Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men

German, Danielle; Grabowski, M Kate; Beyrer, Chris

doi:10.1071/sh16056

Cited by 26 publications

(35 citation statements)

References 61 publications

(73 reference statements)

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“…So far, continued HIV-1 molecular surveillance will be essential for understanding the dynamics of expansion of transmission clusters. This comprehension might allow us to focus preventive efforts in populations with the highest risk of HIV-1 acquisition and continuing transmission [54][55][56][57][58]. Furthermore, it is important in order to monitor the efficacy of public health measure aimed at controlling the epidemic [59].…”

Section: Discussionmentioning

confidence: 99%

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

et al. 2019

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HIV-1 diversity is increasing in European countries due to immigration flows, as well as travels and human mobility, leading to the circulation of both new viral subtypes and new recombinant forms, with important implications for public health. We analyzed 710 HIV-1 sequences comprising protease and reverse-transcriptase (PR/RT) coding regions, sampled from 2011 to 2017, from naive patients in Spedali Civili Hospital, Brescia, Italy. Subtyping was performed by using a combination of different tools; the phylogenetic analysis with a structured coalescence model and Makarov Chain Monte Carlo was used on the datasets, to determine clusters and evolution. We detected 304 (43%) patients infected with HIV-1 non-B variants, of which only 293 sequences were available, with four pure subtypes and five recombinant forms; subtype F1 (17%) and CRF02_AG (51.1%) were most common. Twenty-five transmission clusters were identified, three of which included >10 patients, belonging to subtype CRF02_AG and subtype F. Most cases of alleged transmission were between heterosexual couples. Probably due to strong migratory flows, we have identified different subtypes with particular patterns of recombination or, as in the case of the subtype G (18/293, 6.1%), to a complete lack of relationship between the sequenced strains, revealing that they are all singletons. Continued HIV molecular surveillance is most important to analyze the dynamics of the boost of transmission clusters in order to implement public health interventions aimed at controlling the HIV epidemic.

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Section: Discussionmentioning

confidence: 99%

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

et al. 2019

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“…Contrarily, Kouyos et al 65 found segregation based on location among individuals who were included in a transmission cluster despite having overlapping risk factors. Risk groups may be mixing due to underreporting of risk behaviors or bisexual behavior [65][66][67] . This heterogeneity of risk groups in transmission clusters suggests that focusing on individuals within city areas (e.g., wards in Washington, DC) to concentrate resources and information may help in addressing the HIV-1 epidemic.…”

Section: Pr/rt Int Envmentioning

confidence: 99%

A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing

Gibson

Jair

Castel

et al. 2020

Sci Rep

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the DC Cohort Executive Committee † Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40-49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9-33.8% of the participants into clusters. HIV-TRACE grouped 2.9-12.8% of participants when using consensus sequences and 9.0-64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.Despite recent reductions in HIV-1 prevalence in Washington, DC from 2.5% in 2013 1 to 1.8% in 2018, the United States (US) capital is still experiencing a generalized HIV-1 epidemic -as defined by the World Health Organization 2-4 . There were 340 newly diagnosed cases in DC in 2018, and the DC rate is five times higher than the national rate 3 . Blacks, men, men who have sex with men (MSM), and heterosexuals (HRH) account for the majority of people living with HIV-1 (PLWH) in DC 2,3 . However, ~20% of the newly diagnosed persons had an unknown risk for transmission in both 2016 and 2017 2,3 . Furthermore, the leading group (33.3%) of newly diagnosed cases was between the ages of 20-29 years old 3 . This same age group had the highest percentage (27.5%) of drug resistance mutations (DRM) at diagnosis, suggesting broader spread of HIV-1 drug resistant variants and potential concern for future therapeutic options, especially if these mutations are against first line antiretroviral (ART) drugs for newly infected individuals. With blacks and young adults being the most impacted groups of individuals for HIV-1 in DC, understanding the current HIV-1 phylodynamics can provide informative data to guide programs that prevent and reduce the incidence of HIV-1. Moreover, identifying potential transmission clusters amongst individuals in DC and their associated epidemiological features may help infer otherwise 'unknown' transmission modes and provide insight for more targeted prevention and intervention strategies.In 2011, the DC Cohort, a longitudinal observational NIH-funded co...

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“…describe the use of phylogenetic data to inform public health approaches to HIV surveillance among GBM, 8 arguing that this rapidly evolving field can substantially improve our understanding of the HIV epidemic and describing how social networks, clusters and other factors influence transmission. Although there are appreciable methodological and ethical challenges that need to be addressed, the potential to inform public health approaches for HIV control is notable, particularly if it were available in real time.…”

Section: Surveillancementioning

confidence: 99%

“…1,2 Others describe changes in sexual practices, HIV testing, travel, preventive practices, drug use, mental health and stigma, all of which will affect HIV and STI rate. 1–8 Finally, other authors provide recommendations about how to optimise the health of GBM during this period of rapid change and discuss the unintended consequences of getting this wrong. 9–14 Community responses have always underpinned how individual GBM deal with HIV, but government policy provides the social and structural conditions for those community responses to thrive.…”

Section: Introductionmentioning

confidence: 99%

2020, sexually transmissible infections and HIV in gay, bisexual and other men who have sex with men

et al. 2017

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This editorial accompanies a series of papers dealing with this watershed period for HIV and sexually transmissible infections (STI) infections in gay, bisexual and other men who have sex with men (GBM). We are delighted to share with you the views of some international opinion leaders on what the future may hold and what challenges lie ahead. In this issue of the Journal, authors describe current HIV and STI incidence among GBM and predict the future.

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Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men

Cited by 26 publications

References 61 publications

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing

2020, sexually transmissible infections and HIV in gay, bisexual and other men who have sex with men

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