Phylogenetic insights into regional HIV transmission

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

doi:10.1097/qad.0b013e3283573244

Cited by 61 publications

(52 citation statements)

References 39 publications

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“…Similar results were reported with small sequence datasets when other parts of HIV-1 genome sequences were analyzed 20-22 . This epidemic pattern was different from those in MSM populations in other countries, in which the MSM sequences intermingled with sequences from general HIV-1 infected individuals 40,41 . This unique epidemic pattern indicated that only limited introductions of HIV-1 strains from the general population became predominant strains in the MSM populations in China and the close network resulted in transmission chains mainly among MSM, allowing spreading of the same viruses in all geographic regions across the country.…”

Section: Discussioncontrasting

confidence: 77%

Comprehensive Characterization of the Transmitted/Founder env Genes From a Single MSM Cohort in China

Chen

Zhang

et al. 2015

JAIDS Journal of Acquired Immune Deficiency Syndromes

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Background The men having sex with men (MSM) population has become one of major risk groups for HIV-1 infection in China. However, the epidemiological patterns, function of the env genes, and autologous and heterologous neutralization activity in the same MSM population have not been systematically characterized. Methods The env gene sequences were obtained by the single genome amplification (SGA). The time to the most recent common ancestor (tMRCA) was estimated for each genotype using the Bayesian MCMC approach. Coreceptor usage was determined in NP-2 cells. Neutralization was analyzed using Env pseudoviruses in TZM-bl cells. Results We have obtained 547 full-length env gene sequences by SGA from 30 acute/early HIV-1-infected individuals in the Beijing MSM cohort. Three genotypes (Subtype B, CRF01_AE, and CRF07_BC) were identified and 20% of the individuals were infected with multiple transmitted/founder (T/F) viruses. The tight clusters of the MSM sequences regardless of geographic origins indicated nearly exclusive transmission within the MSM population and limited number of introductions. The tMRCA for each genotype was 10-15 years after each was first introduced in China. Disparate preferences for coreceptor usages among three genotypes might lead to the changes in percentage of different genotypes in the MSM population over time. The genotype-matched and -mismatched neutralization activity varied among the three genotypes. Conclusions Identification of unique characteristics for transmission, coreceptor usage, neutralization profile and epidemic patterns of HIV-1 is critical for the better understanding of transmission mechanisms, development of preventive strategies, and evaluation of vaccine efficacy in the MSM population in China.

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Section: Discussioncontrasting

confidence: 77%

Comprehensive Characterization of the Transmitted/Founder env Genes From a Single MSM Cohort in China

Chen

Zhang

et al. 2015

JAIDS Journal of Acquired Immune Deficiency Syndromes

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“…This cut-off has been used in multiple similar analyses 16,21,26–30 . We considered clusters as groups of greater than two members since transmission pairs may have entered care as part of partners testing and may less likely represent sources of continuous, ongoing transmission 17,27 .…”

Section: Methodsmentioning

confidence: 99%

Transmission Clustering Among Newly Diagnosed HIV Patients in Chicago, 2008 to 2011

Lubelchek

Hoehnen

Hotton

et al. 2015

JAIDS Journal of Acquired Immune Deficiency Syndromes

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Introduction HIV transmission cluster analyses can inform HIV prevention efforts. We describe the first such assessment for transmission clustering among HIV patients in Chicago. Methods We performed transmission cluster analyses using HIV pol sequences from newly diagnosed patients presenting to Chicago’s largest HIV clinic between 2008 and 2011. We compared sequences via progressive pairwise alignment, using neighbor joining to construct an un-rooted phylogenetic tree. We defined clusters as >2 sequences among which each sequence had at least one partner within a genetic distance of ≤ 1.5%. We used multivariable regression to examine factors associated with clustering and used geospatial analysis to assess geographic proximity of phylogenetically clustered patients. Results We compared sequences from 920 patients; median age 35 years; 75% male; 67% Black, 23% Hispanic; 8% had a Rapid Plasma Reagin (RPR) titer ≥ 1:16 concurrent with their HIV diagnosis. We had HIV transmission risk data for 54%; 43% identified as men who have sex with men (MSM). Phylogenetic analysis demonstrated 123 patients (13%) grouped into 26 clusters, the largest having 20 members. In multivariable regression, age < 25, Black race, MSM status, male gender, higher HIV viral load, and RPR ≥ 1:16 associated with clustering. We did not observe geographic grouping of genetically clustered patients. Discussion Our results demonstrate high rates of HIV transmission clustering, without local geographic foci, among young Black MSM in Chicago. Applied prospectively, phylogenetic analyses could guide prevention efforts and help break the cycle of transmission.

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“…21 The HIV-1 pol gene has been used for phylogenetic reconstruction of transmission events 22 and for HIV cluster analysis over the past decade. [3][4][5][6][7]9,[11][12][13]15,19,20,[23][24][25][26][27][28][29][30][31][32] Other HIV-1 genes have also been used for linkage analysis in discordant couples. 33,34 A weaker clustering of subgenomic regions, as compared with the near full-length genome sequences, was demonstrated for HIV-1C from Ethiopia, 35 although the set of viral sequences analyzed was relatively small.…”

Section: Introductionmentioning

confidence: 99%

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering

Novitsky

Moyo

Lei

et al. 2015

AIDS Research and Human Retroviruses

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To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

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Phylogenetic insights into regional HIV transmission

Cited by 61 publications

References 39 publications

Comprehensive Characterization of the Transmitted/Founder env Genes From a Single MSM Cohort in China

Comprehensive Characterization of the Transmitted/Founder env Genes From a Single MSM Cohort in China

Transmission Clustering Among Newly Diagnosed HIV Patients in Chicago, 2008 to 2011

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering

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