Analysis of length variation in the V1-V2 region of env in nonsubtype B HIV type 1 from Uganda
Klevytska, A.M.; Mracna, M.R.; Guay, L.; Becker-Pergola, G.; Furtado, M.; Zhang, L.; Jackson, J.B.; Eshleman, S.H.
Aids Research and Human Retroviruses 18(11): 791-796
2002
ISSN/ISBN: 0889-2229 PMID: 12167271 DOI: 10.1089/08892220260139530Document Number: 259690
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.