Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

Zhang, Xu; Cai, Yuchen; Zhai, Xiaofeng; Liu, Jie; Zhao, Wen; Ji, Senlin; Su, Shuo; Zhou, Jiyong

doi:10.3390/ijms19082397

Cited by 19 publications

(18 citation statements)

References 54 publications

(59 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The effective number of codons (ENC) was calculated to identify bias in the use of synonymous codons. High ENC values (>40) have been identified in many animal viruses, such as porcine circovirus 3 [44], porcine deltacoronavirus [45], and rabies virus [46]. In our study, the mean ENC values of PAstV-2, PAstV-3, PAstV-4, and PAstV-5 were 56.265 ± 0.602, 53.059 ± 0.656, 52.007 ± 0.678, and 53.647 ± 0.316, respectively, demonstrating that a low codon preference was present in the four subtypes of PAstVs.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Bao

Mou

et al. 2020

Viruses

View full text Add to dashboard Cite

Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.

show abstract

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Bao

Mou

et al. 2020

Viruses

View full text Add to dashboard Cite

show abstract

“…Insights on the evolutionary principles of CUB in NSVs have great implications in managing outbreaks of highly pathogenic viruses, such as Ebola virus, influenza virus, and rabies virus. Analyses of codon usage in these viruses (12,36,40,41) found that these NSVs constantly mutate in different hosts, but their CUB was not coincident with that of the host. Our conclusion that optimal viral RNA synthesis regulated by the nucleocapsid is an additional determinant factor in CUB selection of NSVs will lead to an improved algorithm for mapping the evolutionary trajectory of these pathogens.…”

Section: Discussionmentioning

confidence: 99%

Constraints of Viral RNA Synthesis on Codon Usage of Negative-Strand RNA Virus

Gumpper

Luo

2019

J Virol

View full text Add to dashboard Cite

Negative-strand RNA viruses (NSVs) include some of the most pathogenic human viruses known. NSVs completely rely on the host cell for protein translation, but their codon usage bias is often different from that of the host. This discrepancy may have originated from the unique mechanism of NSV RNA synthesis in that the genomic RNA sequestered in the nucleocapsid serves as the template. The stability of the genomic RNA in the nucleocapsid appears to regulate its accessibility to the viral RNA polymerase, thus placing constraints on codon usage to balance viral RNA synthesis. By in situ analyses of vesicular stomatitis virus RNA synthesis, specific activities of viral RNA synthesis were correlated with the genomic RNA sequence. It was found that by simply altering the sequence and not the amino acid that it encoded, a significant reduction, up to an ∼750-fold reduction, in viral RNA transcripts occurred. Through subsequent sequence analysis and thermal shift assays, it was found that the purine/pyrimidine content modulates the overall stability of the polymerase complex, resulting in alteration of the activity of viral RNA synthesis. The codon usage is therefore constrained by the obligation of the NSV genome for viral RNA synthesis. IMPORTANCE Negative-strand RNA viruses (NSVs) include the most pathogenic viruses known. New methods to monitor their evolutionary trends are urgently needed for the development of antivirals and vaccines. The protein translation machinery of the host cell is currently recognized as a main genomic regulator of RNA virus evolution, which works especially well for positive-strand RNA viruses. However, this approach fails for NSVs because it does not consider the unique mechanism of their viral RNA synthesis. For NSVs, the viral RNA-dependent RNA polymerase (vRdRp) must gain access to the genome sequestered in the nucleocapsid. Our work suggests a paradigm shift that the interactions between the RNA genome and the nucleocapsid protein regulate the activity of vRdRp, which selects codon usage.

show abstract

“…In ENC-plot, if the codon usage is only constrained by the GC3s, the observed ENC values just lies on or around the expected curve, and it also indicates that mutation pressure is almost the only factor for evolution. Whereas if several factors constrain the codon usage, the observed ENC values lies far lower than the expected curve (Zhang et al 2018b).…”

Section: Effective Number Of Codon (Enc)mentioning

confidence: 75%

“…The regression line was represented by the straight line and the regression equation was showed on the plot bias in this strain. Low codon usage bias allowed the virus to make use of several codons for each amino acid, which was a benefit for viral replication in the host cells and persistent infection (Chen et al 2014;Zhang et al 2018b). This theory may account for the phenomenon that adult sows and part of piglets did not display any symptoms of CT with APPV viremia (Munoz-Gonzalez et al 2017).…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Liu

et al. 2021

Biochem Genet

View full text Add to dashboard Cite

Atypical porcine pestivirus (APPV) is an emerging novel pestivirus causing the congenital tremor (CT) in piglets. The worldwide distribution characteristic of APPV make it a threat to global swine health. E2 is the major envelope glycoprotein of APPV and the crucial target for vaccine development. Considering the genetic variability of APPV complete genomes and its E2 gene as well as gaps for codon analysis, a comprehensive analysis of codon usage patterns was performed. Relative synonymous codon usage (RSCU) and effective number of codon (ENC) analyses showed that a relatively instable change existed and a slight low codon usage bias (CUB) were displayed in APPV genomes. ENC-plot analysis and correlation analyses of nucleotide compositions and ENC showed that mutation pressure and natural selection both affected the codon usage bias of the APPV and natural selection had a more obvious influence for E2 gene compared with complete genomes. Principal component analysis (PCA) and correlation analyses confirmed the above results. Correlation analyses between Gravy and Aromaticity values and the codon bias showed that natural selection played an important role in shaping the synonymous codon bias. Furthermore, neutrality plot analysis showed that natural selection was the main force while mutation pressure was a minor force influencing the codon usage pattern of the APPV E2 gene and complete genomes. The results could illustrate the codon usage patterns of APPV genomes and provided valuable basic data for further fundamental research of evolution of APPV.

show abstract

Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

Cited by 19 publications

References 54 publications

Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Constraints of Viral RNA Synthesis on Codon Usage of Negative-Strand RNA Virus

Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Contact Info

Product

Resources

About