SARS-CoV-2 Variants Screening in Burkina Faso

In Sub-Saharan Africa, the data on the mutations and variants of circulating SARS-CoV-2 is limited. This study aimed to screen specific mutations and variants of SARS-CoV-2 circulating in Burkina Faso.

This study included symptomatic and asymptomatic individuals who underwent diagnostic testing for SARS-CoV-2 by RT-PCR on nasopharyngeal and oropharyngeal swabs from 7 December 2021 to 12 January 2022. Samples from individuals with a Ct value ≤ 33 were selected for the variants-specific mutation screening. The screening was performed using two kits, “SNPsig® SARS-COV-2 (Escape PLEX)" and "SNPsig® VariPLEX™ (COVID-19) Real-Time PCR Assay".

SARS-CoV-2 prevalence was 18.9% (332/1758). A total of 113 samples (34.04%) had a Ct value less than (≤ 33), with only 20.35% (23/113) belonging to symptomatic patients. The mean age was 39.01±13 years. The Beta variant (B.1.351) was the most detected one comprising 78.8% (89/113) of variants. Gamma and Delta variants were detected at a low proportion of 0.9% (1/113). No mutation or variant was detected in seven (6.2%) samples.

Specific mutation screening detected Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) variants of SARS-CoV-2 circulating in Burkina Faso. The absence of mutations in some samples might suggest variants other than those detected.