Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study
Palanisamy, Navaneethan Osman, Nathan Ohnona, Frédéric Xu, Hong-Tao Brenner, Bluma Mesplède, Thibault Wainberg, Mark A
Palanisamy, Navaneethan
Osman, Nathan
Ohnona, Frédéric
Xu, Hong-Tao
Brenner, Bluma
Mesplède, Thibault
Wainberg, Mark A
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2017-01-07
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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-1 pol sequences from 532 treatment-naive and 52 treatment-experienced individuals, we found that pol 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-1 gag 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: Using pol and gag genes derived from the same HIV-1 genome, we show that antiretroviral therapy changed certain HIV-1 codon frequencies in a subtype specific way.
Citation
Palanisamy, N., Osman, N., Ohnona, F., Xu, H. T., Brenner, B., Mesplède, T., & Wainberg, M. A. (2017). Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study. AIDS Research and Therapy, 14, 1-10. https://doi.org/10.1186/s12981-016-0130-y
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Springer Nature
Journal
AIDS Research and Therapy
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DOI
10.1186/s12981-016-0130-y
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Article
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en
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1742-6405
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Canadian Institutes for Health Research (CIHR)