The early SARS-CoV-2 epidemic in Senegal was driven by the local emergence of B.1.416 and the introduction of B.1.1.420 from Europe

Abstract

Molecular surveillance of SARS-CoV-2 is growing in west Africa, especially in the Republic of Senegal. Here, we present a molecular epidemiology study of the early waves of SARS-CoV-2 infections in this country based on Bayesian phylogeographic approaches. Whereas the first wave in mid-2020 was characterized by a significant diversification of lineages and predominance of B.1.416, the second wave in late-2020 was composed primarily of B.1.1.420. Our results indicate that B.1.416 originated in Senegal and was exported mainly to Europe. In contrast, B.1.1.420 was introduced from Italy, gained fitness in Senegal, and then spread worldwide. Since both B.1.416 and B.1.1.420 lineages carry several positive selected mutations in the spike and nucleocapsid genes, each of which may explain their local dominance, their mutation profiles should be carefully monitored. As the pandemic continues to evolve, molecular surveillance in all regions of Africa will play a key role in stemming its spread.

Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022

“… 30 Phylogenetic analysis showed clustering of most of the alpha Gambian samples with samples from Germany, Ghana, Spain, and the UK, while eta samples clustered with those from the UK, Germany, and Nigeria ( figure 6 ). The B.1.1.420 lineage, which was reported to originate in Italy 25 and later became the dominant lineage in both Senegal 25 and The Gambia's second wave, clustered with sequences mainly from Senegal. Genomic analysis showed mutations in the spike protein associated with immune invasion (N440K) 31 and increased transmission (D614G).…”

“…This timing aligns with the high prevalence of the Senegal–Gambia lineage B.1.416, which was the dominant lineage in the first COVID-19 wave in Senegal (March–August, 2020). 25 This lineage is characterised by few mutations across the genome, the most notable of which is the D614G on the spike protein gene, which is linked to increased viral load and high transmission but not to increased disease severity. 26 So far, The Gambia and Senegal have reported the highest number of cases caused by B.1.416.…”

Genomic epidemiology of SARS-CoV-2 infections in The Gambia, March 2020 to Jan 2022

“…Phylogenetic analysis showed high clustering of most of the Alpha Gambia samples with samples from Germany, Spain , England as well as Ghana while Eta samples clustered more with UK, Germany and Belgium. The B•1•1•420 lineage, reported to originate from Senegal 57 , dominated the second wave in both countries. Overall, sequences from The Gambia clustered closely mainly with sequences from Senegal and from Europe.…”

“…This concurs with the high prevalence of the so-called Senegal/Gambia lineage or B·1·416 11 , which also dominated the first wave in Senegal (March – August 2020). 57 This lineage is characterised by few mutations across the genome, the most notable being the D614G on the spike protein gene linked to increased viral load and high transmission, but not to increased disease severity. 58 So far, The Gambia and Senegal have reported the highest number of B·1·416 cases.…”

Impact and mitigation of sampling bias to determine viral spread: evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations

“…CTMC is a fast algorithm that can handle many sequences while facing little convergence issues, which made it the predominant approach. For example, CTMC and its extensions have been extensively used during the SARS-CoV-2 pandemic (Candido et al 2020; Dellicour, Durkin, et al 2020; Lemey et al 2020; Alteri et al 2021; Butera et al 2021; Dellicour et al 2021; Kaleta et al 2022; Perez et al 2022). In general, researchers analyzed large datasets whose composition was corrected or reflected case counts (Candido et al 2020; Lemey et al 2020) or the number of hospitalizations per geographical location (Dellicour et al 2021).…”