HIV-1 Genetic Diversity in Nairobi Female Sex Workers

Abstract

Sub-Saharan Africa bears 67% of the global HIV-1 infection burden, with more than half of the infections occurring in women above 15 years. The risk of contracting HIV is 30 times higher for female sex workers compared to non-FSW. This group, therefore, bears a double burden of the HIV epidemic. Methods: We assessed HIV tropism and the variables associated with it in recently infected, treatment-naïve female sex workers in Nairobi, Kenya. We analyzed 76 HIV-1 positive plasma samples obtained between November 2020 and April 2021 from female sex workers accessing clinical services at seven Sex Worker Outreach Programme (SWOP) clinics in Nairobi, Kenya. The primary outcome was viral tropism predicted by genotypic algorithms targeting the V3 loop of the env gene. Logistic regression was used to determine the effects of age, HIV-subtype, CD4 count, CD4%, and V3 loop genetic features on the primary outcome. Results:The prevalence of CXCR4-tropic viruses was 26.3%. HIV-1 subtype A1 accounted for 89.5% of subtypes followed by subtype D (6.6%) and subtype C (3.9%). WebPSSM [WebPSSM:R5X4] and Geno2Pheno [G2P:10% FPR, G2P:15% FPR and G2P:20% FPR] were highly concordant at 88% (95% CI 82% –91%) .A unit increase in V3 loop’s net-charge increased the odds of a virus being CXCR4-tropic 75% (OR = 1.75, 95% CI = 1.20-2.70, p = 0.006). The odds of Subjects from Kawangware harboring CXCR4 tropic strains were 256% higher (OR 3.56; 95% CI 0.97-14.7; p = 0.034) compared to the reference group (Thika Road). HIV-1 subtype, age, CD4 count, and CD4 % were not associated with viral tropism. Conclusion We found a relatively higher prevalence of X4 viruses in HIV-1 subtype A1 than previously thought to be present. The most notable finding was the significant association between CCR5 tropism A1 viruses and the presence of the amino acid Alanine at position 22 of the V3 loop. Additional studies with a large dataset are warranted to confirm our findings.