Comprehensive analysis of the codon usage patterns in the polyprotein coding sequences of the honeybee viruses

Area of Science:

• Virology
• Genetics
• Ecology

Background:

• Honeybee viruses (HVs) are major pathogens causing significant economic losses in apiculture globally.
• Understanding HV evolution is crucial for bee health and the beekeeping industry.

Purpose of the Study:

• To analyze codon usage bias (CUB) in four key honeybee viruses: ABPV, KBV, CBPV, and SBV.
• To investigate the evolutionary and adaptive mechanisms shaping HV genomes.

Main Methods:

• Analysis of nucleotide content and Relative Synonymous Codon Usage (RSCU).
• Calculation of Effective Number of Codons (ENC), Codon Adaptation Index (CAI), and Relative Codon Deoptimization Index (RCDI).
• Evaluation of ENC plots, PR2 plots, and neutrality analyses.

Main Results:

• HV polyprotein coding sequences are A/U-rich, with a preference for A/U at the third codon position.
• Higher ENC values indicate lower CUB in these viruses.
• Natural selection, rather than mutation pressure, predominantly shapes codon usage patterns.
• Strong correlations between HVs and their hosts were observed via CAI and RCDI analyses.

Conclusions:

• Codon usage patterns in HVs are shaped by natural selection, reflecting adaptation to host environments.
• Findings provide insights into HV genetic evolution and host-virus interactions.