Coinfections with SARS‐CoV‐2 variants and influenza virus during the 2019 Coronavirus disease pandemic in Burkina Faso: A surveillance study

BACKGROUND AND AIM: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) particularly the variants of concern coinfections with influenza is a public health concern in Africa. We aimed to characterize the SARS‐CoV‐2 variants and determine the rate of coinfections with influenza in Burkina Faso. METHODS: COVID‐19 surveillance study was conducted between August 2021 and January 2022 using reverse transcription polymerase chain reaction (RT‐PCR). Positive specimens were further screened for SARS‐CoV‐2 variants using the multiple variants real‐time PCR kits. In addition, influenza virus strains were detected by RT‐PCR in SARS‐CoV‐2 positive specimens using the CDC primers, probes, and protocols. RESULTS: Of 324 specimens assessed, the Omicron and Delta variants of SARS‐CoV‐2 were the most prevalent with 27.2% [95% confident interval (CI): 22.5–32.4] and 22.2% [95% CI: 17.9–27.2], respectively. The Beta and Gamma variants were detected in 4.3% [95% CI: 2.4–7.1] and 0.3% [95% CI: 0.0–1.7], respectively. Coinfections of Omicron and Beta variants were reported in 21.3% [95% CI: 17.0–26.2], Omicron and Delta variants in 1.2% [95% CI: 0.3–3.1] of specimens, and the Omicron–Gamma variants' coinfections in 0.6% [95% CI: 0.1–2.2]. One COVID‐19 specimen with an undetected SARS‐CoV‐2 variant was also tested positive for the seasonal influenza A (H(3)N(2)) virus. No cases of pandemic influenza A (H(1)N(1))pdm09, seasonal A/H(1)N(1), and influenza B were detected. CONCLUSIONS: The current World Health Organization SARS‐CoV‐2 variants of concern were prevalent and their coinfections with influenza were uncommon. Continuous surveillance of both pathogens is, however, needed because of their public health implications.