Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

Deida, Jemila; Papa Mze, Nasserdine; Beye, Mamadou; Ahmed, Sidi Mohamed; El Bara, Ahmed; Bollahi, Mohamed Abdallahi; Basco, Leonardo; Ould Mohamed Salem Boukhary, Ali; Fournier, Pierre-Edouard

doi:10.3390/genes15030361

Open AccessArticle

Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

by

Jemila Deida

^1,2,

Nasserdine Papa Mze

^3,4

,

Mamadou Beye

^3,4,

Sidi Mohamed Ahmed

²,

Ahmed El Bara

²,

Mohamed Abdallahi Bollahi

²,

Leonardo Basco

^3,4

,

Ali Ould Mohamed Salem Boukhary

^1,3

and

Pierre-Edouard Fournier

^3,4,*

¹

UR-Génomes et Milieux, Université de Nouakchott, Nouakchott BP 880, Mauritania

²

Institut National de Recherche en Santé Publique, Nouakchott BP 695, Mauritania

³

Aix Marseille University, AP-HM, SSA, VITROME, 13005 Marseille, France

⁴

IHU-Méditerranée Infection, 13005 Marseille, France

^*

Author to whom correspondence should be addressed.

Genes 2024, 15(3), 361; https://doi.org/10.3390/genes15030361

Submission received: 20 February 2024 / Revised: 8 March 2024 / Accepted: 12 March 2024 / Published: 14 March 2024

(This article belongs to the Section Viral Genomics)

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Abstract

The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its genomic variation during the course of the epidemic. The purpose of the present study was to document the genomic pattern of SARS-CoV-2 variants from clinical isolates during the COVID-19 outbreak in Mauritania, from September to November 2021. The whole genomes from 54 SARS-CoV-2 strains detected in nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and the Illumina protocol. The mean genome coverage (±standard deviation) was 96.8% (±3.7). The most commonly identified clade was 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), and 20B (9.2%). At the level of lineages, the majority of the samples were Delta variants with the sub-lineage AY.34 (or B.1.617.2.34). Among the 54 SARS-CoV-2 isolates that were successfully sequenced, 33 (61.1%) came from vaccinated individuals, and 21 (38.9%) were from unvaccinated individuals. Several SARS-CoV-2 variants were present in Mauritania between September and November 2021. As Mauritania, like many West African countries, is resource-limited regarding viral genome sequencing facilities, establishment of mutualized sub-regional sequencing platforms will be necessary to ensure continuous monitoring of mutations in viral genomes and track potential reduction in COVID-19 vaccine efficacy, increased transmissibility, and disease severity.

Keywords: coronavirus; COVID-19; Mauritania; SARS-CoV-2; variants

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MDPI and ACS Style

Deida, J.; Papa Mze, N.; Beye, M.; Ahmed, S.M.; El Bara, A.; Bollahi, M.A.; Basco, L.; Ould Mohamed Salem Boukhary, A.; Fournier, P.-E. Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania. Genes 2024, 15, 361. https://doi.org/10.3390/genes15030361

AMA Style

Deida J, Papa Mze N, Beye M, Ahmed SM, El Bara A, Bollahi MA, Basco L, Ould Mohamed Salem Boukhary A, Fournier P-E. Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania. Genes. 2024; 15(3):361. https://doi.org/10.3390/genes15030361

Chicago/Turabian Style

Deida, Jemila, Nasserdine Papa Mze, Mamadou Beye, Sidi Mohamed Ahmed, Ahmed El Bara, Mohamed Abdallahi Bollahi, Leonardo Basco, Ali Ould Mohamed Salem Boukhary, and Pierre-Edouard Fournier. 2024. "Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania" Genes 15, no. 3: 361. https://doi.org/10.3390/genes15030361

APA Style

Deida, J., Papa Mze, N., Beye, M., Ahmed, S. M., El Bara, A., Bollahi, M. A., Basco, L., Ould Mohamed Salem Boukhary, A., & Fournier, P.-E. (2024). Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania. Genes, 15(3), 361. https://doi.org/10.3390/genes15030361

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Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

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