A Cross‐Sectional Study Shows Emergence of the Delta, 19B, 20A, 20B, 19A, and Omicron Variants of SARS‐CoV‐2 in Burkina Faso: A Conundrum Within a Conundrum

ABSTRACT Context and Objective SARS‐CoV‐2 is an RNA virus that emerged in Wuhan, China. Adaptive mutations in its genome can influence the virus's pathogenicity, enhance its ability to evade the host immune system, and complicate vaccine development. This study aimed to identify the circulating SARS‐CoV‐2 variants in Burkina Faso and trace their origin. Methodology Two study populations were included. The first comprised 287 individuals, both asymptomatic and symptomatic, who tested positive for COVID‐19. The second consisted of 318 individuals from the general population without clinical symptoms who were tested for serological evidence of SARS‐CoV‐2 exposure. The study was carried out between January 2021 and December 2022. Sequencing was performed only on the 287 positive samples. Viral RNA was extracted from these clinical specimens, amplified by RT‐PCR, and subsequently sequenced. Phylogenetic analysis was conducted using Nextclade v3.8.2 software, with the Wuhan‐Hu‐1/2019 strain as the reference genome sequence. Results The identified variants were Omicron (47.91%), Delta (29.41%), 19B (10.92%), 20A (5.88%), 20B (4.20%), and 19A (1.68%). Most of these variants (84.04%) were detected in travelers, and 88.24% were identified from naso‐oro‐pharyngeal samples. Among the variants, Omicron was the most prevalent and exhibited the highest number of mutations. Complementary serological testing revealed that approximately 22.7% of the general population had been exposed to SARS‐CoV‐2 during the study period. Conclusion These findings suggest that multiple introductions of SARS‐CoV‐2 into Burkina Faso occurred mainly through international travel, with Omicron rapidly becoming dominant. Despite evidence of widespread viral circulation, COVID‐19 mortality in Burkina Faso has remained relatively low, according to data from the Ministry of Health. Rather than providing definitive explanations for this paradox, our findings generate hypotheses regarding potential protective factors, including demographic characteristics, host genetics, cross‐reactive immunity, and the possibility of underreporting that warrant further investigation guiding responses to future emerging infectious diseases.