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

The role and contribution of civil society and community actors in COVID-19 prevention and control: the case of the COMVID COVID-19 movement in Burkina Faso

Communities should play a crucial role in the fight against public health emergencies but ensuring their effective and sustained engagement remains a challenge in many countries. In this article, we describe the process of mobilising community actors to contribute to the fight against COVID-19 in Burkina Faso. During the early days of the pandemic, the national COVID-19 response plan called for the involvement of community actors, but no strategy had been defined for this purpose. The initiative to involve community actors in the fight against COVID-19 was taken, independently of the government, by 23 civil society organisations gathered through a platform called ‘Health Democracy and Citizen Involvement (DES-ICI)’. In April 2020, this platform launched the movement ‘Communities are committed to Eradicate COVID-19 (COMVID COVID-19)’ which mobilised community-based associations organised into 54 citizen health watch units (CCVS) in Ouagadougou city. These CCVS worked as volunteers, performing door-to-door awareness campaigns. The psychosis created by the pandemic, the proximity of civil society organisations to the communities and the involvement of religious, customary and civil authorities facilitated the expansion of the movement. Given the innovative and promising nature of these initiatives, the movement gained recognition that earned them a seat on the national COVID-19 response plan. This gave them credibility in the eyes of the national and international donors, thus facilitating the mobilisation of resources for the continuity of their activities. However, the decrease in financial resources to offset the community mobilisers gradually reduced the enthusiasm for the movement. In a nutshell, the COMVID COVID-19 movement fostered dialogues and collaboration among civil society, community actors and the Ministry of Health, which plans to engage the CCVS beyond the COVID-19 response, for the implementation of other actions within the national community health policy