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Bibliographic Details
Main Authors:	Rockett, Rebecca J, Agius, Jessica E, Chandra, Shona, Fong, Winkie, Aziz, Ammar, Suster, Carl JE, Basile, Kerri, Lam, Connie, Chen, Sharon C-A, Dwyer, Dominic E, Kok, Jen, Sullivan, Sheena G, Barr, Ian G, Sintchenko, Vitali, Golubchik, Tanya
Format:	Recurso digital
Language:	English
Published:	Zenodo 2026
Subjects:	Australia, Influenza A, H1N1, H3N2, Respiratory viruses, Outbreak, Surveillance
Online Access:	https://doi.org/10.5281/zenodo.20197772
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Table of Contents:

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 COVID-19 pandemic restrictions in 2022, we examined the genomic epidemiology of influenza alongside co-infections of common human respiratory viruses. Using a commercial respiratory viral sequencing method, Respiratory Virus Oligo Panel (RVOP, 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, 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 all co-infections, the viral abundance was predominated by one of the infecting viruses, suggesting 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 contextualise 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 genomic epidemiology, multi-pathogen methodology enables simultaneous detection and characterisation of co-infecting respiratory pathogens, providing insights into the role of viral dynamics during overlapping epidemics.

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