A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing

In 2018, there was an outbreak of African swine fever (ASF) in China, which spread to other provinces in the following 3 years and severely damaged China's pig industry. ASF is caused by the African swine fever virus (ASFV). Given that the genome of the African swine fever virus is very complex...

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Autores principales:	ChiHai Ji, JingZhe Jiang, YingFang Wei, ZhiYuan Wang, YongJie Chen, ZhanZhuo Mai, MengKai Cai, ChenXiao Qin, Yu Cai, HeYou Yi, Guan Liang, Gang Lu, Lang Gong, GuiHong Zhang, Heng Wang
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	African swine fever virus (ASFV) genome virome virus-like particle whole genome sequencing Veterinary medicine SF600-1100
Acceso en línea:	https://doaj.org/article/a07565d1a1794eafb0042b5391487274
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id	oai:doaj.org-article:a07565d1a1794eafb0042b5391487274
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spelling	oai:doaj.org-article:a07565d1a1794eafb0042b53914872742021-11-30T12:05:32ZA Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing2297-176910.3389/fvets.2021.766533https://doaj.org/article/a07565d1a1794eafb0042b53914872742021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fvets.2021.766533/fullhttps://doaj.org/toc/2297-1769In 2018, there was an outbreak of African swine fever (ASF) in China, which spread to other provinces in the following 3 years and severely damaged China's pig industry. ASF is caused by the African swine fever virus (ASFV). Given that the genome of the African swine fever virus is very complex and whole genome information is currently inadequate, it is important to efficiently obtain virus genome sequences for genomic and epidemiological studies. The prevalent ASFV strains have low genetic variability; therefore, whole genome sequencing analysis provides a basis for the study of ASFV. We provide a method for the efficient sequencing of whole genomes, which requires only a small number of tissues. The database construction method was selected according to the genomic types of ASFV, and the whole ASFV genome was obtained through data filtering, host sequence removal, virus classification, data assembly, virus sequence identification, statistical analysis, gene prediction, and functional analysis. Our proposed method will facilitate ASFV genome sequencing and novel virus discovery.ChiHai JiChiHai JiChiHai JiChiHai JiChiHai JiJingZhe JiangYingFang WeiYingFang WeiYingFang WeiYingFang WeiYingFang WeiZhiYuan WangZhiYuan WangZhiYuan WangZhiYuan WangYongJie ChenYongJie ChenYongJie ChenYongJie ChenYongJie ChenZhanZhuo MaiZhanZhuo MaiZhanZhuo MaiZhanZhuo MaiMengKai CaiMengKai CaiMengKai CaiChenXiao QinChenXiao QinChenXiao QinChenXiao QinYu CaiYu CaiYu CaiYu CaiHeYou YiHeYou YiHeYou YiHeYou YiGuan LiangGuan LiangGuan LiangGuan LiangGang LuGang LuLang GongLang GongLang GongLang GongGuiHong ZhangGuiHong ZhangGuiHong ZhangGuiHong ZhangGuiHong ZhangHeng WangHeng WangHeng WangHeng WangHeng WangFrontiers Media S.A.articleAfrican swine fever virus (ASFV)genomeviromevirus-like particlewhole genome sequencingVeterinary medicineSF600-1100ENFrontiers in Veterinary Science, Vol 8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	African swine fever virus (ASFV) genome virome virus-like particle whole genome sequencing Veterinary medicine SF600-1100
