title: Short communication: phylodynamics analysis of the human immunodeficiency virus type 1 envelope gene in mother and child pairs.
abstract: Characterizing the impact of HIV transmission routes on viral genetic diversity can improve the understanding of the mechanisms of virus evolution and adaptation. HIV vertical transmission can occur in utero, during delivery, or while breastfeeding. The present study investigated the phylodynamics of the HIV-1 env gene in mother-to-child transmission by analyzing one chronically infected pair from Brazil and three acutely infected pairs from Zambia, with three to five time points. Sequences from 25 clones from each sample were obtained and aligned using Clustal X. ML trees were constructed in PhyML using the best evolutionary model. Bayesian analyses testing the relaxed and strict molecular clock were performed using BEAST and a Bayesian Skyline Plot (BSP) was construed. The genetic variability of previously described epitopes was investigated and compared between each individual time point and between mother and child sequences. The relaxed molecular clock was the best-fitted model for all datasets. The tree topologies did not show differentiation in the evolutionary dynamics of the virus circulating in the mother from the viral population in the child. In the BSP, the effective population size was more constant in time in the chronically infected patients while in the acute patients it was possible to detect bottlenecks. The genetic variability within viral epitopes recognized by the human immune system was considerably higher among the chronically infected pair in comparison with acutely infected pairs. These results contribute to a better understanding of HIV-1 evolutionary dynamics in mother-to-child transmission.
authors.affiliation: 1 Laboratorio de Hematologia Genética e Biologia Computacional, Centro de Pesquisa Gonçalo Moniz , Fundação Oswaldo Cruz, Salvador, Bahia, Brazil .
authors.forename: Luciane Amorim
authors.initials: LA
authors.lastname: Santos
authors.affiliation: 2 Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine , Gainesville, Florida.
authors.forename: Rebecca R
authors.initials: RR
authors.lastname: Gray
authors.affiliation: 1 Laboratorio de Hematologia Genética e Biologia Computacional, Centro de Pesquisa Gonçalo Moniz , Fundação Oswaldo Cruz, Salvador, Bahia, Brazil .|3 Universidade Federal da Bahia , Bahia, Brazil .
authors.forename: Joana Paixão
authors.initials: JP
authors.lastname: Monteiro-Cunha
authors.affiliation: 4 Hemocentro de Ribeirão Preto, Universidade de São Paulo , São Paulo, Brazil .
authors.forename: Evandra
authors.initials: E
authors.lastname: Strazza
authors.affiliation: 4 Hemocentro de Ribeirão Preto, Universidade de São Paulo , São Paulo, Brazil .
authors.forename: Simone
authors.initials: S
authors.lastname: Kashima
authors.affiliation: 1 Laboratorio de Hematologia Genética e Biologia Computacional, Centro de Pesquisa Gonçalo Moniz , Fundação Oswaldo Cruz, Salvador, Bahia, Brazil .
authors.forename: Edson de Souza
authors.initials: Ede S
authors.lastname: Santos
authors.affiliation: 1 Laboratorio de Hematologia Genética e Biologia Computacional, Centro de Pesquisa Gonçalo Moniz , Fundação Oswaldo Cruz, Salvador, Bahia, Brazil .
authors.forename: Thessika Hialla Almeida
authors.initials: TH
authors.lastname: Araújo
authors.affiliation: 1 Laboratorio de Hematologia Genética e Biologia Computacional, Centro de Pesquisa Gonçalo Moniz , Fundação Oswaldo Cruz, Salvador, Bahia, Brazil .
authors.forename: Marilda de Souza
authors.initials: Mde S
authors.lastname: Gonçalves
authors.affiliation: 2 Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine , Gainesville, Florida.
authors.forename: Marco
authors.initials: M
authors.lastname: Salemi
authors.affiliation: 1 Laboratorio de Hematologia Genética e Biologia Computacional, Centro de Pesquisa Gonçalo Moniz , Fundação Oswaldo Cruz, Salvador, Bahia, Brazil .
authors.forename: Luiz Carlos Junior
authors.initials: LC
authors.lastname: Alcantara
mesh_terms: D000328:Adult; D001499:Bayes Theorem; D001938:Brazil; D002648:Child; D002675:Child, Preschool; D019143:Evolution, Molecular; D005260:Female; D015752:Genes, env; D015658:HIV Infections / Q000635:transmission* / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D018445:Infectious Disease Transmission, Vertical; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D015024:Zambia