Comprehensive analysis of synonymous codon usage patterns in orf3 gene of porcine epidemic diarrhea virus in China

In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli . Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.

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Analysis of synonymous codon usage patterns in different plant mitochondrial genomes

Molecular Biology Reports ◽

10.1007/s11033-008-9414-1 ◽

2008 ◽

Vol 36 (8) ◽

pp. 2039-2046 ◽

Cited By ~ 33

Author(s):

Meng Zhou ◽

Xia Li

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Mitochondrial Genomes ◽

Usage Patterns

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Emergence and evolution of highly pathogenic porcine epidemic diarrhea virus by natural recombination of a low pathogenic vaccine isolate and a highly pathogenic strain in the spike gene

Virus Evolution ◽

10.1093/ve/veaa049 ◽

2020 ◽

Vol 6 (2) ◽

Author(s):

Huinan Wang ◽

Libo Zhang ◽

Yuanbin Shang ◽

Rongrong Tan ◽

Mingxiang Ji ◽

...

Keyword(s):

Porcine Epidemic Diarrhea Virus ◽

Intestinal Epithelial ◽

Orf3 Gene ◽

Highly Pathogenic ◽

Spike Gene ◽

Diarrhea Virus ◽

Attenuated Vaccine ◽

New Variant ◽

Porcine Epidemic Diarrhea ◽

Natural Recombination

Abstract Outbreaks of a new variant of porcine epidemic diarrhea virus (PEDV) at the end of 2010 have raised interest in the mutation and recombination of PEDV. A PEDV strain (CN/Liaoning25/2018) isolated from a clinical outbreak of piglet diarrhea contained a 49-bp deletion in the ORF3 gene. This deletion is considered a genetic characteristic of low pathogenic attenuated vaccine strains. However, CN/Liaoning25/2018 was highly pathogenic. Complete genome sequencing, identity analysis, phylogenetic tree construction, and recombination analysis showed that this virus was a recombinant strain containing the Spike (S) gene from the highly pathogenic CN/GDZQ/2014 strain and the remaining genomic regions from the low pathogenic vaccine isolate SQ2014. Histopathology and immunohistochemistry results confirmed that this strain was highly pathogenic and indicated that intestinal epithelial cell vacuolation was positively correlated with the intensity and density of PEDV antigens. A new natural recombination model for PEDV was identified. Our results suggest that new highly pathogenic recombinant strains in the field may be generated by recombination between low pathogenic attenuated live PEDV vaccines and pathogenic circulating PEDV strains. Our findings also highlight that the 49-bp deletion of the ORF3 gene in low pathogenic attenuated vaccine strains will no longer be a reliable standard to differentiate the classical vaccine attenuated from the field strains.

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Porcine Epidemic Diarrhea Virus (PEDV) ORF3 Enhances Viral Proliferation by Inhibiting Apoptosis of Infected Cells

Viruses ◽

10.3390/v12020214 ◽

2020 ◽

Vol 12 (2) ◽

pp. 214 ◽

Cited By ~ 3

Author(s):

Fusheng Si ◽

Xiaoxia Hu ◽

Chenyang Wang ◽

Bingqing Chen ◽

Ruiyang Wang ◽

...

Keyword(s):

Porcine Epidemic Diarrhea Virus ◽

Underlying Mechanism ◽

Vero Cells ◽

Orf3 Gene ◽

Accessory Gene ◽

Orf3 Protein ◽

Diarrhea Virus ◽

Viral Virulence ◽

Porcine Epidemic Diarrhea

The genomes of coronaviruses carry accessory genes known to be associated with viral virulence. The single accessory gene of porcine epidemic diarrhea virus (PEDV), ORF3, is dispensable for virus replication in vitro, while viral mutants carrying ORF3 truncations exhibit an attenuated phenotype of which the underlying mechanism is unknown. Here, we studied the effect of ORF3 deletion on the proliferation of PEDV in Vero cells. To this end, four recombinant porcine epidemic diarrhea viruses (PEDVs) were rescued using targeted RNA recombination, three carrying the full-length ORF3 gene from different PEDV strains, and one from which the ORF3 gene had been deleted entirely. Our results showed that PEDVs with intact or naturally truncated ORF3 replicated to significantly higher titers than PEDV without an ORF3. Further characterization revealed that the extent of apoptosis induced by PEDV infection was significantly lower with the viruses carrying an intact or C-terminally truncated ORF3 than with the virus lacking ORF3, indicating that the ORF3 protein as well as its truncated form interfered with the apoptosis process. Collectively, we conclude that PEDV ORF3 protein promotes virus proliferation by inhibiting cell apoptosis caused by virus infection. Our findings provide important insight into the role of ORF3 protein in the pathogenicity of PEDV.

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