spellingShingle	African swine fever virus (ASFV) genome virome virus-like particle whole genome sequencing Veterinary medicine SF600-1100 ChiHai Ji ChiHai Ji ChiHai Ji ChiHai Ji ChiHai Ji JingZhe Jiang YingFang Wei YingFang Wei YingFang Wei YingFang Wei YingFang Wei ZhiYuan Wang ZhiYuan Wang ZhiYuan Wang ZhiYuan Wang YongJie Chen YongJie Chen YongJie Chen YongJie Chen YongJie Chen ZhanZhuo Mai ZhanZhuo Mai ZhanZhuo Mai ZhanZhuo Mai MengKai Cai MengKai Cai MengKai Cai ChenXiao Qin ChenXiao Qin ChenXiao Qin ChenXiao Qin Yu Cai Yu Cai Yu Cai Yu Cai HeYou Yi HeYou Yi HeYou Yi HeYou Yi Guan Liang Guan Liang Guan Liang Guan Liang Gang Lu Gang Lu Lang Gong Lang Gong Lang Gong Lang Gong GuiHong Zhang GuiHong Zhang GuiHong Zhang GuiHong Zhang GuiHong Zhang Heng Wang Heng Wang Heng Wang Heng Wang Heng Wang A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing
description	In 2018, there was an outbreak of African swine fever (ASF) in China, which spread to other provinces in the following 3 years and severely damaged China's pig industry. ASF is caused by the African swine fever virus (ASFV). Given that the genome of the African swine fever virus is very complex and whole genome information is currently inadequate, it is important to efficiently obtain virus genome sequences for genomic and epidemiological studies. The prevalent ASFV strains have low genetic variability; therefore, whole genome sequencing analysis provides a basis for the study of ASFV. We provide a method for the efficient sequencing of whole genomes, which requires only a small number of tissues. The database construction method was selected according to the genomic types of ASFV, and the whole ASFV genome was obtained through data filtering, host sequence removal, virus classification, data assembly, virus sequence identification, statistical analysis, gene prediction, and functional analysis. Our proposed method will facilitate ASFV genome sequencing and novel virus discovery.
format	article
author	ChiHai Ji ChiHai Ji ChiHai Ji ChiHai Ji ChiHai Ji JingZhe Jiang YingFang Wei YingFang Wei YingFang Wei YingFang Wei YingFang Wei ZhiYuan Wang ZhiYuan Wang ZhiYuan Wang ZhiYuan Wang YongJie Chen YongJie Chen YongJie Chen YongJie Chen YongJie Chen ZhanZhuo Mai ZhanZhuo Mai ZhanZhuo Mai ZhanZhuo Mai MengKai Cai MengKai Cai MengKai Cai ChenXiao Qin ChenXiao Qin ChenXiao Qin ChenXiao Qin Yu Cai Yu Cai Yu Cai Yu Cai HeYou Yi HeYou Yi HeYou Yi HeYou Yi Guan Liang Guan Liang Guan Liang Guan Liang Gang Lu Gang Lu Lang Gong Lang Gong Lang Gong Lang Gong GuiHong Zhang GuiHong Zhang GuiHong Zhang GuiHong Zhang GuiHong Zhang Heng Wang Heng Wang Heng Wang Heng Wang Heng Wang
author_facet	ChiHai Ji ChiHai Ji ChiHai Ji ChiHai Ji ChiHai Ji JingZhe Jiang YingFang Wei YingFang Wei YingFang Wei YingFang Wei YingFang Wei ZhiYuan Wang ZhiYuan Wang ZhiYuan Wang ZhiYuan Wang YongJie Chen YongJie Chen YongJie Chen YongJie Chen YongJie Chen ZhanZhuo Mai ZhanZhuo Mai ZhanZhuo Mai ZhanZhuo Mai MengKai Cai MengKai Cai MengKai Cai ChenXiao Qin ChenXiao Qin ChenXiao Qin ChenXiao Qin Yu Cai Yu Cai Yu Cai Yu Cai HeYou Yi HeYou Yi HeYou Yi HeYou Yi Guan Liang Guan Liang Guan Liang Guan Liang Gang Lu Gang Lu Lang Gong Lang Gong Lang Gong Lang Gong GuiHong Zhang GuiHong Zhang GuiHong Zhang GuiHong Zhang GuiHong Zhang Heng Wang Heng Wang Heng Wang Heng Wang Heng Wang
author_sort	ChiHai Ji
title	A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing
title_short	A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing
title_full	A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing
title_fullStr	A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing
title_full_unstemmed	A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing
title_sort	method for the analysis of african swine fever by viral metagenomic sequencing
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/a07565d1a1794eafb0042b5391487274
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A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing

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