COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

Abstract

ABSTRACT. West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

“…However, following the emergence of SARS-CoV-2 variants of concern associated with severe clinical signs and symptoms, whole genome sequencing using NGS technique has become the method of choice to timely detect the emergence and spread of new variants with novel mutations and understand the transmission dynamics of the virus worldwide, including in Mauritania [ 16 , 17 , 41 ]. To document COVID-19 dynamics in Mauritania, a set of SARS-CoV-2 clinical isolates collected from Mauritanian COVID-19-positive patients were analyzed for their genomic profile during the period from September to November 2021, corresponding to the third wave of the COVID-19 epidemic in most West African countries [ 42 ]. Starting from 103 quantitative RT-PCR positive nasopharyngeal samples, diagnosed at the INRSP, which was the reference center during the pandemic for SARS-CoV-2 testing in Mauritania, the positivity of 83 of 103 samples was confirmed at the IHU–Méditerranée Infection in Marseille, France.…”

“…Similar findings were reported by Abdelmalick et al in SARS-CoV-2 strains isolated from 13 PCR-positive symptomatic patients sampled five months before our sampling (i.e., 3 March 2021 to 31 May 2021) [ 17 ]. However, comparison with data from other West African countries shows that the predominant lineage in the third epidemic wave in West Africa was sub-lineage B.1.617.2.36 (45% of all sequences) and that lineage B.1.617.2 only represented 6% of the collected samples [ 42 ].…”