Prevalence of endemic respiratory viruses during the COVID-19 pandemic in urban and rural Malawi

Background Non-pharmaceutical interventions (NPI) during the COVID-19 pandemic disrupted respiratory virus circulation. Malawi employed multiple NPI but did not impose a “lockdown”. We aimed to investigate endemic respiratory virus circulation patterns in urban and rural Malawi during this period. Methods Within a prospective cohort of randomly selected households in an urban and rural community in Malawi, adult participants provided upper respiratory tract samples at four timepoints, between February 2021 and April 2022. PCR for SARS-CoV-2, influenza and other endemic respiratory viruses was performed. Results 1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) of samples were PCR-positive for 1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most frequently detected. No influenza A virus was detected. Influenza B and RSV were rare. Significantly higher levels of virus positivity were detected in the rural setting, and at earlier timepoints. Co-infections were infrequent (0.2%; n = 3). Conclusion Endemic respiratory viruses circulated in the community in Malawi during the pandemic, although influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts. Ongoing surveillance is needed to monitor the impact of continuing co-circulation of SARS-CoV-2 with endemic respiratory viruses