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

Lester J Perez; Gregory S Orf; Michael G Berg; Mary A Rodgers; Todd V Meyer; Aurash Mohaimani; Ana Olivo; Barbara Harris; Illya Mowerman; Abdou Padane; Agbogbenkou Tevi Dela-Del Lawson; Aminata Mboup; Moustapha Mbow; Nafissatou Leye; Ndeye Coumba Touré-Kane; Ambroise D Ahouidi; Gavin A Cloherty; Souleymane Mboup

doi:10.1093/ve/veac025

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

Virus Evol. 2022 Mar 21;8(1):veac025. doi: 10.1093/ve/veac025. eCollection 2022.

Authors

Lester J Perez¹, Gregory S Orf¹, Michael G Berg¹, Mary A Rodgers¹, Todd V Meyer¹, Aurash Mohaimani¹, Ana Olivo¹, Barbara Harris¹, Illya Mowerman¹, Abdou Padane², Agbogbenkou Tevi Dela-Del Lawson², Aminata Mboup², Moustapha Mbow², Nafissatou Leye², Ndeye Coumba Touré-Kane², Ambroise D Ahouidi², Gavin A Cloherty¹, Souleymane Mboup²

Affiliations

¹ Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, 100 Abbott Park Rd, Lake Bluff, IL 60044, USA.
² Institut de Recherche en Santé de Surveillance Épidémiologique et de Formation, 4 Rue 2 D1 Pole Urbain de Diamniado, Dakar BP 7325, Senegal.

Abstract

Molecular surveillance of severe acute respiratory syndrome coronavirus 2 (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.

Keywords: Bayesian inference of phylogeny; SARS-CoV-2; Senegal; phylogeography; positive selection analysis; variants of interest; viral surveillance.