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

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 and Ho, Antonia (2023) 'Prevalence of endemic respiratory viruses during the COVID-19 pandemic in urban and rural Malawi'. Open Forum Infectious Diseases, Vol 11, Issue 2, ofad643.

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Abstract

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.

Item Type:	Article
Subjects:	WC Communicable Diseases > Virus Diseases > Viral Respiratory Tract Infections. Respirovirus Infections > WC 505 Viral respiratory tract infections WC Communicable Diseases > Virus Diseases > Viral Respiratory Tract Infections. Respirovirus Infections > WC 506 COVID-19 WF Respiratory System > WF 140 Diseases of the respiratory system (General)
Faculty: Department:	Clinical Sciences & International Health > Malawi-Liverpool-Wellcome Programme (MLW)
Digital Object Identifer (DOI):	https://doi.org/10.1093/ofid/ofad643
SWORD Depositor:	JISC Pubrouter
Depositing User:	JISC Pubrouter
Date Deposited:	05 Feb 2024 10:49
Last Modified:	05 Feb 2024 10:49
URI:	https://archive.lstmed.ac.uk/id/eprint/23772

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