Insight into the codon usage patterns and adaptation of Tembusu Virus

Area of Science:

• Virology
• Evolutionary Biology
• Genomics

Background:

• Tembusu virus (TMUV) emerged in 2010 and has since spread widely in Asian poultry, causing significant economic damage.
• Understanding TMUV's adaptation mechanisms is crucial for managing its impact on poultry health and the economy.

Purpose of the Study:

• To investigate the codon usage patterns (CUPs) that drive TMUV's adaptation and evolution within different host environments.
• To identify the evolutionary lineages of TMUV and their specific adaptations to hosts.

Main Methods:

• Phylogenetic and compositional analyses were used to classify TMUV into evolutionary lineages.
• Codon Adaptation Index (CAI) was employed to assess TMUV's adaptation to the CUPs of various hosts.
• Dinucleotide distribution analysis was performed to understand immune evasion strategies.

Main Results:

• TMUV was classified into four lineages, with Cluster 2 being dominant and showing the highest adaptation to duck CUPs.
• TMUV demonstrated significantly higher adaptation to poultry (duck, goose, chicken) than to humans or mosquitoes.
• The virus genome exhibits suppressed CpG and UpA dinucleotides, indicative of immune evasion, with CpG reduction increasing during transmission.

Conclusions:

• Natural selection predominantly shapes TMUV's CUPs, driving its adaptation to poultry hosts.
• Species-specific adaptation to host CUPs likely influences TMUV's infectivity and clinical outcomes.
• TMUV's genomic adaptations, including CpG suppression, enhance its fitness and persistence within hosts, advancing understanding of its epidemiology and pathogenicity.