Comparative characterization analysis of synonymous codon usage bias in classical swine fever virus

Xu, Xin; Fei, Dongliang; Han, Huansheng; Liu, Honggui; Zhang, Jiayong; Zhou, Youwen; Xu, Chuang; Wang, Hongbin; Cao, Hongwei; Zhang, Hua

doi:10.1016/j.micpath.2017.04.019

Cited by 14 publications

(14 citation statements)

References 17 publications

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“…It is interesting to note that the percentages of nucleotide A and A-end codons are the highest in the APPV genomes. Consistent with previous findings in the BVDV [ 14 ] and CSFV [ 15 ], a high content of nucleotide A in the APPV CDSs might be a genomic characteristic of the genus Pestivirus .…”

Section: Discussionsupporting

confidence: 91%

“…The ENC values of each APPV genome were calculated to estimate the overall codon usage bias. The mean ENC values of APPV genomes (54.832 ± 0.254) were higher than BVDV (51.43 ± 0.46) [ 14 ], CSFV (51.85 ± 0.39) [ 15 ], and BDV (average 51.33 and range from 51.12 to 51.55), suggesting that the overall codon bias of APPV is considerably weaker. Considering that low codon usage bias may be useful for efficient replication with more codon selection options [ 43 ], our results showed that the low codon bias of APPV might facilitate its genome replication and transcription.…”

Section: Discussionmentioning

confidence: 99%

“…The preferentially A/T-ended codons of APPV were found inconsistent with those of BVDV [ 14 ] and CSFV [ 15 ], in which G/C-ended codons were preferentially used. Notably, two (AGA[Arg] and AGG[Arg]) over-represented codons and seven (GCG[Ala], UCG[Ser], ACG[Thr], CGU[Arg], CGC[Arg], CGA[Arg], and CGG[Arg]) under-represented codons were frequently presented in the genomes of APPV, BVDV [ 14 ], and CSFV [ 15 ], indicating a common genomic feature of codon usage patterns of pestiviruses. In conclusion, APPV has a common characteristic of genus Pestivirus as well as its own unique characteristic in the codon usage pattern.…”

Section: Discussionmentioning

confidence: 99%

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Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)

Pan

Mou

et al. 2020

Virulence

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Atypical porcine pestivirus (APPV) has been identified as the main causative agent for congenital tremor (CT) type A-II in piglets, which is threatening the health of the global swine herd. However, the evolution of APPV remains largely unknown. In this study, phylogenetic analysis showed that APPV could be divided into three phylogroups (I, II, and III). Phylogroups I and II included viral strains from China, while phylogroup III contained strains from Europe, North America, and Asia. Phylogroups I and II are tentatively thought to be of Chinese origin. Next, compositional property analysis revealed that a high frequency of nucleotide A and A-end codons was used in the APPV genome. Intriguingly, the analysis of preferred codons revealed that the AGA[Arg] and AGG[Arg] were overrepresented. Dinucleotide CC was found to be overrepresented, and dinucleotide CG was underrepresented. Furthermore, it was found that the weak codon usage bias of APPV was mainly dominated by selection pressures versus mutational forces. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses showed that the codon usage patterns of phylogroup II and III were more similar to the one of a pig than phylogroup I, suggesting that phylogroup II and III may be more adaptive to pigs. Overall, this study provides insights into APPV evolution through phylogeny and codon usage pattern analysis.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)

Pan

Mou

et al. 2020

Virulence

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“…Because the virus relies on the host's cellular machinery for its replication, codon usage bias was suggested to play a role in the adaptation of a virus to its host. Codon usage bias is common in viruses (Butt et al 2014;Castells et al 2017;Cristina et al 2016;He et al 2017;Li et al 2017;Moratorio et al 2013;Singh et al 2016;Su et al 2017;Xu et al 2017;Zang et al 2017;Zhao et al 2016). Efficient replication seemingly requires that a virus and host have similar codon usage patterns to share a tRNA pool.…”

Section: Introductionmentioning

confidence: 99%

The adaptation of codon usage of +ssRNA viruses to their hosts

Tian

Shen

Murphy

et al. 2018

Infection, Genetics and Evolution

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Viruses depend on their host's cellular structure to survive. Most of them do not have tRNAs, their translation relies on hosts' tRNA pools. Over the course of evolution, viruses needed to optimally exploit cellular processes of their host. Thus, codon usage of a virus should coevolve with its host to efficiently and rapidly replicate. Some viruses can invade a broad spectrum of hosts (BSTVs), while others can invade a narrow spectrum only (NSTVs). Consequently, we test the hypothesis that similarity of codon usage preference and the degree of matching between BSTVs and their hosts will be lower than that of NSTVs, which only need to coevolve with few hosts. We compare the patterns of codon usage in 255 virus genomes to test this hypothesis. Our results show that NSTVs have a higher degree of matching to their hosts' tRNA pools than BSTVs. Further, analysis of the effective number of codons (ENC) infers that codon usage bias of NSTVs is relatively stronger than that of BSTVs. Thus, codon usage of NSTVs tends to better match their host than that of BSTVs. This supports the hypothesis that viruses adapt to the expression system of their host(s).

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“…Significantly different synonymous codon usage exists between virus genomes and that of their host species, which reflects different codon usage bias (Zhou et al, 1999;Chen, 2013;Cristina et al, 2016;Xu et al, 2017). Evolution of viruses involves changes in virus nucleotide composition, which ultimately creates variations in the virus genome (Sablok et al, 2011;Zhang et al, 2011).…”

Section: Introductionmentioning

confidence: 99%