Abstract
A new codon-pair bias present in the genomes of different types of influenza virus is described. Codons with fewer network interactions are more frequency paired together than other codon-pairs in influenza A, B, and C genomes. A shared feature among three different influenza types suggests an evolutionary bias. Codon-pair preference can affect both speed of protein translation and RNA structure. This newly identified bias may provide insight into drivers of virus evolution.
Highlights
The limited size of viral genomes places constraints on the evolution that can occur without accruing deleterious mutations (Holmes, 2003)
Genome composition changes over time and evolutionary trends have been reported for different influenza viruses (Wong et al, 2010; Smith et al, 2018; Gu et al, 2019)
We looked to see if the trends in pyrimidine usage at the third codon position were reflected in changes to the relative synonymous codon usage (RSCU)
Summary
The limited size of viral genomes places constraints on the evolution that can occur without accruing deleterious mutations (Holmes, 2003). Open reading frames (ORFs) are the major component of viral genomes. Our understanding of the composition of viral ORFs informs our understanding of the virus itself. A message RNA (mRNA) is transcribed from the viral genome and the host cell ribosomes translate mRNAs into proteins. The proteins that form the virus particles, the enzymes that replicate the viral genomes, and the proteins that counter the host cell response to the intruder are all projected by the triplet codons that lie between the initiation AUG and the termination codon of the ORFs. Different genomic sequences can encode the same proteins, yet preferences exist for codons
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