Article

Phylogenetic insights into regional HIV transmission

aDivision of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA bDepartment of Infection, University College London, London, UK cDepartment of Epidemiology, University of North Carolina, Chapel Hill dCenter for Molecular Biology and Pathology, Laboratory Corporation of America, Research Triangle Park, North Carolina, USA.
AIDS (London, England) (Impact Factor: 5.55). 06/2012; 26(14):1813-22. DOI: 10.1097/QAD.0b013e3283573244
Source: PubMed

ABSTRACT

: Despite prevention efforts, new HIV diagnoses continue in the southern United States, where the epidemic is characterized by significant racial/ethnic disparities. We integrated phylogenetic analyses with clinical data to reveal trends in local HIV transmission.
: Cross-sectional analysis of 1671 HIV-infected individuals each with one B-subtype pol sequence obtained during chronic (82%; UNC Center for AIDS Research Clinical Cohort) or acute/recent (18%; Duke/UNC Acute HIV Consortium) infection.
: Phylogenies were inferred using neighbor joining to select related sequences then confirmed with Bayesian methods. We characterized transmission clusters (clades n ≥ 3 sequences supported by posterior probabilities = 1) by factors including race/ethnicity and transmission risk. Factors associated with cluster membership were evaluated for newly diagnosed patients.
: Overall, 72% were men, 59% black and 39% men who have sex with men (MSM). A total of 557 (33%) sequences grouped in either 108 pairs (n = 216) or 67 clusters (n = 341). Clusters ranged from three to 36 (median 4) members. Composition was delineated primarily by race, with 28% exclusively black, and to a lesser extent by risk group. Both MSM and heterosexuals formed discrete clusters, although substantial mixing was observed. In multivariable analysis, patients with age 30 years or less (P = 0.009), acute infection (P = 0.02), local residence (P = 0.002) and transmitted drug resistance (P = 0.02) were more likely to be cluster members, whereas Latinos were less likely (P < 0.001).
: Integration of molecular, clinical and demographic data offers a unique view into the structure of local transmission networks. Clustering by black race, youth and transmitted drug resistance and inability to identify Latino clusters will inform prevention, testing and linkage to care strategies.

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    • "p = 0.16) (30). Recent studies have suggested that newly diagnosed HIV-positive patients should cluster predominantly with other recently diagnosed HIV-positive[6,8,12,27282932,33]and indicate that transmission occurs early after infection. Debate continues about the possible predominant role of recently infected patients in the dynamics of the HIV epidemics. "
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    • "With the collection of HIV genetic sequences from newly infected individuals and sociodemographic information for partner counseling and referral services, new opportunities have developed for the merger of genetics, geography and epidemiology. Spatial molecular epidemiology has the potential to illuminate patterns of HIV transmission, and of TDR variants in particular, indicating populations and places where surveillance and interventions might best be targeted [24]–[26]. In particular, spatial molecular epidemiology can answer questions about whether urban areas act as reservoirs for rural HIV infection, or whether circulating strains of HIV differ between rural and urban areas. "
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    • "In addition, Bayesian maximum clade credibility (MCC) trees were constructed using BEAST 1.7 [16] to determine the posterior probability values for each network in subtype B, CRF01_AE and CRF51_01B. As previously described elsewhere, transmission network is defined as a network consisting of at least 3 isolates from different individuals [17] of the same geographical (i.e country) origin [18], and a phylogenetic clade supported by bootstrap value of more than 90% and Bayesian posterior probability value of 1.0 at the tree node [17], [19], [20]. "
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