ArticleInternational journal of molecular sciences2020
Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 34 citations in OpenAlex.
- Nanopore direct RNA sequencing reveals transmissible gastroenteritis virus epitranscriptomic and transcriptomic landscapes modulated by gene 7.Microbial genomics · 2026Article
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- Rapid and visual detection of transmissible gastroenteritis virus using a CRISPR/Cas12a system combined with loop-mediated isothermal amplification.BMC veterinary research · 2025Article
- Review
- Comprehensive analysis of the codon usage patterns in the polyprotein coding sequences of the honeybee viruses.Frontiers in veterinary science · 2025Article
- Next-Generation Vaccines for Co-Circulating PEDV and TGEV: Integrating Nucleic Acid Platforms, Mucosal Delivery, and AI-Driven Antigen Design.Transboundary and emerging diseases · 2025Review
- First report of transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV) in pigs from Poland.BMC veterinary research · 2024Article
- All-trans retinoic acid alleviates transmissible gastroenteritis virus-induced intestinal inflammation and barrier dysfunction in weaned piglets.Journal of animal science and biotechnology · 2024Article
- Host and structure-specific codon usage of G genotype (VP7) among group A rotaviruses.Frontiers in veterinary science · 2024Article
- HSP90AB1 Is a Host Factor Required for Transmissible Gastroenteritis Virus Infection.International journal of molecular sciences · 2023Article
- Genetic comparison of transmissible gastroenteritis coronaviruses.Frontiers in veterinary science · 2023Article
- Swine coronaviruses (SCoVs) and their emerging threats to swine population, inter-species transmission, exploring the susceptibility of pigs for SARS-CoV-2 and zoonotic concerns.The veterinary quarterly · 2022Review
- Historical Evolutionary Dynamics and Phylogeography Analysis of Transmissible Gastroenteritis Virus and Porcine Deltacoronavirus: Findings from 59 Suspected Swine Viral Samples from China.International journal of molecular sciences · 2022Article
- Codon usage of host-specific P genotypes (VP4) in group A rotavirus.BMC genomics · 2022Article
- Epidemic and Evolutionary Characteristics of Swine Enteric Viruses in South-Central China from 2018 to 2021.Viruses · 2022Article
- Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion.Memorias do Instituto Oswaldo Cruz · 2022Article
- Cross-species transmission, evolution and zoonotic potential of coronaviruses.Frontiers in cellular and infection microbiology · 2022Review
- Article
- Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype.Frontiers in microbiology · 2021Article
- Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses.Frontiers in microbiology · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Transmissible gastroenteritis virus (TGEV) is a coronavirus associated with diarrhea and high mortality in piglets. To gain insight into the evolution and adaptation of TGEV, a comprehensive analysis of phylogeny and codon usage bias was performed. The phylogenetic analyses of maximum likelihood and Bayesian inference displayed two distinct genotypes: genotypes I and II, and genotype I was classified into subtypes Ia and Ib. The compositional properties revealed that the coding sequence contained a higher number of A/U nucleotides than G/C nucleotides, and that the synonymous codon third position was A/U-enriched. The principal component analysis based on the values of relative synonymous codon usage (RSCU) showed the genotype-specific codon usage patterns. The effective number of codons (ENC) indicated moderate codon usage bias in the TGEV genome. Dinucleotide analysis showed that CpA and UpG were over-represented and CpG was under-represented in the coding sequence of the TGEV genome. The analyses of Parity Rule 2 plot, ENC-plot, and neutrality plot displayed that natural selection was the dominant evolutionary driving force in shaping codon usage preference in genotypes Ia and II. In addition, natural selection played a major role, while mutation pressure had a minor role in driving the codon usage bias in genotype Ib. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses suggested that genotype I might be more adaptive to pigs than genotype II. Current findings contribute to understanding the evolution and adaptation of TGEV.
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