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Defining HIV-1 transmission clusters based on sequence data : a systematic review and perspectives
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- Hassan, Amin S. (author)
- Lund University,Lunds universitet,Klinisk virologi, Malmö,Forskargrupper vid Lunds universitet,Clinical Virology, Malmö,Lund University Research Groups,Centre for Geographic Medicine Research, Kilifi
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- Pybus, Oliver G (author)
- University of Oxford
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- Sanders, Eduard J. (author)
- Centre for Geographic Medicine Research, Kilifi,University of Oxford
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- 2017
- 2017
- English.
- In: AIDS. - 0269-9370. ; 31:9, s. 1211-1222
- Research review (peer-reviewed)
Abstract
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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 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Infektionsmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Infectious Medicine (hsv//eng)
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