Synonymous codon usage of genes in polymerase complex of Newcastle disease virus

Kumar, Chandra Shekhar; Kumar, Sachin

doi:10.1002/jobm.201600740

Cited by 6 publications

(3 citation statements)

References 42 publications

(47 reference statements)

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“…Codon usage bias analysis showed that the F genes of genotype VII NDVs exhibit low codon bias, consistent with the findings of a previous study [ 50 ]. RSCU, ENC-plot, and PR2 analyses suggested that the bias in F genes of genotype VII NDVs was influenced by mutation pressure and natural selection.…”

Section: Discussionsupporting

confidence: 91%

Insights into Genomic Epidemiology, Evolution, and Transmission Dynamics of Genotype VII of Class II Newcastle Disease Virus in China

et al. 2020

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Newcastle disease virus (NDV) is distributed worldwide and has caused significant losses to the poultry industry. Almost all virulent NDV strains belong to class II, among which genotype VII is the predominant genotype in China. However, the molecular evolution and phylodynamics of class II genotype VII NDV strains in China remained largely unknown. In this study, we identified 13 virulent NDV including 11 genotype VII strains and 2 genotype IX strains, from clinical samples during 1997 to 2019. Combined NDV sequences submitted to GenBank, we investigate evolution, and transmission dynamics of class II NDVs in China, especially genotype VII strains. Our results revealed that East and South China have the most genotypic diversity of class II NDV, and East China might be the origin of genotype VII NDVs in China. In addition, genotype VII NDVs in China are presumably transmitted by chickens, as the virus was most prevalent in chickens. Furthermore, codon usage analysis revealed that the F genes of genotype VII NDVs have stronger adaptation in chickens, and six amino acids in this gene are found under positive selection via selection model analysis. Collectively, our results revealed the genetic diversity and evolutionary dynamics of genotype VII NDVs in China, providing important insights into the epidemiology of these viruses in China.

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Section: Discussionsupporting

confidence: 91%

Insights into Genomic Epidemiology, Evolution, and Transmission Dynamics of Genotype VII of Class II Newcastle Disease Virus in China

et al. 2020

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“…This phenomenon has previously been attributed to limiting CpG to evade the host's immune system and to the concept of codon constellation (8,12,(31)(32)(33). More importantly, analyses of codon usages revealed that CUB of NSVs did not result from transitional selection (34)(35)(36). To identify other factors of CUB selection in NSVs, viral proteins that have close interactions with the coding regions of the viral genome are considered.…”

Section: Discussionmentioning

confidence: 99%

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

Gumpper

Luo

2019

J Virol

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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.

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“…If synonymous codon usage bias reflected such trends as mentioned above, the mutation pressure would play a dominant role in the codon usages. During the evolution of the negative-sense single-stranded RNA virus, mutation pressure remained the key factor that influenced the codon bias than natural selection in viral genes (46,47). However, synonymous codon usage bias of PPRV coding sequences showed no AU or GC end, suggesting that the mutation pressure caused by nucleotide usage variation was not predominant in the PPRV evolutionary pathway.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary dynamics of codon usages for peste des petits ruminants virus

Wang

Sun²,

Lu³

et al. 2022

Front. Vet. Sci.

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Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.

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Synonymous codon usage of genes in polymerase complex of Newcastle disease virus

Cited by 6 publications

References 42 publications

Insights into Genomic Epidemiology, Evolution, and Transmission Dynamics of Genotype VII of Class II Newcastle Disease Virus in China

Insights into Genomic Epidemiology, Evolution, and Transmission Dynamics of Genotype VII of Class II Newcastle Disease Virus in China

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

Evolutionary dynamics of codon usages for peste des petits ruminants virus

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