Prevalence of Endemic Respiratory Viruses During the COVID-19 Pandemic in Urban and Rural Malawi

• Published in: Open forum infectious diseases Vol. 11; no. 2; p. ofad643
• Main Authors: Vink, Elen, Banda, Louis, Amoah, Abena S, Kasenda, Stephen, Read, Jonathan M, Jewell, Chris, Denis, Brigitte, Mwale, Annie Chauma, Crampin, Amelia, Anscombe, Catherine, Menyere, Mavis, Ho, Antonia
• Format: Journal Article
• Language: English
• Published: US Oxford University Press 01.02.2024
• Subjects: COVID-19; Influenza; Pandemics; Respiratory syncytial virus; Severe acute respiratory syndrome coronavirus 2; Viruses; Malawi; COVID-19; epidemiology; respiratory viruses; Malawi; community surveillance
• ISSN: 2328-8957; 2328-8957
• DOI: 10.1093/ofid/ofad643

Abstract Background We investigated endemic respiratory virus circulation patterns in Malawi, where no lockdown was imposed, during the COVID-19 pandemic. Methods Within 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. Results 1626 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. Conclusions Endemic 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. Continued circulation of endemic respiratory viruses in Malawi during the pandemic. Influenza/RSV rarely detected. Higher virus positivity detected in the rural setting and at earlier time points. Coinfections infrequent. Distinct differences in demographics between urban and rural cohorts.