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Published on: June 26, 2020
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Using codon usage analysis to speculate potential animal hosts of hepatitis E virus: An exploratory study
Bingzhe Li1, Han Wu1, Ziping Miao2
1Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai 200032, China.
Summary
Hepatitis E virus (HEV) is increasingly found in animals. Codon usage analysis suggests cattle, dogs, rats, cats, and swine may host HEV, aiding in identifying animal reservoirs.
Area of Science:
- Virology
- Genomics
- Comparative Biology
Background:
- Hepatitis E virus (HEV) is a growing global health concern with increasing reports of animal infections.
- Understanding animal hosts is crucial for controlling HEV transmission and preventing zoonotic spread.
Purpose of the Study:
- To investigate potential animal hosts for Hepatitis E virus (HEV) using codon usage analysis.
- To compare nucleotide composition and codon usage bias across different HEV genotypes and potential animal hosts.
Main Methods:
- Collected full-length HEV sequences for six genotypes.
- Analyzed codon usage patterns of 17 potential animal hosts.
- Compared nucleotide composition and codon usage bias between HEV genotypes and animal hosts.
Main Results:
- Analysis for human HEV-1 and humans aligned with epidemiological data.
- All HEV genotypes showed a preference for guanine/cytosine at the third codon position.
- Non-human primates and humans share high-frequency codons with HEV, indicating a strong correlation.
- Cattle, dogs, rats (HEV-A), and cats, dogs, swine (HEV-C1) showed a high preference for HEV.
Conclusions:
- Codon usage bias offers indicative clues for potential HEV animal hosts when integrated with other evidence.
- Specific animals like cattle, dogs, rats, cats, and swine are highlighted as potential reservoirs for different HEV genotypes.
- Further experimental and epidemiological studies are needed to confirm these findings and elucidate HEV host dynamics.
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