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Donor-recipient identification in para- and poly-phyletic trees under alternative HIV-1 transmission hypotheses using approximate bayesian computation

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dc.contributor.authorRomero-Severson, Ethan
dc.contributor.authorBulla, Ingo
dc.contributor.authorHengartner, Nick
dc.contributor.authorBártolo, Inês
dc.contributor.authorAbecasis, Ana B.
dc.contributor.authorAzevedo-Pereira, José M.
dc.contributor.authorTaveira, Nuno
dc.contributor.authorLeitner, Thomas
dc.date.accessioned2023-08-24T10:20:58Z
dc.date.available2023-08-24T10:20:58Z
dc.date.issued2017
dc.date.updated2023-02-03T14:25:17Z
dc.description.abstractDiversity 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.pt_PT
dc.description.sponsorshipResearch reported in this publication was supported by the National Institute of Allergy and Infectious Diseases/National Institutes of Health (NIAID/NIH) under award number R01AI087520, and by grants PTDC/SAU-EPI/122400/2010, VIH/SAU/0029/2011 and UID/Multi/04413/2013 from Fundação para a Ciência e Tecnologia (FCT), Portugal. I.B. was supported by a post-doctoral fellowship (SFRH/BPD/76225/2011) from FCT, Portugal. I.B. was supported by a post-doctoral fellowship (BU 2685/4-1) from the Deutsche Forschungsgemeinschaft.pt_PT
dc.description.versioninfo:eu-repo/semantics/acceptedVersionpt_PT
dc.identifier.citationRomero-Severson EO, Bulla I, Hengartner N, Bártolo I, Abecasis A, Azevedo-Pereira JM, et al. Donor-recipient identification in para- and poly-phyletic trees under alternative hiv-1 transmission hypotheses using approximate bayesian computation. Genetics [Internet]. 1 de novembro de 2017;207(3):1089–101. Disponível em: https://academic.oup.com/genetics/article/207/3/1089/5930734pt_PT
dc.identifier.doi10.1534/genetics.117.300284pt_PT
dc.identifier.eid2-s2.0-85032936267
dc.identifier.slugcv-prod-1108452
dc.identifier.urihttp://hdl.handle.net/10451/58985
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherOxford University Press / Genetics Society of Americapt_PT
dc.relationMolecular epidemiology, drug resistance and pathogenesis of HIV and TB in Angola: the Angolan PErinatal HIV Cohort (APEHC)
dc.relationGlobal Health and Tropical Medicine
dc.relationDESENVOLVIMENTO DE NOVOS MICROBICIDAS PARA PREVENIR A INFECÇÃO POR VIH
dc.relation.publisherversionhttps://academic.oup.com/genetics/article/207/3/1089/5930734pt_PT
dc.subjectcoalescentpt_PT
dc.subjectphylogenypt_PT
dc.subjectapproximate Bayesian computationpt_PT
dc.subjectco-infectionpt_PT
dc.subjectsuperinfectionpt_PT
dc.subjectancestral node statept_PT
dc.titleDonor-recipient identification in para- and poly-phyletic trees under alternative HIV-1 transmission hypotheses using approximate bayesian computationpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleMolecular epidemiology, drug resistance and pathogenesis of HIV and TB in Angola: the Angolan PErinatal HIV Cohort (APEHC)
oaire.awardTitleGlobal Health and Tropical Medicine
oaire.awardTitleDESENVOLVIMENTO DE NOVOS MICROBICIDAS PARA PREVENIR A INFECÇÃO POR VIH
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FSAU-EPI%2F122400%2F2010/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/VIH%2FSAU%2F0029%2F2011/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FMulti%2F04413%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F76225%2F2011/PT
oaire.citation.endPage1101pt_PT
oaire.citation.issue3pt_PT
oaire.citation.startPage1089pt_PT
oaire.citation.titleGeneticspt_PT
oaire.citation.volume207pt_PT
oaire.fundingStream3599-PPCDT
oaire.fundingStream3599-PPCDT
oaire.fundingStream6817 - DCRRNI ID
person.familyNameRomero-Severson
person.familyNameBártolo
person.familyNameAbecasis
person.familyNameAzevedo Pereira
person.familyNameTaveira
person.familyNameLeitner
person.givenNameEthan
person.givenNameInês
person.givenNameAna
person.givenNameJosé Miguel
person.givenNameNuno
person.givenNameThomas
person.identifier652473
person.identifier.ciencia-id661E-F5CB-F85A
person.identifier.ciencia-id0817-056B-9B7C
person.identifier.ciencia-id4A1B-E7AD-9490
person.identifier.ciencia-id7111-3383-A926
person.identifier.orcid0000-0002-8082-1225
person.identifier.orcid0000-0002-2022-8921
person.identifier.orcid0000-0002-3903-5265
person.identifier.orcid0000-0001-7434-7208
person.identifier.orcid0000-0003-0176-5585
person.identifier.orcid0000-0001-8160-2588
person.identifier.ridB-6295-2009
person.identifier.scopus-author-id8835604200
person.identifier.scopus-author-id6506539639
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.cv.cienciaid661E-F5CB-F85A | Inês Bártolo
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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