The role of respiratory co-infections in modulating disease severity remains understudied in southern Africa, particularly in rural areas. We characterized the spectrum of respiratory pathogens in rural southern Zambia and the prognostic impact of co-infections.
Respiratory specimens collected from inpatient and outpatient participants in a viral surveillance program in 2018-2019 were tested for select viruses and atypical bacteria using the Xpert Xpress Flu/RSV assay and FilmArray Respiratory Panel EZ. Participants were followed for 3-5 weeks to assess clinical course. Multivariable regression was used to assess the role of co-infections in influencing disease severity.
Among 671 participants who presented with influenza-like illness, a respiratory pathogen was detected in 63.2% of samples. Common pathogens identified included influenza (18.2% of samples), RSV (11.8%), rhinovirus (26.4%), and coronavirus (6.0%). Overall, 6.4% of participants were co-infected with multiple respiratory pathogens. Compared to mono-infections, co-infections were not associated with severe clinical illness either overall (RR: 0.72; 95% CI: 0.39-1.32) or specifically with influenza virus (RR: 0.80; 95% CI: 0.14-4.46) or RSV infections (RR: 0.44; 95% CI: 0.17-1.11).
Respiratory infections in rural southern Zambia were associated with a wide range of viruses. Respiratory co-infections in this population were not associated with clinical severity.

Copyright © 2020. Published by Elsevier Ltd.