title: Genotypic and phenotypic heterogeneity in the U3R region of HIV type 1 subtype C.
abstract: Approximately 20% of all HIV-1 mother-to-child transmission (MTCT) occurs in utero (IU). In a chronic HIV infection, HIV-1 exists as a complex swarm of genetic variants, and following IU MTCT, viral genomic diversity is restricted through a mechanism that remains to be described. The 5' U3R region of the HIV-1 long terminal repeat (LTR) contains multiple transcription factor (TF) binding sites and regulates viral transcription. In this study, we tested the hypothesis that sequence polymorphisms in the U3R region of LTR are associated with IU MTCT. To this end, we used single template amplification to isolate 517 U3R sequences from maternal, placental, and infant plasma derived from 17 HIV-infected Malawian women: eight whose infants remained HIV uninfected (NT) and nine whose infants became HIV infected IU. U3R sequences show pairwise diversities ranging from 0.2% to 2.3%. U3R sequences from one participant contained two, three, or four putative NF-κB binding sites. Phylogenetic reconstructions indicated that U3R sequences from eight of nine IU participants were consistent with placental compartmentalization of HIV-1 while only one of eight NT cases was consistent with such compartmentalization. Specific TF sequence polymorphisms were not significantly associated with IU MTCT. To determine if replication efficiency of the U3R sequences was associated with IU MTCT, we cloned 90 U3R sequences and assayed promoter activity in multiple cell lines. Although we observed significant, yet highly variable promoter activity and TAT induction of promoter activity in the cell lines tested, there was no association between measured promoter activity and MTCT status. Thus, we were unable to detect a promoter genotype or phenotype associated with IU MTCT.
authors.affiliation: 1 Department of Microbiology, The Ohio State University , Columbus, Ohio.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Mates
authors.forename: Surender B
authors.initials: SB
authors.lastname: Kumar
authors.forename: Jose
authors.initials: J
authors.lastname: Bazan
authors.forename: Megan
authors.initials: M
authors.lastname: Mefford
authors.forename: Igor
authors.initials: I
authors.lastname: Voronkin
authors.forename: Samuel
authors.initials: S
authors.lastname: Handelman
authors.forename: Victor
authors.initials: V
authors.lastname: Mwapasa
authors.forename: William
authors.initials: W
authors.lastname: Ackerman
authors.forename: Daniel
authors.initials: D
authors.lastname: Janies
authors.forename: Jesse J
authors.initials: JJ
authors.lastname: Kwiek
mesh_terms: D024506:5' Flanking Region / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D018791:CD4 Lymphocyte Count; D002460:Cell Line; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D057809:HEK293 Cells; D015658:HIV Infections / Q000635:transmission* / Q000821:virology; D016325:HIV Long Terminal Repeat / Q000235:genetics*; D006679:HIV Seropositivity / Q000097:blood; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D007223:Infant; D018445:Infectious Disease Transmission, Vertical; D019169:Jurkat Cells; D008295:Malawi; D016328:NF-kappa B / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy; D011251:Pregnancy Complications, Infectious / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic; D019562:Viral Load; D055815:Young Adult; D054311:nef Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D016328:NF-kappa B; D014157:Transcription Factors; D054311:nef Gene Products, Human Immunodeficiency Virus; C514837:nef protein, Human immunodeficiency virus 1