A short-term assessment of nascent HIV-1 transmission clusters among newly diagnosed individuals using envelope sequence-based phylogenetic analyses
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AIDS research and human retroviruses ; vol. 35, no. 10, pp. 906-919.Publisher(s)
Mary Ann LiebertAuthor(s)
Affiliation
Abstract(s)
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 1,070 bp with its loop 3 (108 bp) to determine its 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
TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance 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 were
subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped
into 15 distinct small TCs 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 (j) coefficient of 0.59,
p < .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, odds ratio (OR) = 0.25, 95% confidence interval
(CI, 0.04–0.66), p = .002 and OR: 0.17, 95% CI (0.10–0.61), p = .011, respectively. The present 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.
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