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

Journal article

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 non-experts 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.

Authors: Pybus, O; Hassan, A; Sanders, E; Albert, J; Esbjoernsson, J

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Lippincott, Williams & Wilkins
• Journal: AIDS
• Volume: 31
• Issue: 9
• Pages: 1211–1222
• Publication date: 2017-06-01
• Acceptance date: 2017-03-07
• DOI: 10.1097/QAD.0000000000001470
• EISSN: 1473-5571
• ISSN: 0269-9370
• Keywords: transmission clusters; HIV-1; molecular epidemiology; phylogeny