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To achieve this, efficient and timely viral surveillance, and effective public health interventions, are required. Traditional epidemiological methods are largely dependent on the recognition of incident cases with symptomatic illness; acute HIV and HCV infections are commonly asymptomatic, which may lead to delays in the recognition of such new infections. Instead, for these viruses, molecular epidemiology may improve the detection of, and response to, clusters of viral transmission. Molecular epidemiology using historical datasets has highlighted key populations that may have benefitted from a timely intervention. Similar analyses performed on contemporary samples are needed to underpin the 2030 targets, but this requires the generation of a cohesive dataset of viral genome sequences in near\u2010real\u2010time. To generate such data, methodologies harnessing next\u2010generation sequencing (NGS) should be utilised. Here we discuss the opportunity presented by NGS for public health surveillance of HIV and HCV, and discuss three methods that can generate sequences for such analysis. These include full\u2010length genome amplification, utilised for analysis of HCV in the research space; tiling PCR, which was the method of choice for many diagnostic laboratories in the SARS\u2010CoV\u20102 pandemic; and bait\u2010capture hybridisation, which has been utilised in local HIV outbreaks. These techniques could be applied for near\u2010real\u2010time HIV and HCV surveillance, informing public health strategies that will be key to achieving 2030 targets.<\/jats:p>","DOI":"10.1002\/rmv.70001","type":"journal-article","created":{"date-parts":[[2024,10,21]],"date-time":"2024-10-21T03:19:19Z","timestamp":1729480759000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Next\u2010Generation Sequencing Methods for Near\u2010Real\u2010Time Molecular Epidemiology of HIV and HCV"],"prefix":"10.1002","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4263-2351","authenticated-orcid":false,"given":"Bethany A.","family":"Horsburgh","sequence":"first","affiliation":[{"name":"Faculty of Medicine The Kirby Institute University of New South Wales  Sydney Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory J.","family":"Walker","sequence":"additional","affiliation":[{"name":"Virology Research Laboratory Serology and Virology Division (SAViD) Prince of Wales Hospital  Randwick Australia"},{"name":"Faculty of Medicine School of Biomedical Sciences University of New South Wales  Sydney Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony","family":"Kelleher","sequence":"additional","affiliation":[{"name":"Faculty of Medicine The Kirby Institute University of New South Wales  Sydney Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew R.","family":"Lloyd","sequence":"additional","affiliation":[{"name":"Faculty of Medicine The Kirby Institute University of New South Wales  Sydney Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9844-3744","authenticated-orcid":false,"given":"Rowena A.","family":"Bull","sequence":"additional","affiliation":[{"name":"Faculty of Medicine The Kirby Institute University of New South Wales  Sydney Australia"},{"name":"Faculty of Medicine School of Biomedical Sciences University of New South Wales  Sydney Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca Di","family":"Giallonardo","sequence":"additional","affiliation":[{"name":"Faculty of Medicine The Kirby Institute University of New South Wales  Sydney Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,10,20]]},"reference":[{"key":"e_1_2_15_2_1","volume-title":"Global Progress Report on HIV, Viral Hepatitis and Sexually Transmitted Infections","author":"World Health Organization","year":"2021"},{"key":"e_1_2_15_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/jia2.25161"},{"key":"e_1_2_15_4_1","doi-asserted-by":"publisher","DOI":"10.5694\/mja16.00934"},{"key":"e_1_2_15_5_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002552"},{"key":"e_1_2_15_6_1","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.69.8.5087\u20105094.1995"},{"key":"e_1_2_15_7_1","doi-asserted-by":"publisher","DOI":"10.1099\/0022\u20101317\u201081\u20107\u20101631"},{"key":"e_1_2_15_8_1","doi-asserted-by":"publisher","DOI":"10.1097\/QAI.0000000000000809"},{"key":"e_1_2_15_9_1","doi-asserted-by":"publisher","DOI":"10.1097\/qad.0b013e3283578b80"},{"key":"e_1_2_15_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.drugalcdep.2015.04.005"},{"key":"e_1_2_15_11_1","doi-asserted-by":"publisher","DOI":"10.1097\/coh.0000000000000539"},{"key":"e_1_2_15_12_1","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.02390\u201007"},{"key":"e_1_2_15_13_1","volume-title":"Hepatitis C Drug Resistance Webinar: Awareness of Hepatitis C Drug Resistance as Access to Hepatitis C Diagnosis and Treatment Expands","author":"World Health Organization","year":"2023"},{"key":"e_1_2_15_14_1","volume-title":"Australian Needle Syringe Program Survey National Data Report 2018\u20102022: Prevalence of HIV, HCV and Injecting and Sexual Behaviour Among NSP Attendees. 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