Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control

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dc.contributor.authorKitayimbwa, John M.
dc.contributor.authorBbosa, Nicholas
dc.contributor.authorSsemwanga, Deogratius
dc.contributor.authorNsubuga, Rebecca N.
dc.contributor.authorKiwanuka, Noah
dc.contributor.authorBagaya, Bernard S.
dc.contributor.authorSsekagiri, Alfred
dc.contributor.authorGonzalo, Yebra
dc.contributor.authorKaleebu, Pontiano
dc.contributor.authorLeigh-Brown, Andrew
dc.date.accessioned2021-12-22T09:13:31Z
dc.date.available2021-12-22T09:13:31Z
dc.date.issued2021
dc.descriptionThis is a research article discusses the Phylogenetic inference is useful in characterising HIV transmission networks and assessing where prevention is likely to have the greatest impact.en_US
dc.description.abstractPhylogenetic inference is useful in characterising HIV transmission networks and assessing where prevention is likely to have the greatest impact. However, estimating parameters that influence the network structure is still scarce, but important in evaluating determinants of HIV spread. We analyzed 2017 HIV pol sequences (728 Lake Victoria fisherfolk communities (FFCs), 592 female sex workers (FSWs) and 697 general population (GP)) to identify transmission networks on Maximum Likelihood (ML) phylogenetic trees and refined them using time-resolved phylogenies. Network generative models were fitted to the observed degree distributions and network parameters, and corrected Akaike Information Criteria and Bayesian Information Criteria values were estimated. 347 (17.2%) HIV sequences were linked on ML trees (maximum genetic distance _4.5%, _95% bootstrap support) and, of these, 303 (86.7%) that consisted of pure A1 (n = 168) and D (n = 135) subtypes were analyzed in BEAST v1.8.4. The majority of networks (at least 40%) were found at a time depth of _5 years. The waring and yule models fitted best networks of FFCs and FSWs respectively while the negative binomial model fitted best networks in the GP. The network structure in the HIV-hyperendemic FFCs is likely to be scale-free and shaped by preferential attachment, in contrast to the GP. The findings support the targeting of interventions for FFCs in a timely manner for effective epidemic control. Interventions ought to be tailored according to the dynamics of the HIV epidemic in the target population and understanding the network structure is critical in ensuring the success of HIV prevention programs.en_US
dc.identifier.citationKitayimbwa, J.M; Bbosa, N.; Ssemwanga, D.; Nsubuga, R.N.; Kiwanuka, N.; Bagaya, B.S.;.; Ssekagiri, A.; Yebra, G.; Kaleebu, P.; Leigh-Brown, A. Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control. Viruses 2021, 13, 970. https://www.mdpi.com/journal/viruses https://doi.org/10.3390/v13060970en_US
dc.identifier.urihttps://hdl.handle.net/20.500.11951/947
dc.language.isoenen_US
dc.publisherVirusesen_US
dc.subjectHIVen_US
dc.subjectPhylogeneticen_US
dc.subjectTransmission networken_US
dc.subjectPhylodynamicen_US
dc.subjectEpidemic controlen_US
dc.titlePhylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Controlen_US
dc.typeArticleen_US
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