Origin, genomic diversity and evolution of African swine fever virus in East Asia
Abstract Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary feature...
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Veröffentlicht in: | Virus Evolution 2023-12, Vol.9 (2), p.1-vead060 |
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container_title | Virus Evolution |
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creator | Xin, Genyang Kuang, Qiyuan Le, Shijia Wu, Weichen Gao, Qi Gao, Han Xu, Zhiying Zheng, Zezhong Lu, Gang Gong, Lang Wang, Heng Zhang, Guihong Shi, Mang Sun, Yankuo |
description | Abstract
Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620–18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a ‘star-like’ structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention. |
doi_str_mv | 10.1093/ve/vead060 |
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Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620–18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a ‘star-like’ structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.</description><identifier>ISSN: 2057-1577</identifier><identifier>EISSN: 2057-1577</identifier><identifier>DOI: 10.1093/ve/vead060</identifier><language>eng</language><publisher>UK: Oxford University Press</publisher><subject>African swine fever ; Analysis ; Biological diversity ; Care and treatment ; Diagnosis ; Genotype</subject><ispartof>Virus Evolution, 2023-12, Vol.9 (2), p.1-vead060</ispartof><rights>The Author(s) 2023. Published by Oxford University Press. 2023</rights><rights>COPYRIGHT 2023 Oxford University Press</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c487t-1fb25a7d42c037978c81d280f783f64b98dd8162a7160ec8a6cc110e8ca96b7f3</citedby><cites>FETCH-LOGICAL-c487t-1fb25a7d42c037978c81d280f783f64b98dd8162a7160ec8a6cc110e8ca96b7f3</cites><orcidid>0000-0002-4401-8531 ; 0000-0002-6154-4437</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10590196/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10590196/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27903,27904,53769,53771</link.rule.ids></links><search><creatorcontrib>Xin, Genyang</creatorcontrib><creatorcontrib>Kuang, Qiyuan</creatorcontrib><creatorcontrib>Le, Shijia</creatorcontrib><creatorcontrib>Wu, Weichen</creatorcontrib><creatorcontrib>Gao, Qi</creatorcontrib><creatorcontrib>Gao, Han</creatorcontrib><creatorcontrib>Xu, Zhiying</creatorcontrib><creatorcontrib>Zheng, Zezhong</creatorcontrib><creatorcontrib>Lu, Gang</creatorcontrib><creatorcontrib>Gong, Lang</creatorcontrib><creatorcontrib>Wang, Heng</creatorcontrib><creatorcontrib>Zhang, Guihong</creatorcontrib><creatorcontrib>Shi, Mang</creatorcontrib><creatorcontrib>Sun, Yankuo</creatorcontrib><title>Origin, genomic diversity and evolution of African swine fever virus in East Asia</title><title>Virus Evolution</title><description>Abstract
Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620–18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a ‘star-like’ structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.</description><subject>African swine fever</subject><subject>Analysis</subject><subject>Biological diversity</subject><subject>Care and