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Analysis of Dinucleotide Signatures in HIV-1 Subtype B Genomes

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Journal J Genet
Specialty Genetics
Date 2013 Dec 28
PMID 24371162
Citations 4
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Abstract

Dinucleotide usage is known to vary in the genomes of organisms. The dinucleotide usage profiles or genome signatures are similar for sequence samples taken from the same genome, but are different for taxonomically distant species. This concept of genome signatures has been used to study several organisms including viruses, to elucidate the signatures of evolutionary processes at the genome level. Genome signatures assume greater importance in the case of host-pathogen interactions, where molecular interactions between the two species take place continuously, and can influence their genomic composition. In this study, analyses of whole genome sequences of the HIV-1 subtype B, a retrovirus that caused global pandemic of AIDS, have been carried out to analyse the variation in genome signatures of the virus from 1983 to 2007. We show statistically significant temporal variations in some dinucleotide patterns highlighting the selective evolution of the dinucleotide profiles of HIV-1 subtype B, possibly a consequence of host specific selection.

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References
1.
Pandit A, Sinha S . Differential trends in the codon usage patterns in HIV-1 genes. PLoS One. 2012; 6(12):e28889. PMC: 3245234. DOI: 10.1371/journal.pone.0028889. View

2.
Williamson S, Perry S, Bustamante C, Orive M, Stearns M, Kelly J . A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Mol Biol Evol. 2004; 22(3):456-68. DOI: 10.1093/molbev/msi029. View

3.
Dayton A, Sodroski J, Rosen C, Goh W, Haseltine W . The trans-activator gene of the human T cell lymphotropic virus type III is required for replication. Cell. 1986; 44(6):941-7. DOI: 10.1016/0092-8674(86)90017-6. View

4.
Plantier J, Leoz M, Dickerson J, De Oliveira F, Cordonnier F, Lemee V . A new human immunodeficiency virus derived from gorillas. Nat Med. 2009; 15(8):871-2. DOI: 10.1038/nm.2016. View

5.
Pandit A, Sinha S . Using genomic signatures for HIV-1 sub-typing. BMC Bioinformatics. 2010; 11 Suppl 1:S26. PMC: 3009497. DOI: 10.1186/1471-2105-11-S1-S26. View