Subregional origins of emerging SARS-CoV-2 variants during the second pandemic wave in Cote d'Ivoire

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility, virulence and immune escape abilities have heavily altered the COVID-19 pandemic's course. Deciphering local and global transmission patterns of those variants is thus key in building a profound understanding of the virus' spread around the globe. In the present study, we investigate SARS-CoV-2 variant epidemiology in Cote d'Ivoire, Western sub-Saharan Africa. We therefore generated 234 full SARS-CoV-2 genomes stemming from Central and Northern Cote d'Ivoire. Covering the first and second pandemic wave the country had been facing, we identified 20 viral lineages and showed that in Cote d'Ivoire the second pandemic wave in 2021 was driven by the spread of the Alpha (B.1.1.7) and Eta (B.1.525) variant. Our analyses are consistent with a limited number of international introductions of Alpha and Eta into Cote d'Ivoire, and those introduction events mostly stemmed from within the West African subregion. This suggests that subregional travel to Cote d'Ivoire had more impact on local pandemic waves than direct intercontinental travel.

Automated summary

In this study, the epidemiology of SARS-CoV-2 variants in Cote d'Ivoire, Western sub-Saharan Africa, was investigated. It was found that the second wave in 2021 was driven by the spread of the Alpha (B.1.1.7) and Eta (B.1.525) variant. The results suggest that subregional travel had a greater impact on local pandemic waves in Cote d'Ivoire than direct intercontinental travel.