Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study. Issue 1 (December 2017)

• Record Type: Journal Article
• Authors: Palanisamy, Navaneethan; Osman, Nathan; Ohnona, Frédéric; Xu, Hong-Tao; Brenner, Bluma; Mesplède, Thibault; Wainberg, Mark
• Is Part Of: AIDS research and therapy. Volume 14:Issue 1(2017)
• Page Start: 1
• Page End: 10
• Publication Date: 2017-12
• Subjects: HIV-1 -- Codon usage frequency -- Bioinformatics -- Antiretroviral therapy -- Resistance; AIDS (Disease) -- Periodicals; 616.9792005
• DOI: 10.1186/s12981-016-0130-y
• Languages: English
• ISSNs: 1742-6405

Abstract

Abstract Background Codon usage bias has been described for various organisms and is thought to contribute to the regulation of numerous biological processes including viral infections. HIV-1 codon usage has been previously shown to be different from that of other viruses and man. It is evident that the antiretroviral drugs used to restrict HIV-1 replication also select for resistance variants. We wanted to test whether codon frequencies in HIV-1 sequences from treatment-experienced patients differ from those of treatment-naive individuals due to drug pressure affecting codon usage bias. Results We developed a JavaScript to determine the codon frequencies of aligned nucleotide sequences. Irrespective of subtypes, using HIV-1pol sequences from 532 treatment-naive and 52 treatment-experienced individuals, we found thatpol sequences from treatment-experienced patients had significantly increased AGA (arginine; p = 0.0002***) and GGU (glycine; p = 0.0001***), and decreased AGG (arginine; p = 0.0001***) codon frequencies. The same pattern was not observed when subtypes B and C sequences were analyzed separately. Additionally, irrespective of subtypes, using HIV-1gag sequences from 524 treatment-naive and 54 treatment-experienced individuals, gag sequences from treatment-experienced patients had significantly increased CUA (leucine; p < 0.0001***), CAG (glutamine; p = 0.0006***), AUC (isoleucine; p < 0.0001***) and UCU (serine; p = 0.0005***), and decreased AUA (isoleucine; p = 0.0003***) and CAA (glutamine; p = 0.0006***) codon frequencies. Conclusion Usingpol andgag genes derived from the same HIV-1 genome, we show that antiretroviral therapy changed certain HIV-1 codon frequencies in a subtype specific way.