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Factors influencing HIV-1 phylogenetic clustering

Factors influencing HIV-1 phylogenetic clustering Purpose of review A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still no consensus about phylogenetic methodology, sampling coverage, gene target and/or minimum fragment size. Recent findings Several studies use a combined methodology, which includes both a genetic or patristic distance cut-off and a branching support threshold to identify phylogenetic clusters. However, the choice about these thresholds remains an inherently subjective process, which affects the results of these studies. There is still a lack of consensus about the genomic region and the size of fragments that should be used, although there seems to be emerging a consensus that using longer segments, allied with the use of a realistic model of evolution and a codon alignment, increases the likelihood of inferring true transmission clusters. The pol gene is still the most used genomic region, but recent studies have suggested that whole genomes and/or sequences from nef and gp41 are also good targets for cluster reconstruction. Summary The development and application of standard methodologies for phylogenetic clustering analysis will advance our understanding of factors associated with HIV transmission. This will lead to the design of more precise public health interventions. aKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa bCentro Universitário Ritter dos Reis - UniRitter, Porto Alegre, Rio Grande do Sul, Brazil cCollege of Health Sciences, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa dDepartment of Global Health, University of Washington, Seattle, Washington, USA Correspondence to Tulio de Oliveira, KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, K-RITH Tower Building, Ground Floor, 719 Umbilo Rd, Congella, Durban, South Africa. Tel: +27 31 260 4898; e-mail: deoliveira@ukzn.ac.za http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Current Opinion in HIV and Aids Wolters Kluwer Health

Factors influencing HIV-1 phylogenetic clustering

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Publisher
Wolters Kluwer Health
ISSN
1746-630X
eISSN
1746-6318
DOI
10.1097/COH.0000000000000540
Publisher site
See Article on Publisher Site

Abstract

Purpose of review A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still no consensus about phylogenetic methodology, sampling coverage, gene target and/or minimum fragment size. Recent findings Several studies use a combined methodology, which includes both a genetic or patristic distance cut-off and a branching support threshold to identify phylogenetic clusters. However, the choice about these thresholds remains an inherently subjective process, which affects the results of these studies. There is still a lack of consensus about the genomic region and the size of fragments that should be used, although there seems to be emerging a consensus that using longer segments, allied with the use of a realistic model of evolution and a codon alignment, increases the likelihood of inferring true transmission clusters. The pol gene is still the most used genomic region, but recent studies have suggested that whole genomes and/or sequences from nef and gp41 are also good targets for cluster reconstruction. Summary The development and application of standard methodologies for phylogenetic clustering analysis will advance our understanding of factors associated with HIV transmission. This will lead to the design of more precise public health interventions. aKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa bCentro Universitário Ritter dos Reis - UniRitter, Porto Alegre, Rio Grande do Sul, Brazil cCollege of Health Sciences, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa dDepartment of Global Health, University of Washington, Seattle, Washington, USA Correspondence to Tulio de Oliveira, KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, K-RITH Tower Building, Ground Floor, 719 Umbilo Rd, Congella, Durban, South Africa. Tel: +27 31 260 4898; e-mail: deoliveira@ukzn.ac.za

Journal

Current Opinion in HIV and Aids – Wolters Kluwer Health

Published: May 1, 2019

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