期刊
VIRUSES-BASEL
卷 13, 期 6, 页码 -出版社
MDPI
DOI: 10.3390/v13061044
关键词
porcine reproductive and respiratory syndrome virus (PRRSV); lineages; evolutionary analysis; codon bias; codon pair bias; host adaptability; virus attenuation
类别
资金
- National Natural Science Foundation of China [31772759]
- China Agriculture Research System of MOF and MARA [CARS-35]
This study analyzed the codon usage of ORF5 genes from different PRRSV strains in China, revealing a relationship between viral evolution and host adaptation. Results showed that all strains had low codon bias, with lineage 1 showing a higher similarity to pig codon usage patterns and potentially having a predominant epidemic propensity in the field.
Porcine reproductive and respiratory syndrome virus (PRRSV) is economically important and characterized by its extensive variation. The codon usage patterns and their influence on viral evolution and host adaptation among different PRRSV strains remain largely unknown. Here, the codon usage of ORF5 genes from lineages 1, 3, 5, and 8, and MLV strains of type 2 PRRSV in China was analyzed. A compositional property analysis of ORF5 genes revealed that nucleotide C is most frequently used at the third position of codons, accompanied by rich GC3s. The effective number of codon (ENC) and codon pair bias (CPB) values indicate that all ORF5 genes have low codon bias and the differences in CPB scores among four lineages are almost not significant. When compared with host codon usage patterns, lineage 1 strains show higher CAI and SiD values, with a high similarity to pig, which might relate to its predominant epidemic propensity in the field. The CAI, RCDI, and SiD values of ORF5 genes from different passages of MLV JXA1R indicate no relation between attenuation and CPB or codon adaptation decrease during serial passage on non-host cells. These findings provide a novel way of understanding the PRRSV's evolution, related to viral survival, host adaptation, and virulence.
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