{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T10:42:08Z","timestamp":1761129728240,"version":"build-2065373602"},"reference-count":29,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2020,1,27]],"date-time":"2020-01-27T00:00:00Z","timestamp":1580083200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Tailoring public health responses to growing HIV transmission clusters depends on accurately mapping the risk network through which it spreads and identifying acute infections that represent the leading edge of cluster growth. HIV transmission links, especially those involving persons with acute HIV infection (AHI), can be difficult to uncover, or confirm during partner services investigations. We integrated molecular, epidemiologic, serologic and behavioral data to infer and evaluate transmission linkages between participants of a prospective study of AHI conducted in North Carolina, New York City and San Francisco from 2011\u20132013. Among the 547 participants with newly diagnosed HIV with polymerase sequences, 465 sex partners were reported, of whom only 35 (7.5%) had HIV sequences. Among these 35 contacts, 23 (65.7%) links were genetically supported and 12 (34.3%) were not. Only five links were reported between participants with AHI but none were genetically supported. In contrast, phylodynamic inference identified 102 unreported transmission links, including 12 between persons with AHI. Importantly, all putative transmission links between persons with AHI were found among large clusters with more than five members. Taken together, the presence of putative links between acute participants who did not name each other as contacts that are found only among large clusters underscores the potential for unobserved or undiagnosed intermediaries. Phylodynamics identified many more links than partner services alone and, if routinely and rapidly integrated, can illuminate transmission patterns not readily captured by partner services investigations.<\/jats:p>","DOI":"10.3390\/v12020145","type":"journal-article","created":{"date-parts":[[2020,1,27]],"date-time":"2020-01-27T11:41:57Z","timestamp":1580125317000},"page":"145","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Phylodynamic Analysis Complements Partner Services by Identifying Acute and Unreported HIV Transmission"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9535-4420","authenticated-orcid":false,"given":"Ellsworth M.","family":"Campbell","sequence":"first","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, GA 30322, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Patala","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, GA 30322, USA"},{"name":"ICF International, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anupama","family":"Shankar","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, GA 30322, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin-Fen","family":"Li","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, GA 30322, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey A.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, GA 30322, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emily","family":"Westheimer","sequence":"additional","affiliation":[{"name":"New York City Department of Health and Mental Hygiene, New York, NY 10013, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cynthia L.","family":"Gay","sequence":"additional","affiliation":[{"name":"Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephanie E.","family":"Cohen","sequence":"additional","affiliation":[{"name":"San Francisco Department of Public Health, San Francisco, CA 94102, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4591-8731","authenticated-orcid":false,"given":"William M.","family":"Switzer","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, GA 30322, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philip J.","family":"Peters","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, GA 30322, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,1,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2287","DOI":"10.1097\/00002030-200111230-00010","article-title":"Acute HIV infection: Impact on the spread of HIV and transmission of drug resistance","volume":"15","author":"Yerly","year":"2001","journal-title":"AIDS"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1086\/590501","article-title":"HIV-1 Transmission, by Stage of Infection","volume":"198","author":"Hollingsworth","year":"2008","journal-title":"J. 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