| Content Provider | Springer Nature : BioMed Central |
|---|---|
| Author | Palanisamy, Navaneethan Osman, Nathan Ohnona, Frédéric Xu, Hong-Tao Brenner, Bluma Mesplède, Thibault Wainberg, Mark A. |
| 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. |
| Related Links | https://aidsrestherapy.biomedcentral.com/counter/pdf/10.1186/s12981-016-0130-y.pdf |
| Ending Page | 10 |
| Page Count | 10 |
| Starting Page | 1 |
| File Format | HTM / HTML |
| ISSN | 17426405 |
| DOI | 10.1186/s12981-016-0130-y |
| Journal | AIDS Research and Therapy |
| Issue Number | 1 |
| Volume Number | 14 |
| Language | English |
| Publisher | BioMed Central |
| Publisher Date | 2017-01-07 |
| Access Restriction | Open |
| Subject Keyword | Infectious Diseases Virology HIV-1 Codon usage frequency Bioinformatics Antiretroviral therapy Resistance |
| Content Type | Text |
| Resource Type | Article |
| Subject | Molecular Medicine Virology Pharmacology (medical) |
| Journal Impact Factor | 2.1/2023 |
| 5-Year Journal Impact Factor | 2.4/2023 |
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