TY - JOUR
T1 - Analysis of length variation in the V1-V2 region of env in nonsubtype B HIV type 1 from Uganda
AU - Klevytska, Alexandra M.
AU - Mracna, Martin R.
AU - Guay, Laura
AU - Becker-Pergola, Graziella
AU - Furtado, Manohar
AU - Zhang, Linqi
AU - Jackson, J. Brooks
AU - Eshleman, Susan H.
N1 - Copyright:
Copyright 2016 Elsevier B.V., All rights reserved.
PY - 2002
Y1 - 2002
N2 - 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.
AB - 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.
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U2 - 10.1089/08892220260139530
DO - 10.1089/08892220260139530
M3 - Article
C2 - 12167271
AN - SCOPUS:0036346743
SN - 0889-2229
VL - 18
SP - 791
EP - 796
JO - AIDS research and human retroviruses
JF - AIDS research and human retroviruses
IS - 11
ER -