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

Vink, Elen and Banda, Louis and Amoah, Abena S and Kasenda, Stephen and Read, Jonathan M and Jewell, Chris and Denis, Brigitte and Mwale, Annie Chauma and Crampin, Amelia and Anscombe, Catherine and Menyere, Mavis and Ho, Antonia (2024) Prevalence of endemic respiratory viruses during the COVID-19 pandemic in urban and rural Malawi. Open Forum Infectious Diseases, 11 (2). ofad643. ISSN 2328-8957

Abstract

BackgroundWe investigated endemic respiratory virus circulation patterns in Malawi, where no lockdown was imposed, during the COVID-19 pandemic.MethodsWithin a prospective household cohort in urban and rural Malawi, adult participants provided upper respiratory tract (URT) samples at 4 time points between February 2021 and April 2022. Polymerase chain reaction (PCR) was performed for SARS-CoV-2, influenza, and other endemic respiratory viruses.Results1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) samples were PCR- positive for >1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most common. No influenza A virus was detected. Influenza B and respiratory syncytial virus (RSV) were rare. Higher virus positivity were detected in the rural setting and at earlier time points. Coinfections were infrequent.ConclusionsEndemic respiratory viruses circulated in the community in Malawi during the pandemic, though influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts.