Detection of a cluster of Omicron's BA.4 sublineage in Northern Senegal and identification of the first XAS recombinant variant in Senegal

Martin Faye; Modeste Name Faye; Babacar Ndiaye; Moussa Moïse Diagne; Safietou Sankhe; Ndeye Marième Top; Amadou Diallo; Cheikh Loucoubar; Ndongo Dia; Amadou Alpha Sall; Ousmane Faye

doi:10.1016/j.virusres.2023.199259

Detection of a cluster of Omicron's BA.4 sublineage in Northern Senegal and identification of the first XAS recombinant variant in Senegal

Virus Res. 2024 Jan 2:339:199259. doi: 10.1016/j.virusres.2023.199259. Epub 2023 Nov 6.

Affiliations

¹ Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal. Electronic address: martin.faye@pasteur.sn.
² Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal.
³ Biomedical Laboratory, Institut Pasteur de Dakar, Dakar BP220, Senegal.
⁴ Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP220, Senegal.

Abstract

In Senegal, since its first detection in early March 2020, genomic surveillance of SARS-CoV-2 isolates has led to the identification of the emergence of the Omicron BA.4 and BA.5 sublineages from early June 2022. To investigate the origin of a cluster of cases in Northern Senegal on July 2022, isolates were analysed using Next-generation sequencing and phylogeny. Our data provided evidence of the origin of the cluster of BA.4 cases from a XAS recombinant, that is to date, the first reported sequence of this variant from Senegal. Continuous genomic surveillance of positive SARS-CoV-2 samples is a crucial need.

Keywords: First XAS recombinant; Omicron BA.4; SARS-CoV-2 genomic surveillance; Senegal.

MeSH terms

Genomics*
High-Throughput Nucleotide Sequencing*
Phylogeny
SARS-CoV-2 / genetics
Senegal