title: Analysis of length variation in the V1-V2 region of env in nonsubtype B HIV type 1 from Uganda.
abstract: We optimized an assay for analysis of length variation in the V1-V2 region of HIV-1 env in plasma samples from Uganda. V1-V2 env length variation was analyzed in 31 plasma samples containing subtype A, C, D, or A/D recombinant HIV-1. DNA corresponding to the V1-V2 region was amplified by nested PCR. One of the primers in the second step of the PCR was fluorescently labeled. Successful amplification was confirmed by agarose gel electrophoresis. V1-V2 length variation of PCR products was analyzed with an ABI PRISM 3100 genetic analyzer and GeneScan software. A diversity score was generated for each sample on the basis of the degree of fragment length variation. The V1-V2 region was successfully amplified from 30 of 31 samples. Fragment length analysis was successful for all of those 30 samples. The diversity score and lengths of V1-V2 fragments were unique for each sample. This assay can be used for analysis of V1-V2 length variation in subtypes commonly found in Uganda. This assay may be helpful for studies examining the impact of env length diversity on HIV-1 transmission and pathogenesis in regions where these subtypes are prevalent.
authors.affiliation: Department of Pathology, Johns Hopkins Medical Institutions, Ross Building 646, 720 Rutland Avenue, Baltimore, MD 21205, USA.
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Klevytska
authors.forename: Martin R
authors.initials: MR
authors.lastname: Mracna
authors.forename: Laura
authors.initials: L
authors.lastname: Guay
authors.forename: Graziella
authors.initials: G
authors.lastname: Becker-Pergola
authors.forename: Manohar
authors.initials: M
authors.lastname: Furtado
authors.forename: Linqi
authors.initials: L
authors.lastname: Zhang
authors.forename: J Brooks
authors.initials: JB
authors.lastname: Jackson
authors.forename: Susan H
authors.initials: SH
authors.lastname: Eshleman
mesh_terms: D005260:Female; D015752:Genes, env; D014644:Genetic Variation; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D018445:Infectious Disease Transmission, Vertical; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D011247:Pregnancy; D014158:Transcription, Genetic