Journal article
Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies
Immunogenetics (New York), v 67(1), pp 15-24
01 Jan 2015
PMID: 25376343
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Viral epitopes have a distinct codon usage that reflects their dual role in infection and immunity. On the one hand, epitopes are part of proteins important to viral function; on the other hand, they are targets of the immune response. Studies of selection are most commonly based on changes of amino acid and seen through the accumulation of non-synonymous mutations. An independent measure of selection is the codon usage and underlying changeability of the nucleotide sequences. We here use multiple tools and a large-scale analysis of viral genomes to demonstrate that viral epitopes have a distinct codon usage and that this codon usage reflects distinct short- and long-term types of selection during viral evolution. We show that CD8(+) T cell epitopes are encoded by codons more distant from stop codons and more changeable than codons outside epitopes. This biased codon usage reflects the viral population toggling back and forth from a wild-type sequence to an escape mode, which enable them to avoid immune detection when needed, and go back to the functionally favorable form when the threat is removed (i.e., in a new host).
Metrics
Details
- Title
- Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies
- Creators
- Yaakov Maman - Yale UniversityUri Hershberg - Drexel UniversityYoram Louzoun - Bar-Ilan University
- Publication Details
- Immunogenetics (New York), v 67(1), pp 15-24
- Publisher
- Springer Nature
- Number of pages
- 10
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000347161000003
- Scopus ID
- 2-s2.0-84922074376
- Other Identifier
- 991019167428804721
UN Sustainable Development Goals (SDGs)
This publication has contributed to the advancement of the following goals:
InCites Highlights
Data related to this publication, from InCites Benchmarking & Analytics tool:
- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Genetics & Heredity
- Immunology