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Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution.
Infect Genet Evol. 2012 Dec; 12(8):1842-53.IG

Abstract

Hepatitis E virus (HEV) is present in different species and ecological niches. It has been divided into 4 major mammalian genotypes. In this study, 3 new full-length genomes of swine HEV were sequenced and the results did not reveal any particular host determinant in comparison with human isolates belonging to the same genotype. Nucleotide composition and codon usage bias were determined to characterize HEV host restriction and genome evolution. Peculiar nucleotide bias was observed for A and C nucleotides in all HEV genotypes. Apart from the ORF1 hypervariable region and the ORF2/3 overlapping region, no nucleotide bias was observed between the 3 codon positions. CpG dinucleotides were also shown to be under-represented in HEV as in most RNA viruses. The effective number of codon used in HEV genome was high, indicating a lack of codon bias. Correspondence analysis of the relative synonymous codon usage was performed and demonstrated that evolution of HEV is not driven by geographical or host factors, but is representative of HEV phylogeny. These results confirm that HEV genome evolution is mainly based on mutational pressure. Natural selection, for instance involving fine-tuning translation kinetics and escape from the host immune system, may also play a role in shaping the HEV genome, particularly in the ORF1 hypervariable region and the ORF2/3 overlapping region. These regions might be involved in host restriction. Finally this study revealed the need to re-evaluate the possible subtyping classification.

Authors+Show Affiliations

UMR 1161 Virology, ANSES, Laboratoire de Santé Animale, 94706 Maisons-Alfort, France; UMR 1161 Virology, INRA, 94706 Maisons-Alfort, France.No affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

22951575

Citation

Bouquet, Jerome, et al. "Genetic Characterization and Codon Usage Bias of Full-length Hepatitis E Virus Sequences Shed New Lights On Genotypic Distribution, Host Restriction and Genome Evolution." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 12, no. 8, 2012, pp. 1842-53.
Bouquet J, Cherel P, Pavio N. Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution. Infect Genet Evol. 2012;12(8):1842-53.
Bouquet, J., Cherel, P., & Pavio, N. (2012). Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 12(8), 1842-53. https://doi.org/10.1016/j.meegid.2012.07.021
Bouquet J, Cherel P, Pavio N. Genetic Characterization and Codon Usage Bias of Full-length Hepatitis E Virus Sequences Shed New Lights On Genotypic Distribution, Host Restriction and Genome Evolution. Infect Genet Evol. 2012;12(8):1842-53. PubMed PMID: 22951575.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution. AU - Bouquet,Jerome, AU - Cherel,Pierre, AU - Pavio,Nicole, Y1 - 2012/08/21/ PY - 2012/05/13/received PY - 2012/07/27/revised PY - 2012/07/29/accepted PY - 2012/9/7/entrez PY - 2012/9/7/pubmed PY - 2013/6/19/medline SP - 1842 EP - 53 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect Genet Evol VL - 12 IS - 8 N2 - Hepatitis E virus (HEV) is present in different species and ecological niches. It has been divided into 4 major mammalian genotypes. In this study, 3 new full-length genomes of swine HEV were sequenced and the results did not reveal any particular host determinant in comparison with human isolates belonging to the same genotype. Nucleotide composition and codon usage bias were determined to characterize HEV host restriction and genome evolution. Peculiar nucleotide bias was observed for A and C nucleotides in all HEV genotypes. Apart from the ORF1 hypervariable region and the ORF2/3 overlapping region, no nucleotide bias was observed between the 3 codon positions. CpG dinucleotides were also shown to be under-represented in HEV as in most RNA viruses. The effective number of codon used in HEV genome was high, indicating a lack of codon bias. Correspondence analysis of the relative synonymous codon usage was performed and demonstrated that evolution of HEV is not driven by geographical or host factors, but is representative of HEV phylogeny. These results confirm that HEV genome evolution is mainly based on mutational pressure. Natural selection, for instance involving fine-tuning translation kinetics and escape from the host immune system, may also play a role in shaping the HEV genome, particularly in the ORF1 hypervariable region and the ORF2/3 overlapping region. These regions might be involved in host restriction. Finally this study revealed the need to re-evaluate the possible subtyping classification. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/22951575/Genetic_characterization_and_codon_usage_bias_of_full_length_Hepatitis_E_virus_sequences_shed_new_lights_on_genotypic_distribution_host_restriction_and_genome_evolution_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1567-1348(12)00257-2 DB - PRIME DP - Unbound Medicine ER -