Defining HIV-1 transmission clusters based on sequence data: a systematic review and perspectives

Amin S. Hassan, Oliver G Pybus, Eduard J. Sanders, Jan Albert, Joakim Esbjörnsson

Research output: Contribution to journalReview articlepeer-review


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 summarising the most popular 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 languageEnglish
Pages (from-to)1211-1222
Issue number9
Early online date2017 Mar 28
Publication statusPublished - 2017

Subject classification (UKÄ)

  • Infectious Medicine


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