Palanisamy, NavaneethanOsman, NathanOhnona, FrédéricXu, Hong-TaoBrenner, BlumaMesplède, ThibaultWainberg, Mark A2025-06-162025-06-162017-01-07Palanisamy, 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-y1742-640510.1186/s12981-016-0130-yhttp://hdl.handle.net/10034/629471Background: 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.Electronicenhttp://creativecommons.org/licenses/by/4.0/HIV-1Codon usage frequencyBioinformaticsAntiretroviral therapyResistanceAnti-HIV AgentsBase SequenceCodonComputational BiologyDrug Resistance, ViralGenes, polGenome, ViralHIV InfectionsHIV IntegraseHIV ProteaseHIV-1HumansPhylogenySequence AnalysisVirus Replicationgag Gene Products, Human Immunodeficiency Viruspol Gene Products, Human Immunodeficiency VirusAnti-HIV AgentsBase SequenceCodonComputational BiologyDrug Resistance, ViralGenes, polGenome, ViralHIV InfectionsHIV IntegraseHIV ProteaseHIV-1HumansPhylogenySequence AnalysisVirus Replicationgag Gene Products, Human Immunodeficiency Viruspol Gene Products, Human Immunodeficiency VirusHumansHIV-1HIV InfectionsHIV ProteaseHIV IntegraseCodonAnti-HIV AgentsSequence AnalysisComputational BiologyPhylogenyDrug Resistance, ViralVirus ReplicationBase SequenceGenes, polGenome, Viralgag Gene Products, Human Immunodeficiency Viruspol Gene Products, Human Immunodeficiency VirusArticleAIDS Research and Therapy2025-06-1314