A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.

The epidemiology of HIV-1 in China has unique features that may have led to unique viral strains. We therefore tested the hypothesis that it is possible to find distinctive patterns in HIV-1 genomes sampled in China. Using a rule inference algorithm we could indeed extract from sequences of the thir...

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Autores principales:	Yan Wang, Reda Rawi, Christoph Wilms, Dominik Heider, Rongge Yang, Daniel Hoffmann
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6fce960e34494932b30f3c76a2ed932d
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spelling	oai:doaj.org-article:6fce960e34494932b30f3c76a2ed932d2021-11-18T07:52:57ZA small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.1932-620310.1371/journal.pone.0058804https://doaj.org/article/6fce960e34494932b30f3c76a2ed932d2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23527028/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The epidemiology of HIV-1 in China has unique features that may have led to unique viral strains. We therefore tested the hypothesis that it is possible to find distinctive patterns in HIV-1 genomes sampled in China. Using a rule inference algorithm we could indeed extract from sequences of the third variable loop (V3) of HIV-1 gp120 a set of 14 signature patterns that with 89% accuracy distinguished Chinese from non-Chinese sequences. These patterns were found to be specific to HIV-1 subtype, i.e. sequences complying with pattern 1 were of subtype B, pattern 2 almost exclusively covered sequences of subtype 01_AE, etc. We then analyzed the first of these signature patterns in depth, namely that L and W at two V3 positions are specifically occurring in Chinese sequences of subtype B/B' (3% false positives). This pattern was found to be in agreement with the phylogeny of HIV-1 of subtype B inside and outside of China. We could neither reject nor convincingly confirm that the pattern is stabilized by immune escape. For further interpretation of the signature pattern we used the recently developed measure of Direct Information, and in this way discovered evidence for physical interactions between V2 and V3. We conclude by a discussion of limitations of signature patterns, and the applicability of the approach to other genomic regions and other countries.Yan WangReda RawiChristoph WilmsDominik HeiderRongge YangDaniel HoffmannPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 3, p e58804 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yan Wang Reda Rawi Christoph Wilms Dominik Heider Rongge Yang Daniel Hoffmann A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.
description	The epidemiology of HIV-1 in China has unique features that may have led to unique viral strains. We therefore tested the hypothesis that it is possible to find distinctive patterns in HIV-1 genomes sampled in China. Using a rule inference algorithm we could indeed extract from sequences of the third variable loop (V3) of HIV-1 gp120 a set of 14 signature patterns that with 89% accuracy distinguished Chinese from non-Chinese sequences. These patterns were found to be specific to HIV-1 subtype, i.e. sequences complying with pattern 1 were of subtype B, pattern 2 almost exclusively covered sequences of subtype 01_AE, etc. We then analyzed the first of these signature patterns in depth, namely that L and W at two V3 positions are specifically occurring in Chinese sequences of subtype B/B' (3% false positives). This pattern was found to be in agreement with the phylogeny of HIV-1 of subtype B inside and outside of China. We could neither reject nor convincingly confirm that the pattern is stabilized by immune escape. For further interpretation of the signature pattern we used the recently developed measure of Direct Information, and in this way discovered evidence for physical interactions between V2 and V3. We conclude by a discussion of limitations of signature patterns, and the applicability of the approach to other genomic regions and other countries.
format	article
author	Yan Wang Reda Rawi Christoph Wilms Dominik Heider Rongge Yang Daniel Hoffmann
author_facet	Yan Wang Reda Rawi Christoph Wilms Dominik Heider Rongge Yang Daniel Hoffmann
author_sort	Yan Wang
title	A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.
title_short	A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.
title_full	A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.
title_fullStr	A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.
title_full_unstemmed	A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.
title_sort	small set of succinct signature patterns distinguishes chinese and non-chinese hiv-1 genomes.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/6fce960e34494932b30f3c76a2ed932d
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A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.

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