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

Abstract

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 Côte d'Ivoire, Western sub-Saharan Africa. We therefore generated 234 full SARS-CoV-2 genomes stemming from Central and Northern Côte d'Ivoire. Covering the first and second pandemic wave the country had been facing, we identified 20 viral lineages and showed that in Côte 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 Côte d'Ivoire, and those introduction events mostly stemmed from within the West African subregion. This suggests that subregional travel to Côte d'Ivoire had more impact on local pandemic waves than direct intercontinental travel.

Keywords: Phylogeography; SARS-CoV-2; Sub-Saharan Africa; VOC; VOI; Whole-genome sequencing.

Fig. 1

Distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral lineages among 234 genomes sequenced at the Centre Hospitalier et Universitaire de Bouaké in Côte d’Ivoire. Data were subdivided into six sample collection periods, aiming to balance sampling effort: May–July 2020 (N  = 62), August–December 2020 (N  = 29), January 2021 (N = 16), February 2021 (N  = 50), March 2021 (N = 43), April–May 2021 (N  = 34). Viral lineage assignment was conducted using pangolin (version 2.3.8, April 2nd 2021), and the plot was drawn with R, package Treemap.

Fig. 2

A, C Subsampled time-scaled phylogeny of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage Alpha (A) and Eta (C). 300 sequences were subsampled from a global dataset as to maximize genetic distances, while retaining all genomes from Côte d’Ivoire. The branches are scaled in decimal time, and sampling dates are capped at May 31st 2021 (decimal date 2021.41), the latest sampling month in Côte d’Ivoire in this study. Sequences originating from West Africa are indicated by large circles. B, D Number of importation events of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage Alpha (B) and Eta (D) into Côte d’Ivoire. Sampling dates are capped at May 31st 2021, the latest sampling month in Côte d’Ivoire in this study. Standard error bars are derived from replicating the introduction analysis ten times starting from different maximum likelihood phylogenetic trees.