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

2017-11-01Journal article Restricted access
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dc.contributor.authorRomero-Severson, Ethan O.
dc.contributor.authorBulla, Ingo
dc.contributor.authorHengartner, Nick
dc.contributor.authorBártolo, Inês
dc.contributor.authorAbecasis, Ana
dc.contributor.authorAzevedo-Pereira, José M.
dc.contributor.authorTaveira, Nuno
dc.contributor.authorLeitner, Thomas
dc.date.accessioned2017-11-22T12:08:18Z
dc.date.available2017-11-22T12:08:18Z
dc.date.issued2017-11-01
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.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationEthan O. Romero-Severson, Ingo Bulla, Nick Hengartner, Inês Bártolo, Ana Abecasis, José M. Azevedo-Pereira, Nuno Taveira and View ORCID ProfileThomas Leitner. GENETICS November 1, 2017 vol. 207 no. 3 1089-1101; https://doi.org/10.1534/genetics.117.300284pt_PT
dc.identifier.doi10.1534/genetics.117.300284pt_PT
dc.identifier.issn0016-6731
dc.identifier.issn1943-2631
dc.identifier.urihttp://hdl.handle.net/10400.26/19467
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherGenetics Society of Americapt_PT
dc.relationMolecular epidemiology, drug resistance and pathogenesis of HIV and TB in Angola: the Angolan PErinatal HIV Cohort (APEHC)
dc.relationDESENVOLVIMENTO DE NOVOS MICROBICIDAS PARA PREVENIR A INFECÇÃO POR VIH
dc.relation.publisherversionhttps://doi.org/10.1534/genetics.117.300284pt_PT
dc.subjectCoalescentpt_PT
dc.subjectPhylogenypt_PT
dc.subjectApproximate Bayesian computationpt_PT
dc.subjectCoinfectionpt_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.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/5876/UID%2FMulti%2F04413%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F76225%2F2011/PT
oaire.citation.endPage1101pt_PT
oaire.citation.startPage1089pt_PT
oaire.citation.titleGeneticspt_PT
oaire.citation.volume207(3)pt_PT
oaire.fundingStream3599-PPCDT
oaire.fundingStream3599-PPCDT
oaire.fundingStream5876
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.rightsrestrictedAccesspt_PT
rcaap.typearticlept_PT
relation.isProjectOfPublicationc3b60260-41c1-4212-93cd-191d5b2e6133
relation.isProjectOfPublicatione63cde82-fa32-4aed-90e7-c9443427f2e1
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