Evolutionary dynamics of codon usages for peste des petits ruminants virus

Area of Science:

• Virology
• Evolutionary Biology
• Genomics

Background:

• Peste des petits ruminants virus (PPRV) causes significant disease in small ruminants.
• The evolutionary dynamics of PPRV, particularly concerning codon usage, remain underexplored.

Purpose of the Study:

• To investigate the genetic features and evolutionary dynamics of PPRV through synonymous codon usage analysis.
• To understand PPRV's adaptation to its hosts and identify factors influencing its evolution.

Main Methods:

• Analysis of 45 whole PPRV genomes using information entropy, relative synonymous codon usage, similarity indexes, and codon adaptation index.
• Examination of codon usage patterns across six PPRV genes (N, P, M, F, H, L).

Main Results:

• PPRV exhibits universal, lineage-specific, and gene-specific codon usage features, indicating evolutionary plasticity.
• High PPRV host adaptation is suggested by codon usage, despite selection of rare codons and avoidance of CpG dinucleotides.
• PPRV strains from China (2007-2008, 2013-2014) showed independent evolutionary paths within the universal lineage IV pattern.

Conclusions:

• Synonymous codon usage in PPRV reflects evolutionary independence and host adaptation.
• Mutation pressure and natural selection are key drivers of PPRV's evolutionary dynamics and host fitness.