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This study retrospectively investigated the genetic characteristics of influenza viruses circulating in NSW in 2019 and identified genetic markers related to antiviral resistance and potential virulence.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>The complete genomes of influenza A and B viruses were amplified using reverse transcription\u2010polymerase chain reaction (PCR) and sequenced with an Illumina MiSeq platform.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>When comparing the sequencing data with the vaccine strains and reference sequences, the phylogenetic analysis revealed that most NSW A\/H3N2 viruses (<jats:italic>n<\/jats:italic>\u00a0=\u200968; 94%) belonged to 3C.2a1b and a minority (<jats:italic>n<\/jats:italic>\u00a0=\u20094; 6%) belonged to 3C.3a. These viruses all diverged from the vaccine strain A\/Switzerland\/8060\/2017. All A\/H1N1pdm09 viruses (<jats:italic>n<\/jats:italic>\u00a0=\u200920) showed genetic dissimilarity from vaccine strain A\/Michigan\/45\/2015, with subclades 6B.1A.5 and 6B.1A.2 identified. All B\/Victoria\u2010lineage viruses (<jats:italic>n<\/jats:italic>\u00a0=\u200921) aligned with clade V1A.3, presenting triple amino acid deletions at positions 162\u2013164 in the hemagglutinin protein, significantly diverging from the vaccine strain B\/Colorado\/06\/2017. Multiple amino acid substitutions were also found in the internal proteins of influenza viruses, some of which have been previously reported in hospitalized influenza patients in Thailand. Notably, the oseltamivir\u2010resistant marker H275Y was present in one immunocompromised patient infected with A\/H1N1pdm09 and the resistance\u2010related mutation I222V was detected in another A\/H3N2\u2010infected patient.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Considering antigenic drift and the constant evolution of circulating A and B strains, we believe continuous monitoring of influenza viruses in NSW via the high\u2010throughput sequencing approach provides timely and pivotal information for both public health surveillance and clinical treatment.<\/jats:p><\/jats:sec>","DOI":"10.1111\/irv.13252","type":"journal-article","created":{"date-parts":[[2024,1,30]],"date-time":"2024-01-30T01:50:24Z","timestamp":1706579424000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genome characterization of influenza A and B viruses in New South Wales, Australia, in 2019: A retrospective study using high\u2010throughput whole genome sequencing"],"prefix":"10.1111","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2703-5505","authenticated-orcid":false,"given":"Xinye","family":"Wang","sequence":"first","affiliation":[{"name":"School of Biomedical Sciences, Faculty of Medicine and Health University of New South Wales  Sydney New South Wales Australia"},{"name":"Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology Prince of Wales Hospital  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ki Wook","family":"Kim","sequence":"additional","affiliation":[{"name":"Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology Prince of Wales Hospital  Sydney New South Wales Australia"},{"name":"Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health University of New South Wales  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory","family":"Walker","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences, Faculty of Medicine and Health University of New South Wales  Sydney New South Wales Australia"},{"name":"Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology Prince of Wales Hospital  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sacha","family":"Stelzer\u2010Braid","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences, Faculty of Medicine and Health University of New South Wales  Sydney New South Wales Australia"},{"name":"Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology Prince of Wales Hospital  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5100-9724","authenticated-orcid":false,"given":"Matthew","family":"Scotch","sequence":"additional","affiliation":[{"name":"Biodesign Center for Environmental Health Engineering, Biodesign Institute Arizona State University  Phoenix Arizona USA"},{"name":"College of Health Solutions Arizona State University  Phoenix Arizona USA"},{"name":"Kirby Institute University of New South Wales  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William D.","family":"Rawlinson","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences, Faculty of Medicine and Health University of New South Wales  Sydney New South Wales Australia"},{"name":"Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology Prince of Wales Hospital  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,1,29]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2008.07.039"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.118"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12879\u2010020\u201005670\u20108"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10096\u2010020\u201003822\u2010x"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/irv.12772"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms18081650"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.2105\/AJPH.2018.304609"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciab625"},{"key":"e_1_2_11_10_1","unstructured":"Australian Government.2019 influenza season in Australia. 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