Journal of medical virologyOct 3, 2024

Tracking flu cases during the COVID-19 omicron surge in a major city in southern Brazil

Updated Apr 6, 2026

Abstract

32% of respiratory samples tested positive for SARS-CoV-2 during the summer of 2021-22.

A total of 694 respiratory samples were analyzed from patients in Rio Grande do Sul, Brazil.
7% of samples tested positive for the influenza A virus (H3 subtype), with no detections of influenza B virus.
Co-infections of influenza A and SARS-CoV-2 were found in 1.7% of the positive samples.
Fifteen complete genomes of the H3N2 subtype were sequenced, revealing genetic evolution marked by 72 amino acid substitutions.
The study identified a specific phylogenetic classification of the influenza viruses, indicating dominance in southern Brazil.
Current surveillance systems were found to have limitations, suggesting a need for enhanced data collection to improve understanding of influenza epidemiology.

Simplified

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 the circulation of FLUAV, FLUBV and SARS-CoV-2 and characterize the influenza genomes in respiratory samples using high-throughput sequencing technology (HTS). Respiratory samples (n = 694) from patients in RS were selected between July 2021 and August 2022. The samples were typed using reverse transcriptase real-time PCR (RT-qPCR) and showed 32% (223/694) of the samples to be positive for SARS-CoV-2, 7% for FLUAV (H3) (49/694). FLUBV was not detected. RT-qPCR data also resulted in FLUAV and SARS-CoV-2 co-infections in 1.7% (4/223) of samples tested. Whole genome sequencing of FLUAV produced 15 complete genomes of the H3N2 subtype, phylogenetically classified in the 3C.2a1b.2a.2a.3 subclade and revealing the dominance of viruses in the southern region of Brazil. Mutation analysis identified 72 amino acid substitutions in all genes, highlighting ongoing genetic evolution with potential implications for vaccine effectiveness, viral fitness, and pathogenicity. This study underscores limitations in current surveillance systems, advocating for comprehensive data inclusion to enhance understanding of influenza epidemiology in southern Brazil. These findings contribute valuable insights to inform more effective public health responses and underscore the critical need for continuous genomic surveillance.

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Tracking flu cases during the COVID-19 omicron surge in a major city in southern Brazil

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