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

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...

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Autores principales:	Shuonan Pan, Chunxiao Mou, Huiguang Wu, Zhenhai Chen
Formato:	article
Lenguaje:	EN
Publicado:	Taylor & Francis Group 2020
Materias:	atypical porcine pestivirus phylogenetics codon usage mutation pressure selection pressure Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/b441df11afa744f0917b0334b715cb4c
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spelling	oai:doaj.org-article:b441df11afa744f0917b0334b715cb4c2021-11-17T14:21:58ZPhylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)2150-55942150-560810.1080/21505594.2020.1790282https://doaj.org/article/b441df11afa744f0917b0334b715cb4c2020-12-01T00:00:00Zhttp://dx.doi.org/10.1080/21505594.2020.1790282https://doaj.org/toc/2150-5594https://doaj.org/toc/2150-5608Atypical 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.Shuonan PanChunxiao MouHuiguang WuZhenhai ChenTaylor & Francis Grouparticleatypical porcine pestivirusphylogeneticscodon usagemutation pressureselection pressureInfectious and parasitic diseasesRC109-216ENVirulence, Vol 11, Iss 1, Pp 916-926 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	atypical porcine pestivirus phylogenetics codon usage mutation pressure selection pressure Infectious and parasitic diseases RC109-216
spellingShingle	atypical porcine pestivirus phylogenetics codon usage mutation pressure selection pressure Infectious and parasitic diseases RC109-216 Shuonan Pan Chunxiao Mou Huiguang Wu Zhenhai Chen Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)
description	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.
format	article
author	Shuonan Pan Chunxiao Mou Huiguang Wu Zhenhai Chen
author_facet	Shuonan Pan Chunxiao Mou Huiguang Wu Zhenhai Chen
author_sort	Shuonan Pan
title	Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)
title_short	Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)
title_full	Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)
title_fullStr	Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)
title_full_unstemmed	Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)
title_sort	phylogenetic and codon usage analysis of atypical porcine pestivirus (appv)
publisher	Taylor & Francis Group
publishDate	2020
url	https://doaj.org/article/b441df11afa744f0917b0334b715cb4c
work_keys_str_mv	AT shuonanpan phylogeneticandcodonusageanalysisofatypicalporcinepestivirusappv AT chunxiaomou phylogeneticandcodonusageanalysisofatypicalporcinepestivirusappv AT huiguangwu phylogeneticandcodonusageanalysisofatypicalporcinepestivirusappv AT zhenhaichen phylogeneticandcodonusageanalysisofatypicalporcinepestivirusappv
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Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)

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