HIV type 2 protease, reverse transcriptase, and envelope viral variation in the PBMC and genital tract of ARV-naive women in Senegal

Abstract

Unique viral variants and resistance mutations may occur in the genital tract of HIV-2 ARV-naive infected women. We sequenced and phylogenetically analyzed protease (PR), reverse transcriptase (RT), and envelope (ENV) from PBMC and genital tract samples from four ARV-naive women in Senegal. HIV-2 protease polymorphisms that predict HIV-1 protease inhibitor (PI) resistance were common. Two subjects had protease mutations (T77I and I64V) in genital tract samples that were not found in PBMCs. One subject had the HIV-2 reverse transcriptase M184I mutation in CVL DNA (but not PBMCs) that is known to confer 3TC/FTC resistance in HIV-2. In another subject, the reverse transcriptase A62V mutation was also found in CVL-RNA but not PBMCs. We found no significant difference in ENV variants between PBMCs and the genital tract. HIV-2 RT and PR mutations in the genital tract of ARV-naive females may have implications for transmitted HIV-2 resistance and ARV therapy.

FIG. 1.

HIV protease sequences (amino acids 1–99) from HIV-1 (HXB2), HIV-2 (ROD), and subject's PBMCs (HIV-2 DNA) and genital tract [cervicovaginal lavage (CVL) cell-associated HIV-2 DNA (CVL-DNA) and genital secretion-associated HIV-2 RNA (CVL-RNA)]. IAS-USA and Stanford HIV database predicted protease resistance mutations known to be associated with PI resistance in HIV-1 are shown (sites of predicted HIV-1 PI major resistance mutations are bolded and underlined and sites of potential HIV-1 resistance that are polymorphic between HIV-1 and HIV-2 are shaded). Note: Numbers in parentheses represent the number of identical sequences from that source; (−) represents the presence of a stop codon in the original nucleotide sequence.

FIG. 2.

Maximum-likelihood phylogenetic tree of HIV-2 RT sequences from PBMCs, CVL-RNA, and CVL-DNA from four ARV-naive females. Potential ARV resistance mutations (M184I, A62V) found in CVL of two subjects are shown. Inset: Example of Slatkin–Maddison test for compartmentalization of CVL versus PBMC sequences for subject MIN1974. The tree shows traced character states corresponding to CVL (black lines) and PBMCs (white lines). There are two steps required to move along the tree between CVL and PBMCs. The histogram shows the of number of steps found during 1000 random character (taxa) shuffles on the ML tree.

FIG. 3.

Maximum-likelihood phylogenetic trees of HIV-2 Env sequences from PBMC, CVL-RNA and CVL-DNA from subject MIN652. (A) Boxes represent longitudinal HIV-2 Env PBMC sequences between March, 1995 and August, 1998. Open and closed circles represent HIV-2 Env sequences from April, 1998 CVL-RNA and CVL-DNA, respectively. Estimated most recent common ancestor (MRCA) is shown, as is HIV-2 ROD (M15390) used as an outgroup. Inset shows box-plots of the levels of divergence of CVL and PBMC sequences from MRCA. (B) Maximum-likelihood phylogenetic tree of HIV-2 Env sequences from PBMC, CVL-RNA, and CVL-DNA from April, 1998. Inset shows box-plots of the levels of diversity of CVL and PBMC sequences. P-values are nonparametric (Wilcoxon) between groups, PBMC vs. CVL or CVL-DNA vs. CVL-RNA. Box-plots show median, 25–75% IQR and range.

FIG. 3.

Maximum-likelihood phylogenetic trees of HIV-2 Env sequences from PBMC, CVL-RNA and CVL-DNA from subject MIN652. (A) Boxes represent longitudinal HIV-2 Env PBMC sequences between March, 1995 and August, 1998. Open and closed circles represent HIV-2 Env sequences from April, 1998 CVL-RNA and CVL-DNA, respectively. Estimated most recent common ancestor (MRCA) is shown, as is HIV-2 ROD (M15390) used as an outgroup. Inset shows box-plots of the levels of divergence of CVL and PBMC sequences from MRCA. (B) Maximum-likelihood phylogenetic tree of HIV-2 Env sequences from PBMC, CVL-RNA, and CVL-DNA from April, 1998. Inset shows box-plots of the levels of diversity of CVL and PBMC sequences. P-values are nonparametric (Wilcoxon) between groups, PBMC vs. CVL or CVL-DNA vs. CVL-RNA. Box-plots show median, 25–75% IQR and range.