Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses.
Authors: Kumar Naveen, Bera Bidhan Chandra, Greenbaum Benjamin D, Bhatia Sandeep, Sood Richa, Selvaraj Pavulraj, Anand Taruna, Tripathi Bhupendra Nath, Virmani Nitin
Journal: PloS one
Summary
# Editorial Summary: Codon Usage Bias in Equine Influenza Viruses Understanding how influenza viruses adapt to equine hosts at a molecular level is crucial for predicting outbreak severity and viral evolution, yet the genetic mechanisms underlying this adaptation remain poorly characterised. Researchers examined codon usage patterns—the virus's "preference" for particular synonymous codons—across 92 equine influenza virus (EIV) strains of both H3N8 and H7N7 subtypes using relative synonymous codon usage (RSCU) analysis and multivariate statistical methods. The H3N8 subtype, responsible for most field outbreaks, demonstrated significantly better adaptation to equine cellular machinery than H7N7, showing lower overall codon bias and greater compatibility with the horse's transfer RNA (tRNA) pool—suggesting H3N8 achieves more efficient viral protein synthesis within equine cells. Codon usage in EIVs appears governed by a complex interplay of mutational pressures and host-driven selection rather than biased mutation alone, with nucleotide composition playing a substantial constraining role. For equine professionals involved in biosecurity, vaccination strategy, or surveillance programmes, these findings offer insights into why certain viral strains persist and spread more readily in horse populations, potentially informing risk assessment during reported outbreaks and contributing to a more nuanced understanding of EIV epidemiology and zoonotic potential.
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Practical Takeaways
- •Understanding EIV codon adaptation mechanics may inform future vaccine development and strain prediction strategies for H3N8 and emerging subtypes
- •H7N7's weaker host adaptation suggests it may pose lower long-term epidemiological risk compared to the dominant H3N8 subtype
- •Genomic codon analysis could become a tool to assess emerging EIV strains' evolutionary potential and virulence trajectory
Key Findings
- •EIV codon usage shows preference for A/U-ended codons with overall bias mainly driven by nucleotide compositional constraints
- •H7N7 subtype demonstrates lower host adaptation fitness compared to H3N8, with higher codon bias and poorer alignment with equine tRNA pools
- •Viral codon usage patterns governed by interplay of mutation pressure, natural selection from host, and undefined evolutionary factors