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
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.
(Less)
- author
- Hassan, Amin S.
LU
; Pybus, Oliver G
; Sanders, Eduard J.
; Albert, Jan
and Esbjörnsson, Joakim
LU
- organization
- publishing date
- 2017-03-28
- type
- Contribution to journal
- publication status
- published
- subject
- in
- AIDS
- volume
- 31
- issue
- 9
- pages
- 1211 - 1222
- publisher
- Lippincott Williams & Wilkins
- external identifiers
-
- scopus:85016438495
- pmid:28353537
- 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
- 2024-02-29 13:51:57
@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}},
}