We sought to predict virus coreceptor utilization using a simple bioinformatics method based on genotypic analysis of human immunodeficiency virus types 1 (HIV-1) env V3 loop sequences of 28 infected but drug-naive women during pregnancy and their infected infants and to better understand coreceptor usage in vertical transmission dynamics. The HIV-1 env V3 loop was sequenced from plasma samples and analyzed for viral coreceptor usage and subtype in a cohort of HIV-1-infected pregnant women. Predicted maternal frequencies of the X4, R5X4, and R5 genotypes were 7%, 11%, and 82%, respectively. Antenatal plasma viral load was higher, with a mean log(10) (SD) of 4.8 (1.6) and 3.6 (1.2) for women with the X4 and R5 genotypes, respectively, p = 0.078. Amino acid substitution from the conserved V3 loop crown motif GPGQ to GPGR and lymphadenopathy were associated with the X4 genotype, p = 0.031 and 0.043, respectively. The maternal viral coreceptor genotype was generally preserved in vertical transmission and was predictive of the newborn's viral genotype. Infants born to mothers with X4 genotypes were more likely to have lower birth weights relative to those born to mothers with the R5 genotype, with a mean weight (SD) of 2870 (±332) and 3069 (±300) g, respectively. These data show that at least in HIV-1 subtype C, R5 coreceptor usage is the most predominant genotype, which is generally preserved following vertical transmission and is associated with the V3 GPGQ crown motif. Therefore, antiretroviral-naive pregnant women and their infants can benefit from ARV combination therapies that include R5 entry inhibitors following prediction of their coreceptor genotype using simple bioinformatics methods.

To characterize phylogenetic relatedness of plasma HIV-1 RNA subtype C env gp120 viral variants capable of establishing an infection following heterosexual and subsequent vertical transmission events a 650-base pair fragment within the C2-V5 subregion was sequenced from four HIV-1-infected families each consisting of biological parent(s), index children (first), and subsequent (second) siblings. None of the family members had received antiretroviral therapy at the time of sample collection. Sequence alignment and analysis were done using Gene Doc, Clustal X, and MEGA software programs. Second siblings' sequences were homogeneous and clustered in a single branch while first siblings' sequences were more heterogeneous, clustering in separate branches, suggestive of more than one donor variants responsible for the infection or evolution from founder variant(s) could have occurred. While the directionality for heterosexual transmission could not be determined, homogeneous viral variants were a unique characteristic of maternal variants as opposed to the more heterogeneous paternal variants. Analysis of families' sequences demonstrated a localized expansion of the subtype C infection. We demonstrated that families' sequences clustered quite closely with other regional HIV-1 subtype C sequences supported by a bootstrap value of 86%, confirming the difficulty of classifying subtype C sequences on a geographic basis. Data are indicative of several mechanisms that may be involved in both vertical and heterosexual transmission. Larger studies are warranted to address the caveats of this study and build on the strengths. Our study could be the beginning of family-based HIV-1 intervention research in Zimbabwe.

Objective: To ascertain the role of HIV-1 gp120 env PNGs variations and sequence length polymorphism following transmission events as possible supporting forensic evidence to determine directionality of HIV transmission. Method: An observational study of HIV-1 infected family members, where median and range values of the amino acid lengths and PNGs for the genotyped C2V5 region were calculated. Wilcoxon rank-sum test was used to determine differences in these parameters between different family members. Results: For heterosexual transmission, two mothers had longer C3 sequences relative to that of their spouses; p = 0.006 and p = 0.025 whilst the opposite was observed for one mother, p = 0.028. No clear trends were observed for PNGs. In three families, index children had longer C2V5 amino acid sequences compared to their mothers; p= 0.013, 0.040 and 0.043. Second siblings' V4 and V5 sequences were generally shorter relative to the maternal ones; p = 0.039 and 0.028, respectively. Generally adults had longer V3 amino acid sequences compared to the children; p = 0.018. Similar trends were also observed regarding PNGs within the entire C2V5 region, C3 and V4 sub-regions; p= 0.0025, 0.005 and 0.008, respectively. First siblings' C2V5 and C3 sequence lengths were significantly longer relative to those of the second siblings; p = 0.005 and 0.007, respectively. Conclusion: Our results are suggestive that HIV-1 env C2V5 amino acid length polymorphism and PNGs tend to increase with age and HIV disease progression. Though sensitive and should be cautiously handled, it is tempting to propose the directionality of the HIV transmission events with respect to C3 sequence length polymorphisms. Correlating HIV-1 env C2V5 amino acid length polymorphism and age of infection may be the first step towards a possible valuable piece of forensic evidence which may be useful in criminalisation of willful HIV infections. However, bigger studies are warranted to substantiate the authenticity of this potentially useful application.