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

Hassan, Amin S.Lund University,Lunds universitet,Klinisk virologi, Malmö,Forskargrupper vid Lunds universitet,Clinical Virology, Malmö,Lund University Research Groups,Centre for Geographic Medicine Research, Kilifi (författare)

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.

Pybus, Oliver GUniversity of Oxford (författare)
Sanders, Eduard J.Centre for Geographic Medicine Research, Kilifi,University of Oxford (författare)
Albert, JanKarolinska Institute (författare)
Esbjörnsson, JoakimKarolinska Institute,University of Oxford(Swepub:lu)med-jes (författare)
Klinisk virologi, MalmöForskargrupper vid Lunds universitet (creator_code:org_t)

Av författaren/redakt...: Hassan, Amin S.; Pybus, Oliver G; Sanders, Eduard ...; Albert, Jan; Esbjörnsson, Joa ...

Om ämnet

MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Klinisk medicin; och Infektionsmedici ...

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