{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T06:15:53Z","timestamp":1777011353572,"version":"3.51.4"},"reference-count":28,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2019,5,27]],"date-time":"2019-05-27T00:00:00Z","timestamp":1558915200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["P300PA_174462"],"award-info":[{"award-number":["P300PA_174462"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP1074467"],"award-info":[{"award-number":["APP1074467"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP1092852)"],"award-info":[{"award-number":["APP1092852)"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP117907"],"award-info":[{"award-number":["APP117907"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["FL170100022"],"award-info":[{"award-number":["FL170100022"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Australia\u2019s response to the human immunodeficiency virus type 1 (HIV-1) pandemic led to effective control of HIV transmission and one of the world\u2019s lowest HIV incidence rates\u20140.14%. Although there has been a recent decline in new HIV diagnoses in New South Wales (NSW), the most populous state in Australia, there has been a concomitant increase with non-B subtype infections, particularly for the HIV-1 circulating recombinant form CRF01_AE. This aforementioned CRF01_AE sampled in NSW, were combined with those sampled globally to identify NSW-specific viral clades. The population growth of these clades was assessed in two-year period intervals from 2009 to 2017. Overall, 109 NSW-specific clades were identified, most comprising pairs of sequences; however, five large clades comprising \u226510 sequences were also found. Forty-four clades grew over time with one or two sequences added to each in different two-year periods. Importantly, while 10 of these clades have seemingly discontinued, the remaining 34 were still active in 2016\/2017. Seven such clades each comprised \u226510 sequences, and are representative of individual sub-epidemics in NSW. Thus, although the majority of new CRF01_AE infections were associated with small clades that rarely establish ongoing chains of local transmission, individual sub-epidemics are present and should be closely monitored.<\/jats:p>","DOI":"10.3390\/v11050482","type":"journal-article","created":{"date-parts":[[2019,5,27]],"date-time":"2019-05-27T11:19:27Z","timestamp":1558955967000},"page":"482","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8749-4095","authenticated-orcid":false,"given":"Francesca","family":"Di Giallonardo","sequence":"first","affiliation":[{"name":"The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3583-9490","authenticated-orcid":false,"given":"Angie N.","family":"Pinto","sequence":"additional","affiliation":[{"name":"The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia"},{"name":"Department of Infectious Diseases &amp; Microbiology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2678-0645","authenticated-orcid":false,"given":"Phillip","family":"Keen","sequence":"additional","affiliation":[{"name":"The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ansari","family":"Shaik","sequence":"additional","affiliation":[{"name":"The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Carrera","sequence":"additional","affiliation":[{"name":"New South Wales State Reference Laboratory for HIV\/AIDS, Darlinghurst, New South Wales 2010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanan","family":"Salem","sequence":"additional","affiliation":[{"name":"New South Wales Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barbara","family":"Telfer","sequence":"additional","affiliation":[{"name":"Health Protection New South Wales, New South Wales Health, NSW, North Sydne, New South Wales 2060, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Craig","family":"Cooper","sequence":"additional","affiliation":[{"name":"Positive Life New South Wales, Surry Hills, New South Wales 2010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen","family":"Price","sequence":"additional","affiliation":[{"name":"ACON Health Ltd., Surry Hills, New South Wales 2010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine","family":"Selvey","sequence":"additional","affiliation":[{"name":"Health Protection New South Wales, New South Wales Health, NSW, North Sydne, New South Wales 2060, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanne","family":"Holden","sequence":"additional","affiliation":[{"name":"Centre for Population Health, New South Wales Ministry of Health, North Sydney, New South Wales 2059, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadine","family":"Bachmann","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederick J.","family":"Lee","sequence":"additional","affiliation":[{"name":"New South Wales Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia"},{"name":"Department of Clinical Immunology &amp; Allergy, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia"},{"name":"Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dominic E.","family":"Dwyer","sequence":"additional","affiliation":[{"name":"New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2863-0907","authenticated-orcid":false,"given":"Sebasti\u00e1n","family":"Duch\u00eane","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9596-3552","authenticated-orcid":false,"given":"Edward C.","family":"Holmes","sequence":"additional","affiliation":[{"name":"Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia"},{"name":"Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew E.","family":"Grulich","sequence":"additional","affiliation":[{"name":"The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony D.","family":"Kelleher","sequence":"additional","affiliation":[{"name":"The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,5,27]]},"reference":[{"key":"ref_1","unstructured":"UNAIDS (2014). 90-90-90 An Ambitious Treatment Target to Help End the AIDS Epidemic, UNAIDS."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Insight Start Study Group, Lundgren, J.D., Babiker, A.G., Gordin, F., Emery, S., Grund, B., Sharma, S., Avihingsanon, A., Cooper, D.A., and Fatkenheuer, G. 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