Tracking severe acute respiratory syndrome coronavirus 2 transmission and co‐infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya

BACKGROUND: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been the most significant public health challenge in over a century. SARS‐CoV‐2 has infected over 765 million people worldwide, resulting in over 6.9 million deaths. This study aimed to detect community transmission of SARS‐CoV‐2 and monitor the co‐circulation of SARS‐CoV‐2 with other acute respiratory pathogens in Rift Valley, Kenya. METHODS: We conducted a cross‐sectional active sentinel surveillance for the SARS‐CoV‐2 virus among patients with acute respiratory infections at four sites in Rift Valley from January 2022 to December 2022. One thousand two hundred seventy‐one patients aged between 3 years and 98 years presenting with influenza‐like illness (ILI) were recruited into the study. Nasopharyngeal swab specimens from all study participants were screened using a reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR) for SARS‐CoV‐2, influenza A, influenza B and respiratory syncytial virus (RSV). RESULTS: The samples that tested positive for influenza A (n = 73) and RSV (n = 12) were subtyped, while SARS‐CoV‐2 (n = 177) positive samples were further screened for 12 viral and seven bacterial respiratory pathogens. We had a prevalence of 13.9% for SARS‐CoV‐2, 5.7% for influenza A, 2% for influenza B and 1% for RSV. Influenza A‐H1pdm09 and RSV B were the most dominant circulating subtypes of influenza A and RSV, respectively. The most common co‐infecting pathogens were Streptococcus pneumoniae (n = 29) and Haemophilus influenzae (n = 19), accounting for 16.4% and 10.7% of all the SARS‐CoV‐2 positive samples. CONCLUSIONS: Augmenting syndromic testing in acute respiratory infections (ARIs) surveillance is crucial to inform evidence‐based clinical and public health interventions.