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

Forskningsoutput: TidskriftsbidragÖversiktsartikel


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.


Enheter & grupper
Externa organisationer
  • Centre for Geographic Medicine Research, Kilifi
  • University of Oxford
  • Karolinska Institute

Ämnesklassifikation (UKÄ) – OBLIGATORISK

  • Infektionsmedicin
Sidor (från-till)1211-1222
Tidigt onlinedatum2017 mar 28
StatusPublished - 2017
Peer review utfördJa