{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T22:16:13Z","timestamp":1792448173604,"version":"4.5.0"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T00:00:00Z","timestamp":1782518400000},"content-version":"vor","delay-in-days":177,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Prevention Research Support Program"},{"name":"Investigator Grants","award":["GNT2018222"],"award-info":[{"award-number":["GNT2018222"]}]},{"name":"Investigator Grants","award":["GNT2025445"],"award-info":[{"award-number":["GNT2025445"]}]},{"name":"National Health and Medical Research Council, Australia"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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.<\/jats:p>","DOI":"10.1093\/ve\/veag036","type":"journal-article","created":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T11:48:23Z","timestamp":1782388103000},"source":"Crossref","is-referenced-by-count":1,"title":["Respiratory virus genomic epidemiology during post-pandemic re-emergence of influenza in Australia"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4329-5198","authenticated-orcid":false,"given":"Rebecca J","family":"Rockett","sequence":"first","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology - Public Health, Redbank Road, Westmead Hospital , Westmead, New South Wales 2145 ,","place":["Australia"]},{"name":"Sydney Institute for Infectious Diseases, The University of Sydney , Hawkesbury Road, Westmead Hospital, New South Wales 2006 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8735-1222","authenticated-orcid":false,"given":"Jessica E","family":"Agius","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology - Public Health, Redbank Road, Westmead Hospital , Westmead, New South Wales 2145 ,","place":["Australia"]},{"name":"Sydney Institute for Infectious Diseases, The University of Sydney , Hawkesbury Road, Westmead Hospital, New South Wales 2006 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2092-8917","authenticated-orcid":false,"given":"Shona","family":"Chandra","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology - Public Health, Redbank Road, Westmead Hospital , Westmead, New South Wales 2145 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Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Redbank Road, Westmead Hospital , Westmead, New South Wales 2145 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Connie","family":"Lam","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology - Public Health, Redbank Road, Westmead Hospital , Westmead, New South Wales 2145 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9983-6603","authenticated-orcid":false,"given":"Sharon C-A","family":"Chen","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology - Public Health, Redbank Road, Westmead Hospital , Westmead, New South Wales 2145 ,","place":["Australia"]},{"name":"Sydney Institute for Infectious Diseases, The University of Sydney , Hawkesbury Road, Westmead Hospital, New South Wales 2006 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Westmead, New South Wales 2145 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8796-283X","authenticated-orcid":false,"given":"Jen","family":"Kok","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology - Public Health, Redbank Road, Westmead Hospital , Westmead, New South Wales 2145 ,","place":["Australia"]},{"name":"Sydney Institute for Infectious Diseases, The University of Sydney , Hawkesbury Road, Westmead Hospital, New South Wales 2006 ,","place":["Australia"]},{"name":"Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Redbank Road, Westmead Hospital , Westmead, New South Wales 2145 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheena G","family":"Sullivan","sequence":"additional","affiliation":[{"name":"World Health Organization 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