Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Sep 10;26(14):1813-22.
doi: 10.1097/QAD.0b013e3283573244.

Phylogenetic insights into regional HIV transmission

Ann M Dennis  1 , Stéphane Hué, Christopher B Hurt, Sonia Napravnik, Joseph Sebastian, Deenan Pillay, Joseph J Eron
Affiliations

Phylogenetic insights into regional HIV transmission

Ann M Dennis et al. AIDS. .

Abstract

Objectives: 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.

Design: 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.

Methods: 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.

Results: 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).

Conclusion: 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.

PubMed Disclaimer

Conflict of interest statement

Conflicts of Interest and Source of Funding: AD has received grant support from the Bristol-Myer Squibb Virology Fellows research training program. SN has received grant support from Pfizer, Bristol-Myers Squibb, and Merck. JS is an employee of Laboratory Corporation of America. JJE has received consulting fees from Tibotec, Bristol-Myers Squibb, Merck, GlaxoSmithKline and ViiV, lecture fees from Roche and Bristol-Myers Squibb, and grant support from GlaxoSmithKline, Merck, ViiV and BMS.

Figures

Figure 1
Figure 1
Cluster size distribution and example sections of Bayesian phylogenetic tree showing two large clusters characterized by risk group. Nodes with posterior probability=1 are indicated. Numbers at tips represent date of sequencing. Note. MSM, men who have sex with men; HET, heterosexual; OTH, Other/Unknown risk A. Distribution of cluster sizes (n≥3 sequences). Median cluster size 4 (IQR 3-5) members. B. Cluster n=18, Predominant MSM (83%) and Black (78%). C. Cluster n=13, Homogenous HET (100%) and Predominant Black (69%).
See this image and copyright information in PMC

References

    1. Centers for Disease Control and Prevention. [Accessed Aug 13, 2011];HIV Surveillance Report. 2009 vol. 21 Available from http://www.cdc.gov/hiv/topics/surveillance/resources/reports/. Published February 2010.
    1. North Carolina Department of Health and Human Services. [Accessed March 27, 2011];Epidemiologic Profile for HIV/STD Prevention & Care Planning. Available from http://www.epi.state.nc.us/epi/hiv/. Published December 2010.
    1. North Carolina Department of Health and Human Services. [Accessed March 27, 2011];1999 STD Surveillance Report. Available from http://www.epi.state.nc.us/epi/hiv.
    1. Branson BM, Handsfield HH, Lampe MA, Janssen RS, Taylor AW, Lyss SB, et al. Revised recommendations for HIV testing of adults, adolescents, and pregnant women in health-care settings. Morbidity and Mortality Weekly Report Recommendations and Reports. 2006 Sep 22;55(RR-14):1–17. - PubMed
    1. Althoff K, Gange S, Klein M, Brooks J, Hogg R, Bosch R, et al. Late Presentation for Human Immunodeficiency Virus Care in the United States and Canada. Clinical Infectious Diseases. 2010;50(11):1512–1520. - PMC - PubMed

Publication types

MeSH terms

Substances