{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T02:16:47Z","timestamp":1784081807701,"version":"3.55.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,9,13]],"date-time":"2017-09-13T00:00:00Z","timestamp":1505260800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections, there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods, and the reconstruction of epidemiologic histories. To infer who-infected-whom, and to compute the probability of alternative transmission scenarios while explicitly taking phylogenetic uncertainty into account, we created an approximate Bayesian computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a suspected heterosexual transmission case involving three individuals, showing a complex monophyletic-paraphyletic-polyphyletic phylogenetic topology. We detected that seven phylogenetic lineages had been transmitted between two of the individuals based on the available samples, implying that many more unsampled lineages had also been transmitted. Testing whether the lineages had been transmitted at one time or over some length of time suggested that an ongoing superinfection process over several years was most likely. While one individual was found unlinked to the other two, surprisingly, when evaluating two competing epidemiological priors, the donor of the two that did infect each other was not identified by the host root-label, and was also not the primary suspect in that transmission. This highlights that it is important to take epidemiological information into account when analyzing support for one transmission hypothesis over another, as results may be nonintuitive and sensitive to details about sampling dates relative to possible infection dates. Our study provides a formal inference framework to include information on infection and sampling times, and to investigate ancestral node-label states, transmission direction, transmitted genetic diversity, and frequency of transmission.<\/jats:p>","DOI":"10.1534\/genetics.117.300284","type":"journal-article","created":{"date-parts":[[2017,9,15]],"date-time":"2017-09-15T01:20:17Z","timestamp":1505438417000},"page":"1089-1101","source":"Crossref","is-referenced-by-count":15,"title":["Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation"],"prefix":"10.1093","volume":"207","author":[{"given":"Ethan O","family":"Romero-Severson","sequence":"first","affiliation":[{"name":"Theoretical Biology and Biophysics Group , Los Alamos National Laboratory, New Mexico 87545"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingo","family":"Bulla","sequence":"additional","affiliation":[{"name":"Theoretical Biology and Biophysics Group , Los Alamos National Laboratory, New Mexico 87545"},{"name":"Institut f\u00fcr Mathematik und Informatik , Universit\u00e4t Greifswald, 17487, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nick","family":"Hengartner","sequence":"additional","affiliation":[{"name":"Theoretical Biology and Biophysics Group , Los Alamos National Laboratory, New Mexico 87545"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"In\u00eas","family":"B\u00e1rtolo","sequence":"additional","affiliation":[{"name":"HIV Evolution , Epidemiology and Prevention, Research Institute for Medicines \/Instituto de Investiga\u00e7\u00e3o do Medicamento (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa, 1649-003 Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Abecasis","sequence":"additional","affiliation":[{"name":"Global Health and Tropical Medicine (GHTM) , Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa (UNL), 1349-008 Lisboa, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 M","family":"Azevedo-Pereira","sequence":"additional","affiliation":[{"name":"Host-Pathogen Interaction Unit , Research Institute for Medicines \/Instituto de Investiga\u00e7\u00e3o do Medicamento (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa, 1649-003 Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuno","family":"Taveira","sequence":"additional","affiliation":[{"name":"HIV Evolution , Epidemiology and Prevention, Research Institute for Medicines \/Instituto de Investiga\u00e7\u00e3o do Medicamento (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa, 1649-003 Portugal"},{"name":"Centro de Investiga\u00e7\u00e3o Interdisciplinar Egas Moniz (CiiEM) , Instituto Superior Ci\u00eancias da Sa\u00fade Egas Moniz, Monte de Caparica, 2829-511 Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Leitner","sequence":"additional","affiliation":[{"name":"Theoretical Biology and Biophysics Group , Los Alamos National Laboratory, New Mexico 87545"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,9,13]]},"reference":[{"key":"2022110414555039700_bib1","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/nature01200","article-title":"HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus.","volume":"420","author":"Altfeld","year":"2002","journal-title":"Nature"},{"key":"2022110414555039700_bib2","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1080\/10635150600755453","article-title":"Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative.","volume":"55","author":"Anisimova","year":"2006","journal-title":"Syst. 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