PMID: 28353537
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.
Date: 1970-08-22
Year: 2018
Journal: AIDS
PMID Author: Hassan AS, Pybus OG, Sanders EJ, Albert J, Esbjörnsson J
Defining HIV-1 transmission clusters based on sequence data. AIDS 2017;31(9):1211-1222 doi: 10.1097/QAD.0000000000001470

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