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

Adamou Lagaré Issaka Aboubacar Adakal A. Yacouba T. A. C. Gnimadi Safiétou Sankhe Santou Mamadou Mouhamed Kane Moussa Issa Younoussa Otto Adamou Rachida Salibi Moumpatla Jacqueline Ndiaye Issifi Kollo Abdoulkader Maimouna Mbanne Fatimata Hassane R. Lazoumar Habibatou Idé Amadou S. Ousmane A. Diallo É. Adehossi Ndongo Dia M. Doutchi Mamadou Saidou R. Jambou Martin Faye S. Wohl M. Diagne
Jul 2026 · Infection, Genetics and Evolution · pp. 106000 · 0 citations · 53 references
Medicine

Abstract

Background

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.

Method

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.

Results

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.

Conclusion

This study helps to understand the SARS-CoV-2 evolution and dynamics in Niger Republic, where diagnostic capacities and containment measures were challenging.

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