Phylogenetic Studies of Transmission Dynamics in Generalized HIV Epidemics

Dennis, Ann M.; Herbeck, Joshua T.; Brown, Andrew J. Leigh; Kellam, Paul; Oliveira, Túlio de; Pillay, Daisy; Fraser, Christophe; Cohen, Myron S.

doi:10.1097/qai.0000000000000271

Cited by 85 publications

(86 citation statements)

References 136 publications

(135 reference statements)

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“…The study of HIV transmission networks provides insight into the spread of HIV, and thus into opportunities for intervention [1–5]. By using HIV nucleotide sequence data, we can construct transmission networks that link persons who are infected with genetically similar HIV variants [5–7].…”

Section: Introductionmentioning

confidence: 99%

“…Linked persons are likely to have a direct or indirect epidemiologic connection and represent potential transmission partners. The extent to which transmission occurs between people who are similar or different with respect to race/ethnicity and risk characteristics is unclear, and network data can aid in understanding transmission dynamics (reviewed in [1]). For example, understanding the links between different populations can be particularly useful in elucidating transmission routes for heterosexual women, who are often unaware of the HIV risk behaviors of their partners [8, 9].…”

Section: Introductionmentioning

confidence: 99%

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Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States

et al. 2015

JAIDS Journal of Acquired Immune Deficiency Syndromes

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Background Studying HIV transmission networks provides insight into the spread of HIV and opportunities for intervention. We identified transmission dynamics among risk groups and racial/ethnic groups in the United States. Methods For HIV-1 pol sequences reported to the U.S. National HIV Surveillance System during 2001–2012, we calculated pairwise genetic distance, identified linked pairs of sequences (those with distance ≤1.5%), and examined transmission category and race/ethnicity of these potential transmission partners. Results Of 40,950 sequences, 12,910 (32%) linked to ≥1 other sequence. Of men who have sex with men (MSM) who linked to ≥1 sequence, 88% were linked to other MSM and only 4% were linked to heterosexual women. Of heterosexual women for whom we identified potential transmission partners, 29% linked to MSM, 21% to heterosexual men, and 12% to persons who inject drugs. Older and black MSM were more likely to be linked to heterosexual women. Assortative mixing was present for all racial/ethnic groups; 81% of blacks/African Americans linked to other blacks. Conclusions This analysis is the first use of U.S. surveillance data to infer an HIV transmission network. Our data suggest that HIV infections among heterosexual women predominantly originate from MSM, followed by heterosexual men. Although few MSM were linked to women, suggesting that a minority of MSM are involved in transmission with heterosexual women, these transmissions represent a substantial proportion of HIV acquisitions by heterosexual women. Interventions that reduce transmissions involving MSM are likely to also reduce HIV acquisition among other risk groups.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States

et al. 2015

JAIDS Journal of Acquired Immune Deficiency Syndromes

138

130

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“…6–11 By building transmission networks based on HIV nucleotide sequence data, we can identify persons who have closely related sequences, indicating that they have a direct or indirect epidemiologic connection and represent potential transmission partners. 11 Exploring who are the potential transmission partners of foreign-born persons with a diagnosis of HIV infection in the United States may allow us to determine whether transmissions involving this group occur primarily with other foreign-born persons or with U.S.-born persons.…”

Section: Introductionmentioning

confidence: 99%

HIV Transmission Dynamics Among Foreign-Born Persons in the United States

Valverde

Oster

et al. 2017

JAIDS Journal of Acquired Immune Deficiency Syndromes

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Background In the United States (U.S.), foreign-born persons are disproportionately affected by HIV and differ epidemiologically from U.S.-born persons with diagnosed HIV infection. Understanding HIV transmission dynamics among foreign-born persons is important to guide HIV prevention efforts for these populations. We conducted molecular transmission network analysis to describe HIV transmission dynamics among foreign-born persons with diagnosed HIV. Methods Using HIV-1 polymerase nucleotide sequences reported to the U.S. National HIV Surveillance System for persons with diagnosed HIV infection during 2001–2013, we constructed a genetic distance based transmission network using HIV-TRACE and examined the birth region of potential transmission partners in this network. Results Of 77,686 people, 12,064 (16%) were foreign-born. Overall, 28% of foreign-born persons linked to at least one other person in the transmission network. Of potential transmission partners, 62% were born in the United States, 31% were born in the same region as the foreign-born person, and 7% were born in another region of the world. The majority of transmission partners of male foreign-born persons (63%) were born in the United States, whereas the majority of transmission partners of female foreign-born (57%) were born in their same world region. Discussion These finding suggests that a majority of HIV infections among foreign-born persons in our network occurred after immigrating to the United States. Efforts to prevent HIV infection among foreign-born persons in the U.S. should include information of the transmission networks in which these individuals acquire or transmit HIV in order to develop more targeted HIV prevention interventions.

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“…Through the phylogenetic relation between viral nucleic acid sequences, phylogenetic analyses can be informative of transmission events between risk groups [18]. Phylodynamics and phylogeography can also help provide data on the evolutionary history of a certain viral population.…”

Section: Introductionmentioning

confidence: 99%

Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain

et al. 2016

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BackgroundSince 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain.Patients & MethodsWe studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005–2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain). Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6.ResultsOf the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3). The rest (133/234) were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133) were men who have sex with men (MSM) grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02) men (p< 0.001), MSM (p<0.001) younger than 35 years (p = 0.001) and with a CD4+ T-cell count above 350 cells/ul (p<0.001). We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965–1987), with an evolutionary rate of 2.4 (95%CI: 1.7–3.1) x 10−3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980–1990 and 2005–2008. The most significant migration routes for subtype B went from inland cities to seaside locations.ConclusionsWe provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.

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Phylogenetic Studies of Transmission Dynamics in Generalized HIV Epidemics

Cited by 85 publications

References 136 publications

Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States

Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States

HIV Transmission Dynamics Among Foreign-Born Persons in the United States

Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain

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