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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 (2017) In AIDS
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
organization
publishing date
type
Contribution to journal
publication status
epub
subject
in
AIDS
publisher
Lippincott Williams & Wilkins
external identifiers
  • scopus:85016438495
  • wos:000401197400002
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
2017-09-18 13:33:47
@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},
  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},
  year         = {2017},
}