Respiratory virus genomic epidemiology during post-pandemic re-emergence of influenza in Australia

Simultaneous genomic sequencing of multiple respiratory pathogens from clinical samples can provide real-time data on viral evolution, co-circulation, and co-infection during seasonal epidemics. Influenza is a major global respiratory pathogen, with a well-established genomic epidemiology framework, that has yet to be integrated with genomic surveillance of other co-circulating respiratory viruses. Leveraging existing well-integrated community influenza sampling during the first major Australian winter influenza season after the lifting of the Coronavirus Disease 2019 (COVID-19) pandemic restrictions in 2022, we examined the genomic epidemiology of influenza A alongside co-infections of common human respiratory viruses. Using a commercial respiratory viral sequencing method, Respiratory Virus Oligo Panel (Illumina), we recovered full-length human influenza A genomes from 75% (117/157) of samples with nucleic acid amplification test-confirmed influenza, as well as 19 genomes of co-infecting viruses from 17 samples, including respiratory syncytial virus (RSV-B), human bocavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), human metapneumovirus, and coronaviruses 229E and OC43. The observed incidence of co-infecting viruses (RSV and SARS-CoV-2) was temporally consistent with national epidemic trends. In the majority of co-infections, the viral abundance was predominated by one of the infecting viruses, which may suggest either consecutive infections, or within-host dynamics favouring the dominance of one of the infecting viruses. The dominant influenza subtype was A/H3N2, with a minority of A/H1N1 infections persisting throughout the winter season, consistent with national surveillance. We contextualize our representative sample set within the global genomic diversity of A/H3N2 and the ongoing evolution of influenza A/H3N2 in the following Northern Hemisphere 2022/2023 winter. In addition to influenza A genomic epidemiology, multi-pathogen methodology enables simultaneous detection and characterization of co-infecting respiratory pathogens, providing insights into the role of viral dynamics during overlapping epidemics.