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

The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression.
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Wasson MK, Borkakoti J, Kumar A, Biswas B, Vivekanandan P,


Wasson MK, Borkakoti J, Kumar A, Biswas B, Vivekanandan P, (click to view)

Wasson MK, Borkakoti J, Kumar A, Biswas B, Vivekanandan P,

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Scientific reports 2017 08 157(1) 8162 doi 10.1038/s41598-017-08716-1

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.

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