Related Experiment Video
Updated: Sep 9, 2025
13:41
Use of Interferon-γ Enzyme-linked Immunospot Assay to Characterize Novel T-cell Epitopes of Human Papillomavirus
Published on: March 8, 2012
12.5K
Codon Usage Pattern of Papillomavirus E6, E7, and L1 Genes Across Hosts
Xudong Liu1, Kexin Li2,3, Xiaojing Chen1,4,5
1National Infrastructures for Translational Medicine, the State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China.
Current Microbiology
|August 29, 2025
Summary
Papillomavirus codon usage varies by host, influenced by natural selection and mutation. Key genes L1, E6, and E7 show distinct evolutionary patterns across different papillomavirus clades.
Area of Science:
- Virology
- Evolutionary Biology
- Bioinformatics
Background:
- Papillomaviruses (PVs) are a diverse group of viruses with significant host specificity.
- Understanding codon usage patterns can reveal insights into viral evolution and adaptation.
Purpose of the Study:
- To investigate papillomavirus codon usage preferences across various hosts.
- To examine the evolutionary relationships of essential PV genes (L1, E6, E7).
Main Methods:
- Retrieved 86 complete PV genome sequences from the PaVE database.
- Constructed phylogenetic trees using MAFFT and ITOL.
- Calculated codon usage indices (RSCU, ENC, CAI, GC3) with CodonW and performed ENC-GC3, Neutrality, and PR2-bias analyses.
Main Results:
- Papillomavirus genomes were classified into five clades, showing variations in codon usage indices (CAI, ENC).
- Phylogenetic analysis identified three distinct gene clusters for L1, E6, and E7.
- Both natural selection and mutation pressure were found to shape codon usage patterns.
Conclusions:
- Papillomavirus codon usage and the evolution of L1, E6, and E7 genes are host-dependent.
- These variations are driven by a combination of evolutionary forces, including selection and mutation.
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