Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective.

Area of Science:

• Virology
• Evolutionary Biology
• Genomics

Background:

• Transmissible gastroenteritis virus (TGEV) causes significant diarrhea and mortality in piglets.
• Understanding TGEV evolution and adaptation is crucial for disease control.

Purpose of the Study:

• To perform a comprehensive analysis of TGEV phylogeny and codon usage bias.
• To investigate the evolutionary driving forces shaping TGEV codon usage.
• To assess the adaptive potential of different TGEV genotypes in pigs.

Main Methods:

• Phylogenetic analyses (maximum likelihood, Bayesian inference).
• Codon usage bias analysis (RSCU, ENC, dinucleotide analysis, Parity Rule 2 plot, ENC-plot, neutrality plot).
• Adaptation assessment (CAI, RCDI, SiD).

Main Results:

• Two distinct TGEV genotypes (I and II) were identified, with Genotype I further classified into subtypes Ia and Ib.
• Codon usage patterns were genotype-specific, with A/U enrichment and moderate bias (ENC).
• Natural selection was the dominant force shaping codon usage in Genotypes Ia and II, with mutation pressure playing a minor role in Ib.
• Genotype I appears more adaptive to pigs than Genotype II.

Conclusions:

• Phylogenetic and codon usage analyses reveal distinct evolutionary paths for TGEV genotypes.
• Natural selection significantly influences TGEV codon usage and adaptation.
• Genotype I's higher adaptability to pigs warrants further investigation for targeted disease management strategies.