INFLUENZA OUTBREAK DURING THE SURGE OF SARS-CoV-2 OMICRON IN A METROPOLITAN AREA FROM SOUTHERN BRAZIL: GENOMIC SURVEILLANCE.

Influenza circulation was significantly affected in 2020–21 by the COVID-19 pandemic. During this time, few influenza cases were recorded. However, in the summer of 2021–22, an increase in atypical influenza cases was observed, leading to the resurgence of influenza in the southernmost state of Brazil, Rio Grande do Sul (RS). The present study aimed to identify FLUAV, FLUBV, and SARS-CoV-2 circulation and characterize influenza genomes in suspected COVID-19 patients using high-throughput sequencing technology. Respiratory samples (n = 694) from patients in RS were selected between July 2021 and August 2022. The samples were typed reverse transcriptase real-time PCR (RT-qPCR) and showed 32.13% (223/694) of the samples to be positive for SARS-CoV-2, 7.06% for FLUAV (49/694). FLUBV was not detected. RT-qPCR data also showed 0.57% of the cases had FLUAV and SARS-CoV-2 co-infections. Whole genome sequencing of the FLUAV positive specimens produced 15 complete genomes of H3N2 subtype with phylogenetic placement in the 3C.2a1b.2a.2a.3 subclade. Mutation analysis showed 73 amino acid substitutions in addition to several nonsynonymous mutations. The detected percentage of FLUAV (7.06%) is relatively similar to the total number of flu cases requiring hospitalization in RS state (8.9%), including those admitted to intensive care units for severe complications. This study provides insights into influenza virus circulation in the south of Brazil during the Omicron wave of the COVID-19 pandemic and reinforces the importance of H3N2 as a major driver of severe respiratory disease in the region along with the SARS-CoV-2 Omicron wave at the beginning of 2022.