Selection pressure in CD8⁺ T-cell epitopes in the pol gene of HIV-1 infected individuals in Colombia. A bioinformatic approach
| Autor: | Francisco J. Díaz, Rodrigo Ochoa, Paula Andrea Velilla-Hernández, María Teresa Rugeles, Liliana Acevedo-Sáenz, Patricia Olaya-García |
|---|---|
| Rok vydání: | 2014 |
| Předmět: |
CD8+ T-cells
lcsh:QR1-502 Mutation Missense Epitopes T-Lymphocyte HIV Infections Human leukocyte antigen Biology CD8-Positive T-Lymphocytes Colombia lcsh:Microbiology Epitope Article Genetic drift HLA Antigens positive selection Virology Drug Resistance Viral Humans Genetic variability Binding site Selection Genetic Genetics Binding Sites human immunodeficiency virus Computational Biology epitopes Reverse transcriptase HIV Reverse Transcriptase Infectious Diseases Anti-Retroviral Agents Docking (molecular) pol Gene Products Human Immunodeficiency Virus docking HIV-1 Synonymous substitution Protein Binding |
| Zdroj: | Viruses Viruses, Vol 7, Iss 3, Pp 1313-1331 (2015) Volume 7 Issue 3 Pages 1313-1331 |
| ISSN: | 1999-4915 |
| Popis: | One of the main characteristics of the human immunodeficiency virus is its genetic variability and rapid adaptation to changing environmental conditions. This variability, resulting from the lack of proofreading activity of the viral reverse transcriptase, generates mutations that could be fixed either by random genetic drift or by positive selection. Among the forces driving positive selection are antiretroviral therapy and CD8+ T-cells, the most important immune mechanism involved in viral control. Here, we describe mutations induced by these selective forces acting on the pol gene of HIV in a group of infected individuals. We used Maximum Likelihood analyses of the ratio of non-synonymous to synonymous mutations per site (dN/dS) to study the extent of positive selection in the protease and the reverse transcriptase, using 614 viral sequences from Colombian patients. We also performed computational approaches, docking and algorithmic analyses, to assess whether the positively selected mutations affected binding to the HLA molecules. We found 19 positively-selected codons in drug resistance-associated sites and 22 located within CD8+ T-cell epitopes. A high percentage of mutations in these epitopes has not been previously reported. According to the docking analyses only one of those mutations affected HLA binding. However, algorithmic methods predicted a decrease in the affinity for the HLA molecule in seven mutated peptides. The bioinformatics strategies described here are useful to identify putative positively selected mutations associated with immune escape but should be complemented with an experimental approach to define the impact of these mutations on the functional profile of the CD8+ T-cells. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|