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: 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.

Original publication

DOI

10.1097/QAD.0000000000001470

Type

Journal article

Journal

AIDS

Publication Date

01/06/2017

Volume

31

Pages

1211 - 1222

Keywords

Cluster Analysis, Genotype, HIV Infections, HIV-1, Humans, Molecular Epidemiology, Sequence Analysis, DNA