treatment</subject><subject>Diagnosis</subject><subject>Genotype</subject><issn>2057-1577</issn><issn>2057-1577</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNp9kcFKJDEQhhtRUFwvPkEugiyOW-me7qRPMojrCoIXPYdMUhlLepIx6e7Ft5lnmSfb6Ayil6UKKlR9_0-oKopTDpcc2urXiDm1hQb2iqMSajHhtRD7X96HxUlKLwDA60pMeXVUPD5EWpC_YAv0YUmGWRoxJurfmPZ2s8YxdENPwbPgNuuZi2S0Z-kveWQOM8pGikNi5DfrG516NkukfxQHTncJT3b1uHj6ffN4_Wdy_3B7dz27n5ipFP2Eu3lZa2GnpYFKtEIayW0pwQlZuWY6b6W1kjelFrwBNFI3xnAOKI1um7lw1XFxtfVdDfMlWoO-j7pTq0hLHd9U0KS-Tzw9q0UYFYe6Bd422eF85xDD64CpV0tKBrtOewxDUqWUIMuqqSCjl1t0oTtU5F3IliaHxby34NFR7s-EhPZDlQU_twITQ0oR3efHOKj3g6kR1e5gGT7bwmFY_Y_7BylrmYI</recordid><startdate>20231201</startdate><enddate>20231201</enddate><creator>Xin, Genyang</creator><creator>Kuang, Qiyuan</creator><creator>Le, Shijia</creator><creator>Wu, Weichen</creator><creator>Gao, Qi</creator><creator>Gao, Han</creator><creator>Xu, Zhiying</creator><creator>Zheng, Zezhong</creator><creator>Lu, Gang</creator><creator>Gong, Lang</creator><creator>Wang, Heng</creator><creator>Zhang, Guihong</creator><creator>Shi, Mang</creator><creator>Sun, Yankuo</creator><general>Oxford University Press</general><scope>TOX</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IAO</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-4401-8531</orcidid><orcidid>https://orcid.org/0000-0002-6154-4437</orcidid></search><sort><creationdate>20231201</creationdate><title>Origin, genomic diversity and evolution of African swine fever virus in East Asia</title><author>Xin, Genyang ; Kuang, Qiyuan ; Le, Shijia ; Wu, Weichen ; Gao, Qi ; Gao, Han ; Xu, Zhiying ; Zheng, Zezhong ; Lu, Gang ; Gong, Lang ; Wang, Heng ; Zhang, Guihong ; Shi, Mang ; Sun, Yankuo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c487t-1fb25a7d42c037978c81d280f783f64b98dd8162a7160ec8a6cc110e8ca96b7f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>African swine fever</topic><topic>Analysis</topic><topic>Biological diversity</topic><topic>Care and treatment</topic><topic>Diagnosis</topic><topic>Genotype</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Xin, Genyang</creatorcontrib><creatorcontrib>Kuang, Qiyuan</creatorcontrib><creatorcontrib>Le, Shijia</creatorcontrib><creatorcontrib>Wu, Weichen</creatorcontrib><creatorcontrib>Gao, Qi</creatorcontrib><creatorcontrib>Gao, Han</creatorcontrib><creatorcontrib>Xu, Zhiying</creatorcontrib><creatorcontrib>Zheng, Zezhong</creatorcontrib><creatorcontrib>Lu, Gang</creatorcontrib><creatorcontrib>Gong, Lang</creatorcontrib><creatorcontrib>Wang, Heng</creatorcontrib><creatorcontrib>Zhang, Guihong</creatorcontrib><creatorcontrib>Shi, Mang</creatorcontrib><creatorcontrib>Sun, Yankuo</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>CrossRef</collection><collection>Gale Academic OneFile</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Virus Evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xin, Genyang</au><au>Kuang, Qiyuan</au><au>Le, Shijia</au><au>Wu, Weichen</au><au>Gao, Qi</au><au>Gao, Han</au><au>Xu, Zhiying</au><au>Zheng, Zezhong</au><au>Lu, Gang</au><au>Gong, Lang</au><au>Wang, Heng</au><au>Zhang, Guihong</au><au>Shi, Mang</au><au>Sun, Yankuo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Origin, genomic diversity and evolution of African swine fever virus in East Asia</atitle><jtitle>Virus Evolution</jtitle><date>2023-12-01</date><risdate>2023</risdate><volume>9</volume><issue>2</issue><spage>1</spage><epage>vead060</epage><pages>1-vead060</pages><issn>2057-1577</issn><eissn>2057-1577</eissn><abstract>Abstract
Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620–18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a ‘star-like’ structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.</abstract><cop>UK</cop><pub>Oxford University Press</pub><doi>10.1093/ve/vead060</doi><orcidid>https://orcid.org/0000-0002-4401-8531</orcidid><orcidid>https://orcid.org/0000-0002-6154-4437</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | African swine fever Analysis Biological diversity Care and treatment Diagnosis Genotype |
title | Origin, genomic diversity and evolution of African swine fever virus in East Asia |
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