Metagenomic surveillance reveals off-season circulation of respiratory viruses during the COVID-19 pandemic in Salvador, Brazil

Background Evidence from multiple countries suggests that the COVID-19 pandemic disrupted the transmission of other respiratory viruses. We characterized respiratory virus transmission during the pandemic in Salvador, Brazil, a tropical region in the Southern Hemisphere. Methods From November 2021 to October 2022, we conducted biweekly household visits in an urban informal settlement to screen individuals with respiratory symptoms. Symptomatic individuals and their contacts were interviewed, and nasal swabs collected. Virus identification was performed using multiplex RT-qPCR, followed by metagenomic analysis in a subset of symptomatic participants with negative RT-qPCR results. Results We screened 3174 residents from 1174 households, identifying 669 symptomatic episodes and detecting 219 respiratory viruses. including coinfections, SARS-CoV-2 was the most common with 118 cases (54%), followed by Influenza A with 39 (18%), Rhinovirus with 22 (10%), Human Parainfluenza Virus with 15 (7%), Respiratory Syncytial Virus with 13 (6%), and seasonal Human Coronaviruses with 12 (5%). Co-infections were observed, with combinations involving SARS-CoV-2, Influenza A, and Respiratory Syncytial Virus being the most common. Peaks of Influenza, HPIV, and RSV occurred in late 2021 during low Delta circulation, while Omicron BA.1 emerged in January 2022. Influenza and RSV showed low transmission during Brazil's winter months, and seasonal coronaviruses reappeared two years after the pandemic onset. Conclusion Multiplex RT-qPCR and metagenomic analysis allowed rapid detection and sequencing. An off-season influenza peak was identified, possibly due to relaxed hygiene measures or accumulated susceptibility after SARS-CoV-2 interventions. The household secondary attack rate for influenza was lower than for Omicron BA.1, possibly reflecting lower transmissibility or pre-existing immunity.