Search

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.

The presence of alphaviruses, such as chikungunya virus (CHIKV), has never been reported in Mauritania. We assessed the seroprevalence of CHIKV among Nouakchott residents. A cross-sectional study involving 1300 non-febrile patients consulting at the Nouakchott hospital center was conducted between January and June 2021. The presence of anti-CHIKV IgG and neutralizing antibodies against CHIKV, O'nyong-nyong virus (ONNV), and Semliki Forest virus (SFV) was determined by an enzyme-linked immunosorbent assay (ELISA) and a serum neutralization test, respectively, and the associated risk factors were investigated. Of the 1300 study participants, serological evidence of previous exposure to CHIKV was observed in 37 individuals (2.8%). Sex, age, reported use of repellants, and bed net ownership and usage were not associated with CHIKV seropositivity. Our results showed the co-circulation of two other alphaviruses, ONNV and SFV, in Nouakchott in 30 (2.3%) individuals. This is the first study that documents the co-circulation of CHIKV, ONNV, and SFV in Mauritania, albeit at low prevalence. Surveillance and routine testing for alphaviruses and other arboviruses in symptomatic patients should be implemented in health facilities to assess the health burden associated with these viruses. Efforts should also be made to strengthen the vector control measures.