ArticleVirulence2019
Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern.
Article in Virulence, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 32 citations in OpenAlex.
- Comprehensive analysis of complete chloroplast genome sequence of Morina L.Scientific reports · 2025Article
- Influenza D in Domestic and Wild Animals.Viruses · 2023Review
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- Insights into the Epidemiology, Phylodynamics, and Evolutionary Changes of Lineage GI-7 Infectious Bronchitis Virus.Transboundary and emerging diseases · 2023Article
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- Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases.Computational and structural biotechnology journal · 2022Review
- Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16.Viruses · 2021Article
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- Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers candidate therapeutics for COVID-19.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Insights into Genomic Epidemiology, Evolution, and Transmission Dynamics of Genotype VII of Class II Newcastle Disease Virus in China.Pathogens (Basel, Switzerland) · 2020Article
- Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus.International journal of molecular sciences · 2020Article
- Article
- Article
- Emerging Influenza D Virus Threat: What We Know so Far!Journal of clinical medicine · 2019Review
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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