title: Common genetic arrangements among human immunodeficiency virus type 1 subtype A and D recombinant genomes vertically transmitted in Tanzania.
abstract: Human immunodeficiency virus type 1 (HIV-1) subtypes A, C, and D are cocirculating in Tanzania, and large numbers of recombinant genomes have been reported from this region. Here we describe full-length sequences of six unlinked HIV-1 subtype A and D recombinants. The samples came from newborns, indicating that the recombination patterns were vertically transmitted and were functionally competent. All six genomes had different recombination patterns with one to eight cross-over points frequently located at the beginning or end of functionally defined regions. In five of the six viruses most of gag, pol, tat, and rev and the intracytoplasmic domain of gp41 were classified as subtype D. In all but one genome, the external domain of gp41 and the majority of gp120 belonged to subtype A. A recombination site common to four of the six genomes was located at the transmembrane domain of gp41, at the end of the rev response element. The identification of subtype patterns among intersubtype recombinant genomes from recently infected individuals may reveal genetic determinants of improved viral fitness or advantage for transmission.
authors.affiliation: Harvard AIDS Institute and Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
authors.forename: Irene N
authors.initials: IN
authors.lastname: Koulinska
authors.forename: Gernard
authors.initials: G
authors.lastname: Msamanga
authors.forename: Davis
authors.initials: D
authors.lastname: Mwakagile
authors.forename: Max
authors.initials: M
authors.lastname: Essex
authors.forename: Boris
authors.initials: B
authors.lastname: Renjifo
mesh_terms: D004279:DNA, Viral / Q000032:analysis; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D018445:Infectious Disease Transmission, Vertical; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013636:Tanzania
chemical_list: D004279:DNA, Viral