Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern
The codon usage pattern can reveal the adaptive changes that allow virus survival and fitness adaptation to their particular host, as well as the external environment. Although still considered a novel influenza virus, there is an increasing number of influenza D viruses (IDVs) reported. Considering...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2019-01-01
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| Series: | Virulence |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/21505594.2018.1551708 |
| _version_ | 1818422916617863168 |
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| author | Ziqing Yan Ruyi Wang Letian Zhang Binger Shen Ningning Wang Qiuhua Xu Wei He Wanting He Gairu Li Shuo Su |
| author_facet | Ziqing Yan Ruyi Wang Letian Zhang Binger Shen Ningning Wang Qiuhua Xu Wei He Wanting He Gairu Li Shuo Su |
| author_sort | Ziqing Yan |
| collection | DOAJ |
| description | The codon usage pattern can reveal the adaptive changes that allow virus survival and fitness adaptation to their particular host, as well as the external environment. Although still considered a novel influenza virus, there is an increasing number of influenza D viruses (IDVs) reported. Considering the vital role of the hemagglutinin-esterase fusion (HEF) gene in receptor binding, receptor degradation, and membrane fusion, we investigated the codon usage pattern of the IDV HEF gene to better understand its adaptive changes during evolution. Based on the HEF gene, three groups including, D/OK, D/660, and D/Japan were identified. We found a low codon usage bias, which allowed IDV to replicate in the corresponding hosts by reducing competition during evolution, that was mainly driven by natural selection and mutation pressure, with a profound role of natural selection. Furthermore, the interaction between the codon adaption index (CAI) and the relative codon deoptimization index (RCDI) revealed the adaption of IDV to multiple hosts, especially cattle which is currently considered its reservoir. Additionally, similarity index (SiD) analysis revealed that the swine exerted a stronger evolutionary pressure on IDV than cattle, though cattle is considered the primary reservoir. In addition, the conserved PB1 gene showed a similar pattern of codon usage compared to HEF. Therefore, we hypothesized that IDV has a preference to maintain infection in multiple hosts. The study aids the understanding of the evolutionary changes of IDV, which could assist this novel virus prevention and control. |
| first_indexed | 2024-12-14T13:33:51Z |
| format | Article |
| id | doaj.art-dcf34a80ec7e48d1a5ba5351e5e44110 |
| institution | Directory Open Access Journal |
| issn | 2150-5594 2150-5608 |
| language | English |
| last_indexed | 2024-12-14T13:33:51Z |
| publishDate | 2019-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Virulence |
| spelling | doaj.art-dcf34a80ec7e48d1a5ba5351e5e441102022-12-21T22:59:38ZengTaylor & Francis GroupVirulence2150-55942150-56082019-01-011011910.1080/21505594.2018.15517081551708Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage patternZiqing Yan0Ruyi Wang1Letian Zhang2Binger Shen3Ningning Wang4Qiuhua Xu5Wei He6Wanting He7Gairu Li8Shuo Su9Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityThe codon usage pattern can reveal the adaptive changes that allow virus survival and fitness adaptation to their particular host, as well as the external environment. Although still considered a novel influenza virus, there is an increasing number of influenza D viruses (IDVs) reported. Considering the vital role of the hemagglutinin-esterase fusion (HEF) gene in receptor binding, receptor degradation, and membrane fusion, we investigated the codon usage pattern of the IDV HEF gene to better understand its adaptive changes during evolution. Based on the HEF gene, three groups including, D/OK, D/660, and D/Japan were identified. We found a low codon usage bias, which allowed IDV to replicate in the corresponding hosts by reducing competition during evolution, that was mainly driven by natural selection and mutation pressure, with a profound role of natural selection. Furthermore, the interaction between the codon adaption index (CAI) and the relative codon deoptimization index (RCDI) revealed the adaption of IDV to multiple hosts, especially cattle which is currently considered its reservoir. Additionally, similarity index (SiD) analysis revealed that the swine exerted a stronger evolutionary pressure on IDV than cattle, though cattle is considered the primary reservoir. In addition, the conserved PB1 gene showed a similar pattern of codon usage compared to HEF. Therefore, we hypothesized that IDV has a preference to maintain infection in multiple hosts. The study aids the understanding of the evolutionary changes of IDV, which could assist this novel virus prevention and control.http://dx.doi.org/10.1080/21505594.2018.1551708idvhefcodon usagemutation pressurenatural selectionevolution |
| spellingShingle | Ziqing Yan Ruyi Wang Letian Zhang Binger Shen Ningning Wang Qiuhua Xu Wei He Wanting He Gairu Li Shuo Su Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern Virulence idv hef codon usage mutation pressure natural selection evolution |
| title | Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern |
| title_full | Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern |
| title_fullStr | Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern |
| title_full_unstemmed | Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern |
| title_short | Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern |
| title_sort | evolutionary changes of the novel influenza d virus hemagglutinin esterase fusion gene revealed by the codon usage pattern |
| topic | idv hef codon usage mutation pressure natural selection evolution |
| url | http://dx.doi.org/10.1080/21505594.2018.1551708 |
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