Analysis of length variation in the V1-V2 region of env in nonsubtype B HIV type 1 from Uganda

Alexandra M. Klevytska, Martin R. Mracna, Laura Guay, Graziella Becker-Pergola, Manohar Furtado, Linqi Zhang, J. Brooks Jackson, Susan H. Eshleman

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)791-796
Number of pages6
JournalAIDS Research and Human Retroviruses
Volume18
Issue number11
DOIs
StatePublished - 2002

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