A short-term assessment of nascent HIV-1 transmission clusters among newly diagnosed individuals using envelope sequence-based phylogenetic analyses.

The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1070 bp with its loop 3 (108 bp) to determine their utility in inferring HIV-1 transmission clustering.Serum samples of recently (n=106) and chronically (n=156) HIV-1 infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 transmission clusters. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distances of ≤ 10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering.Ninety-eight distinct consensus envelope sequences subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small transmission clusters while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's Kappa (κ) coefficient of 0.59, p<0.00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, OR= 0.25, 95% CI [0.04-0.66], P=0.002 and OR: 0.17 95% CI [0.10-0.61, P=0.011, respectively.The current study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.