TRACKING SARS-COV-2 TRANSMISSION AND CO-INFECTION WITH OTHER ACUTE
RESPIRATORY PATHOGENS USING A SENTINEL SURVEILLANCE SYSTEM IN RIFT
VALLEY, KENYA
Abstract
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. 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. 1271 patients of all ages presenting with influenza-like
illness were recruited into the study. Nasopharyngeal swab specimens
were screened using a multiplex RT–qPCR for SARS-CoV-2, Influenza A,
Influenza B and RSV. Influenza A and RSV samples were subtyped, and all
the SARS-CoV-2 positive samples were further screened for 12 viral and 7
bacterial respiratory pathogens. We had a prevalence of 13.93%
SARS-CoV-2, Influenza A 5.7%, Influenza B 1.96% and 0.94%. 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 and Haemophilus influenzae,
accounting for 16.4% and 10.7% of all the SARS-CoV-2 positive samples.
Augmenting syndromic testing in ARI surveillance is crucial to inform
evidence-based clinical and public health interventions.