Abstract
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 (κ) 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.
Highlights
In 2015, a total of 609 HIV cases were reported to the Public Health Laboratory in Quebec (LSPQ), including 299 new diagnoses.[1]
The mean age (
This moderate level of amplification success could be mediated by multiple factors affecting the specimen quality such as the long-term storage of serum, viral RNA extraction procedures and enzymes used in the PCR amplification as well as the viral loads of infected individuals (VL < 20,000 copies/ml)
Summary
In 2015, a total of 609 HIV cases were reported to the Public Health Laboratory in Quebec (LSPQ), including 299 new diagnoses.[1] To better characterize transmission patterns,[2,3] we evaluated molecular epidemiology methods using phylogenetic analyses of HIV genome sequences obtained from infected individuals. Pairwise genetic distances (PWDs) derived from env, gag, and pol nucleotide sequences were used to assess the relationship between sequences and define study HIV transmission dynamics.[4,5] Combining sequence-based clustering with risk factors and sociodemographic, clinical, and geographical parameters may help identify patterns of transmission in the HIV-infected population.[6,7,8,9,10,11]. Each subregion and each domain of the env play a key role in HIV pathogenesis.[16,18,20]
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