Defining HIV-1 transmission clusters based on sequence data

• Published in: AIDS (London) Vol. 31; no. 9; pp. 1211 - 1222
• Main Authors: Hassan, Amin S, Pybus, Oliver G, Sanders, Eduard J, Albert, Jan, Esbjörnsson, Joakim
• Format: Journal Article
• Language: English
• Published: England Copyright Wolters Kluwer Health, Inc 01.06.2017; Lippincott Williams & Wilkins
• Subjects: AIDS/HIV; Cluster Analysis; Genotype; HIV Infections - transmission; HIV-1 - classification; HIV-1 - genetics; HIV-1 - isolation & purification; Humans; Medicin och hälsovetenskap; Molecular Epidemiology - methods; Sequence Analysis, DNA - methods
• ISSN: 0269-9370; 1473-5571; 1473-5571
• DOI: 10.1097/QAD.0000000000001470

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 summarizing the most common 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.