Nucleotide composition and synonymous codon usage of open reading frames in Norovirus GII.4 variants

Area of Science:

• Virology
• Molecular Biology
• Bioinformatics

Background:

• Norovirus GII.4 variants are major causes of nonbacterial gastroenteritis outbreaks.
• These viruses possess a single-stranded positive-sense RNA genome with three Open Reading Frames (ORFs).

Purpose of the Study:

• To analyze nucleotide composition and synonymous codon usage patterns in Norovirus GII.4 strains.
• To investigate the factors driving codon usage bias and identify temporal changes.

Main Methods:

• Bioinformatic analysis of 292 Norovirus GII.4 strains isolated between 1974 and 2016.
• Assessment of nucleotide composition, codon bias, and evolutionary pressures using tools like CodonW and SPSS.
• Correspondence analysis and ENC plots were employed to evaluate codon usage patterns.

Main Results:

• Norovirus GII.4 genomes are enriched in Adenine (A) and show a bias against Guanine (G) at the third codon position.
• ORF2 and ORF3 share similar nucleotide composition and codon bias patterns, distinct from ORF1.
• Temporal variations in codon usage were observed, with natural selection being a dominant force, especially for ORF2 and ORF3.

Conclusions:

• Codon usage bias in Norovirus GII.4 is shaped by both natural selection and mutational pressure.
• Understanding these patterns provides insights into the evolutionary mechanisms of this significant human pathogen.