Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species
Abstract The intraspecies genomic diversity of the single‐strand RNA (+) virus species hepatitis A virus (Hepatovirus), hepatitis C virus (Hepacivirus), and hepatitis E virus (Orthohepevirus) was compared. These viral species all can cause liver inflammation (hepatitis), but share no gene similarity...
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| Format: | Article |
| Language: | English |
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Wiley
2020-02-01
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| Series: | MicrobiologyOpen |
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| Online Access: | https://doi.org/10.1002/mbo3.973 |
| _version_ | 1818136960586219520 |
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| author | Trudy M. Wassenaar Se‐Ran Jun Michael Robeson David W. Ussery |
| author_facet | Trudy M. Wassenaar Se‐Ran Jun Michael Robeson David W. Ussery |
| author_sort | Trudy M. Wassenaar |
| collection | DOAJ |
| description | Abstract The intraspecies genomic diversity of the single‐strand RNA (+) virus species hepatitis A virus (Hepatovirus), hepatitis C virus (Hepacivirus), and hepatitis E virus (Orthohepevirus) was compared. These viral species all can cause liver inflammation (hepatitis), but share no gene similarity. The codon usage of human hepatitis A virus (HAV) is suboptimal for replication in its host, a characteristic it shares with taxonomically related rodent, simian, and bat hepatitis A virus species. We found this codon usage to be strikingly similar to that of Triatoma virus that infects blood‐sucking kissing bugs. The codon usage of that virus is well adapted to its insect host. The codon usage of HAV is also similar to other invertebrate viruses of various taxonomic families. An evolutionary ancestor of HAV and related virus species is hypothesized to be an insect virus that underwent a host jump to infect mammals. The similarity between HAV and invertebrate viruses goes beyond codon usage, as they also share amino acid composition characteristics, while not sharing direct sequence homology. In contrast, hepatitis C virus and hepatitis E virus are highly similar in codon usage preference, nucleotide composition, and amino acid composition, and share these characteristics with Human pegivirus A, West Nile virus, and Zika virus. We present evidence that these observations are only partly explained by differences in nucleotide composition of the complete viral codon regions. We consider the combination of nucleotide composition, amino acid composition, and codon usage preference suitable to provide information on possible evolutionary similarities between distant virus species that cannot be investigated by phylogeny. |
| first_indexed | 2024-12-11T09:48:43Z |
| format | Article |
| id | doaj.art-1b59a8580805474685bdcfa665f0200c |
| institution | Directory Open Access Journal |
| issn | 2045-8827 |
| language | English |
| last_indexed | 2024-12-11T09:48:43Z |
| publishDate | 2020-02-01 |
| publisher | Wiley |
| record_format | Article |
| series | MicrobiologyOpen |
| spelling | doaj.art-1b59a8580805474685bdcfa665f0200c2022-12-22T01:12:28ZengWileyMicrobiologyOpen2045-88272020-02-0192n/an/a10.1002/mbo3.973Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus speciesTrudy M. Wassenaar0Se‐Ran Jun1Michael Robeson2David W. Ussery3Molecular Microbiology and Genomics Consultants Zotzenheim GermanyDepartment of Biomedical Informatics University of Arkansas for Medical Sciences Little Rock AR USADepartment of Biomedical Informatics University of Arkansas for Medical Sciences Little Rock AR USADepartment of Biomedical Informatics University of Arkansas for Medical Sciences Little Rock AR USAAbstract The intraspecies genomic diversity of the single‐strand RNA (+) virus species hepatitis A virus (Hepatovirus), hepatitis C virus (Hepacivirus), and hepatitis E virus (Orthohepevirus) was compared. These viral species all can cause liver inflammation (hepatitis), but share no gene similarity. The codon usage of human hepatitis A virus (HAV) is suboptimal for replication in its host, a characteristic it shares with taxonomically related rodent, simian, and bat hepatitis A virus species. We found this codon usage to be strikingly similar to that of Triatoma virus that infects blood‐sucking kissing bugs. The codon usage of that virus is well adapted to its insect host. The codon usage of HAV is also similar to other invertebrate viruses of various taxonomic families. An evolutionary ancestor of HAV and related virus species is hypothesized to be an insect virus that underwent a host jump to infect mammals. The similarity between HAV and invertebrate viruses goes beyond codon usage, as they also share amino acid composition characteristics, while not sharing direct sequence homology. In contrast, hepatitis C virus and hepatitis E virus are highly similar in codon usage preference, nucleotide composition, and amino acid composition, and share these characteristics with Human pegivirus A, West Nile virus, and Zika virus. We present evidence that these observations are only partly explained by differences in nucleotide composition of the complete viral codon regions. We consider the combination of nucleotide composition, amino acid composition, and codon usage preference suitable to provide information on possible evolutionary similarities between distant virus species that cannot be investigated by phylogeny.https://doi.org/10.1002/mbo3.973codon biascomparative genomicsevolutionHepactovirus Ahepatitis A virus |
| spellingShingle | Trudy M. Wassenaar Se‐Ran Jun Michael Robeson David W. Ussery Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species MicrobiologyOpen codon bias comparative genomics evolution Hepactovirus A hepatitis A virus |
| title | Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species |
| title_full | Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species |
| title_fullStr | Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species |
| title_full_unstemmed | Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species |
| title_short | Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species |
| title_sort | comparative genomics of hepatitis a virus hepatitis c virus and hepatitis e virus provides insights into the evolutionary history of hepatovirus species |
| topic | codon bias comparative genomics evolution Hepactovirus A hepatitis A virus |
| url | https://doi.org/10.1002/mbo3.973 |
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