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