Abstract
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.
Highlights
Porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped, singlestranded positive-sense RNA (+ssRNA) virus, which is classified into the genus Porartevirus of the family Arteriviridae in the order Nidovirales [1,2,3]
It is the etiological agent of porcine reproductive and respiratory syndrome (PRRS), which is clinically characterized by reproductive failure in sows, including abortion and elevated fetal losses, as well as respiratory disorders in pigs of all ages, leading to elevated mortality and poor growth performance, especially in weaning and nursery herds [4]
In Principal component analysis (PCA) analysis based on Relative synonymous codon usage (RSCU) values of the 59 synonymous codons, the first two principal axes of PRRSV ORF5 genes accounted for 31.8% and 8.8% of the synonymous codon usage, and we explored the distribution of each lineage based on the first two axes (Figure 3)
Summary
Porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped, singlestranded positive-sense RNA (+ssRNA) virus, which is classified into the genus Porartevirus of the family Arteriviridae in the order Nidovirales [1,2,3]. It is the etiological agent of porcine reproductive and respiratory syndrome (PRRS), which is clinically characterized by reproductive failure in sows, including abortion and elevated fetal losses, as well as respiratory disorders in pigs of all ages, leading to elevated mortality and poor growth performance, especially in weaning and nursery herds [4]. In the late 1980s, PRRSV first emerged as a “mystery” disease progressing through pig farms in both Europe and North
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