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A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses.

Authors
  • Kafando, Alexis1
  • Serhir, Bouchra2
  • Doualla-Bell, Florence2
  • Fournier, Eric2
  • Sangaré, Mohamed Ndongo3
  • Martineau, Christine2
  • Sylla, Mohamed4
  • Chamberland, Annie4
  • El-Far, Mohamed4
  • Charest, Hugues1, 2
  • Tremblay, Cécile L1, 2, 4
  • 1 Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada. , (Canada)
  • 2 Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada. , (Canada)
  • 3 Département de Médecine Sociale et Préventive, École de Santé Publique, Université de Montréal, Montréal, Canada. , (Canada)
  • 4 Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada. , (Canada)
Type
Published Article
Journal
AIDS Research and Human Retroviruses
Publisher
Mary Ann Liebert
Publication Date
Oct 01, 2019
Volume
35
Issue
10
Pages
906–919
Identifiers
DOI: 10.1089/AID.2019.0142
PMID: 31407606
Source
Medline
Keywords
Language
English
License
Unknown

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.

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