title: Defining HIV-1 transmission clusters based on sequence data.
abstract: : Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.
authors.affiliation: aKEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research (Coast), Kilifi, Kenya bDepartment of Laboratory Medicine, Lund University, Lund, Sweden cDepartment of Zoology dNuffield Department of Medicine, University of Oxford, Oxford, UK eDepartment of Clinical Microbiology, Karolinska University Hospital fDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
authors.forename: Amin S
authors.initials: AS
authors.lastname: Hassan
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.forename: Eduard J
authors.initials: EJ
authors.lastname: Sanders
authors.forename: Jan
authors.initials: J
authors.lastname: Albert
authors.forename: Joakim
authors.initials: J
authors.lastname: Esbjörnsson
mesh_terms: D016000:Cluster Analysis; D005838:Genotype; D015658:HIV Infections / Q000635:transmission*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*