SARS-CoV-2 variants circulating in West and Central Africa between 2020 and 2022: A retrospective study

Abstract

OBJECTIVE: The study aims to identify and characterize the SARS-Cov-2 variants circulating in West and Central Africa during the pandemic, between 2020 and 2022. METHODS: From early 2020 to late 2022, naso-pharyngeal or oro-pharyngeal samples were collected in five countries: Burkina Faso, Côte d'Ivoire, Mali, Republic of Congo and Chad. SARS-CoV-2 positive samples (Ct-value < 30) were sequenced to identify the circulating variants in these countries during the different waves of the pandemic. RESULTS: Overall, 793 whole genomes of SARS-Cov-2 were generated: 308 in Côte d'Ivoire, 244 in the Republic of Congo, 91 in Chad, 87 in Burkina Faso and 63 in Mali. In 2020, early variants detected included B.1 and B.1.1. Lineage A.21 was identified in both Burkina Faso and Mali, while lineages A and A.18 were detected in Côte d'Ivoire and Mali. Some variants appeared to be country-specific, such as lineage B.1.1.404 in Burkina Faso. Chad exhibited a distinct pattern compared with the other countries, with Delta variants detected earlier than in the other locations. In 2021, the diversity of circulating variants increased and differed more markedly between countries. In 2022, the variant landscape was dominated by Omicron lineages in all countries. CONCLUSION: This study provides new resources concerning the SARS-CoV-2 variants circulating in West and Central Africa between 2020 and 2022, which are less represented in global datasets. The variants identified in this study were similar to the variants observed in other regions of the world.