The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression

Abstract The clinical course of HIV-1 varies greatly among infected individuals. Despite extensive research, virus factors associated with slow-progression remain poorly understood. Identification of unique HIV-1 genomic signatures linked to slow-progression remains elusive. We investigated CpG dinu...

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Autores principales:	Mishi Kaushal Wasson, Jayanta Borkakoti, Amit Kumar, Banhi Biswas, Perumal Vivekanandan
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/18d528d0998a464fb55c4b3b8b11c5ac
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spelling	oai:doaj.org-article:18d528d0998a464fb55c4b3b8b11c5ac2021-12-02T11:41:10ZThe CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression10.1038/s41598-017-08716-12045-2322https://doaj.org/article/18d528d0998a464fb55c4b3b8b11c5ac2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08716-1https://doaj.org/toc/2045-2322Abstract The clinical course of HIV-1 varies greatly among infected individuals. Despite extensive research, virus factors associated with slow-progression remain poorly understood. Identification of unique HIV-1 genomic signatures linked to slow-progression remains elusive. We investigated CpG dinucleotide content in HIV-1 envelope gene as a potential virus factor in disease progression. We analysed 1808 HIV-1 envelope gene sequences from three independent longitudinal studies; this included 1280 sequences from twelve typical-progressors and 528 sequences from six slow-progressors. Relative abundance of CpG dinucleotides and relative synonymous codon usage (RSCU) for CpG-containing codons among HIV-1 envelope gene sequences from typical-progressors and slow-progressors were analysed. HIV-1 envelope gene sequences from slow-progressors have high-CpG dinucleotide content and increased number of CpG-containing codons as compared to typical-progressors. Our findings suggest that observed differences in CpG-content between typical-progressors and slow-progressors is not explained by differences in the mononucleotide content. Our results also highlight that the high-CpG content in HIV-1 envelope gene from slow-progressors is observed immediately after seroconversion. Thus CpG dinucleotide content of HIV-1 envelope gene is a potential virus-related factor that is linked to disease progression. The CpG dinucleotide content of HIV-1 envelope gene may help predict HIV-1 disease progression at early stages after seroconversion.Mishi Kaushal WassonJayanta BorkakotiAmit KumarBanhi BiswasPerumal VivekanandanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-8 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mishi Kaushal Wasson Jayanta Borkakoti Amit Kumar Banhi Biswas Perumal Vivekanandan The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression
description	Abstract The clinical course of HIV-1 varies greatly among infected individuals. Despite extensive research, virus factors associated with slow-progression remain poorly understood. Identification of unique HIV-1 genomic signatures linked to slow-progression remains elusive. We investigated CpG dinucleotide content in HIV-1 envelope gene as a potential virus factor in disease progression. We analysed 1808 HIV-1 envelope gene sequences from three independent longitudinal studies; this included 1280 sequences from twelve typical-progressors and 528 sequences from six slow-progressors. Relative abundance of CpG dinucleotides and relative synonymous codon usage (RSCU) for CpG-containing codons among HIV-1 envelope gene sequences from typical-progressors and slow-progressors were analysed. HIV-1 envelope gene sequences from slow-progressors have high-CpG dinucleotide content and increased number of CpG-containing codons as compared to typical-progressors. Our findings suggest that observed differences in CpG-content between typical-progressors and slow-progressors is not explained by differences in the mononucleotide content. Our results also highlight that the high-CpG content in HIV-1 envelope gene from slow-progressors is observed immediately after seroconversion. Thus CpG dinucleotide content of HIV-1 envelope gene is a potential virus-related factor that is linked to disease progression. The CpG dinucleotide content of HIV-1 envelope gene may help predict HIV-1 disease progression at early stages after seroconversion.
format	article
author	Mishi Kaushal Wasson Jayanta Borkakoti Amit Kumar Banhi Biswas Perumal Vivekanandan
author_facet	Mishi Kaushal Wasson Jayanta Borkakoti Amit Kumar Banhi Biswas Perumal Vivekanandan
author_sort	Mishi Kaushal Wasson
title	The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression
title_short	The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression
title_full	The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression
title_fullStr	The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression
title_full_unstemmed	The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression
title_sort	cpg dinucleotide content of the hiv-1 envelope gene may predict disease progression
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/18d528d0998a464fb55c4b3b8b11c5ac
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The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression

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