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

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...

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Bibliographic Details
Published in:Scientific reports 2017-08, Vol.7 (1), p.8162-8, Article 8162
Main Authors: Wasson, Mishi Kaushal, Borkakoti, Jayanta, Kumar, Amit, Biswas, Banhi, Vivekanandan, Perumal
Format: Article
Language:English
Subjects:
45
631/326/596/1787
631/326/596/2555
Cloning
Codons
CpG islands
Datasets
Env gene
Genomes
HIV
Human immunodeficiency virus
Humanities and Social Sciences
Infections
Longitudinal studies
multidisciplinary
Pathogenesis
Relative abundance
Science
Science (multidisciplinary)
Seroconversion
Viruses
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-017-08716-1