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

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One Health Advances 2023年第1期1卷 10-25页

作者： Chang-zhan Xie Ping Zhang Yi-mo Tao Qi Wang Ning-yi Jin Hui-jun Lu Institute of Urban Agriculture Chinese Academy of Agricultural SciencesChengdu National Agricultural Science&Technology CenterChengdu 610213China Chinese Academy of Agricultural Sciences Chang-chun Veterinary Research InstituteChangchunChina Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences ChangchunChina.

Porcine reproductive and respiratory syndrome(PRRS)is a problem that has significant economic impact on the global pig *** 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)***,codon usage patterns and their effects on the evolution and adaptation of these new input PRRSV sub-types in hosts remain *** investigate this,we employed a Bayesian approach to analyze two novel imported PRRSV sub-types,namely,NADC30-like and NADC34-like *** sub-types have different codon ***,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 *** on the codon Adaptation Index(CAI),NADC30-like showed the highest similarity to the host,aligning with the main prevalence trend of the *** 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 *** 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 *** study provides new insights into the disease,origin,evolutionary patterns,and host adaptation of these newly imported PRRSV sub-types in *** also contributes to the development of theoretical frameworks for studying genetics and the evolution of PRRSV.

关键词： PRRSV NADC30-like NADC34-like codon usage preference

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