites despite the HPAIV outbreak and did not prospect other breeding colonies. They performed regular foraging trips at sea, similar to their behaviour before the outbreak. Comparison with GPS-tracking data gathered in 2019, i.e. before the HPAIV outbreak, suggested lower foraging effort in birds which survived HPAIV in 2022, potentially as a consequence of reduced intra- and interspecific food competition. Breeding colony fidelity of surviving adult northern gannets following HPAIV mass-mortalities indicates limited capacity for viral spread during our study. This may contrast with the behaviour of adults during the initial disease outbreak, and with that of younger individuals