Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China
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...
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MDPI AG
2021-05-01
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| Online Access: | https://www.mdpi.com/1999-4915/13/6/1044 |
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| author | Weixin Wu Xinna Ge Yongning Zhang Jun Han Xin Guo Lei Zhou Hanchun Yang |
| author_facet | Weixin Wu Xinna Ge Yongning Zhang Jun Han Xin Guo Lei Zhou Hanchun Yang |
| author_sort | Weixin Wu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T10:49:43Z |
| format | Article |
| id | doaj.art-5f1f23438a08443d8d4658238d354f37 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T10:49:43Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
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| series | Viruses |
| spelling | doaj.art-5f1f23438a08443d8d4658238d354f372023-11-21T22:17:17ZengMDPI AGViruses1999-49152021-05-01136104410.3390/v13061044Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in ChinaWeixin Wu0Xinna Ge1Yongning Zhang2Jun Han3Xin Guo4Lei Zhou5Hanchun Yang6Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Agricultural University, Beijing 100193, ChinaKey Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Agricultural University, Beijing 100193, ChinaKey Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Agricultural University, Beijing 100193, ChinaKey Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Agricultural University, Beijing 100193, ChinaKey Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Agricultural University, Beijing 100193, ChinaKey Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Agricultural University, Beijing 100193, ChinaKey Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Agricultural University, Beijing 100193, ChinaPorcine 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.https://www.mdpi.com/1999-4915/13/6/1044porcine reproductive and respiratory syndrome virus (PRRSV)lineagesevolutionary analysiscodon biascodon pair biashost adaptability |
| spellingShingle | Weixin Wu Xinna Ge Yongning Zhang Jun Han Xin Guo Lei Zhou Hanchun Yang Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China Viruses porcine reproductive and respiratory syndrome virus (PRRSV) lineages evolutionary analysis codon bias codon pair bias host adaptability |
| title | Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China |
| title_full | Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China |
| title_fullStr | Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China |
| title_full_unstemmed | Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China |
| title_short | Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China |
| title_sort | evolutionary patterns of codon usage in major lineages of porcine reproductive and respiratory syndrome virus in china |
| topic | porcine reproductive and respiratory syndrome virus (PRRSV) lineages evolutionary analysis codon bias codon pair bias host adaptability |
| url | https://www.mdpi.com/1999-4915/13/6/1044 |
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