期刊
AIDS
卷 31, 期 9, 页码 1211-1222出版社
LIPPINCOTT WILLIAMS & WILKINS
DOI: 10.1097/QAD.0000000000001470
关键词
HIV-1; molecular epidemiology; phylogeny; transmission clusters
资金
- Swedish Research Council [350-2012-6628, 2016-01417]
- Swedish Society for Medical Research
- Wellcome Trust [077092, 107752/Z/15/Z]
- International AIDS Vaccine Initiative (IAVI)
- American people through United States Agency for International Development (USAID)
- African Research Excellence Fund (AREF) [MRF-157-0002-F-HASSA]
- Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE), a DELTAS Africa Initiative [DEL-15-006]
- African Academy of Sciences (AAS)'s Alliance for Accelerating Excellence in Science in Africa (AESA)
- New Partnership for Africa's Development Planning and Coordinating Agency (NEPAD Agency)
- UK government
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. Copyright (C) 2017 Wolters Kluwer Health, Inc. All rights reserved.
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