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

Hassan, Amin S. LU ; Pybus, Oliver G ; Sanders, Eduard J. ; Albert, Jan and Esbjörnsson, Joakim LU orcid (2017) In AIDS 31(9). p.1211-1222
Abstract

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... (More)

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.

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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
AIDS
volume
31
issue
9
pages
1211 - 1222
publisher
Lippincott Williams & Wilkins
external identifiers
  • pmid:28353537
  • wos:000401197400002
  • scopus:85016438495
ISSN
0269-9370
DOI
10.1097/QAD.0000000000001470
language
English
LU publication?
yes
id
f8635823-82a0-4f37-bf10-dcc2e28f635b
date added to LUP
2017-05-02 16:24:48
date last changed
2022-08-02 04:39:43
@article{f8635823-82a0-4f37-bf10-dcc2e28f635b,
  abstract     = {{<p>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.</p>}},
  author       = {{Hassan, Amin S. and Pybus, Oliver G and Sanders, Eduard J. and Albert, Jan and Esbjörnsson, Joakim}},
  issn         = {{0269-9370}},
  language     = {{eng}},
  month        = {{03}},
  number       = {{9}},
  pages        = {{1211--1222}},
  publisher    = {{Lippincott Williams & Wilkins}},
  series       = {{AIDS}},
  title        = {{Defining HIV-1 transmission clusters based on sequence data : a systematic review and perspectives}},
  url          = {{http://dx.doi.org/10.1097/QAD.0000000000001470}},
  doi          = {{10.1097/QAD.0000000000001470}},
  volume       = {{31}},
  year         = {{2017}},
}