Codon usage and evolutionary dynamics of genetic diversity of novel imported porcine reproductive and respiratory syndrome virus in China

Porcine reproductive and respiratory syndrome (PRRS) is a problem that has significant economic impact on the global pig industry. In recent years, there has been an increased importation of pork into China, contributing to the emergence of novely imported porcine reproductive and respiratory syndrome virus (PRRSV) sub-types. Nevertheless, codon usage patterns and their effects on the evolution and adaptation of these new input PRRSV sub-types in hosts remain elusive. To investigate this, we employed a Bayesian approach to analyze two novel imported PRRSV sub-types, namely, NADC30-like and NADC34-like viruses. These sub-types have different codon preferences. Besides, the Effective Number of Codon (ENC) analysis revealed that both NADC30-like and NADC34-like fall within the expected curve distribution, describing a balanced codon usage for both NADC30-like and NADC34-like virus. Based on the Codon Adaptation Index (CAI), NADC30-like showed the highest similarity to the host, aligning with the main prevalence trend of the host. In contrast, NADC34-like exhibited the highest frequency of optimal codon usage; this analysis is based on Frequency of Optimal Codons (FOP). Moreover, the Relative Codon Deoptimization Index (RCDI) indicates that NADC30-like sub-types have a greater degree of inverse optimization sub-type. These findings suggest that mutational pressure affects codon usage preferences of genes in newly imported PRRSV, and that natural selection plays a vital role in determining PRRSV gene codon preferences. Our study provides new insights into the disease, origin, evolutionary patterns, and host adaptation of these newly imported PRRSV sub-types in China. It also contributes to the development of theoretical frameworks for studying genetics and the evolution of PRRSV.