Genetic diversity and evolution of SARS-CoV-2 in the republic of Niger over 3 years.

Authors

Adamou Lagare, Issaka Aboubacar Adakal, Abdourahamane Yacouba, Thibaut Armel Chérif Gnimadi, Safiétou Sankhe, Santou Mamadou, Mouhamed Kane, Moussa Issa, Younoussa Otto Adamou, Rachida Salibi Moumpatla, Jacqueline Ndiaye, Issifi Kollo Abdoulkader, Maïmouna Mbanne, Fatimata Hassane, Ramatoulaye Hamidou Lazoumar, Habibatou Idé Amadou, Sani Ousmane, Amadou Diallo, Eric Adehossi, Ndongo Dia, Mahamadou Doutchi, Mamadou Saidou, Ronan Jambou, Martin Faye, Shirlee Wohl, Moussa Moise Diagne

Published in

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. Pages 106000. Jul 27, 2026. Epub Jul 27, 2026.

Abstract

Since the beginning of the COVID-19 pandemic, a large number of SARS-CoV-2 variants have emerged from the reference strain (Wuhan-Hu-1, NC_045512.2). Using these variants to understand the genetic diversity and temporal dynamics of SARS-CoV-2 in Niger is essential for developing and implementing effective public health interventions.
SARS-CoV-2 detection was performed on nasopharyngeal samples collected from travelers and symptomatic patients at the National Reference Laboratory in Niger from March 2020 to March 2023 using RT-qPCR techniques. A subset of samples with a cycle threshold <28 were selected for whole-genome sequencing and genomic analysis, which included phylogenetic reconstruction to study the evolutionary relationships of SARS-CoV-2 variants detected in Niger.
Among 286,872 samples from suspected cases tested, we confirmed 8266 positives for SARS-CoV-2, resulting in a positivity rate of 2.88%. Of the positive cases, 268 (3.24%) resulted in death and 5577 (67.48%) were travelers. All the WHO-designated Variants of Concern (VOCs), including Alpha B.1.1.7 (n = 2), Beta B.1.351 (n = 1), Delta B.1.617 (n = 20) and Omicron B.1.1.529 (n = 95) circulated in Niger during the study period. Among the Variants of Interest (VOIs) and Variants Under Monitoring (VUMs), the A27 lineage (n = 49) was the predominant virus detected and co-circulated with Eta lineage B.1.525 (n = 21). Phylogeographic analysis identified at least 60 independent introductions of SARS-CoV-2 into Niger, the majority of which were closely related to published sequences from other African countries (n = 25) and European countries (n = 24). Phylogenetic analysis of the four predominant variants revealed a temporal progression of SARS-CoV-2 lineages in Niger, with well-supported clades. A high number of mutations were observed, mainly located in the spike protein, ORF1a, and ORF1b genes.
This study helps to understand the SARS-CoV-2 evolution and dynamics in Niger Republic, where diagnostic capacities and containment measures were challenging.

PMID:
42508551
Bibliographic data and abstract were imported from PubMed on 28 Jul 2026.

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