Molecular-based investigation and genetic characterization of porcine stool-associated RNA virus (posavirus) lineages 1 to 3 in pigs in South Korea from 2017 to 2019
Recent results on the detection and genetic characterization of stool-associated RNA viruses from different species have increased the knowledge about the extreme genetic diversity of picornaviruses. This study aimed to investigate the presence of unclassified porcine stool-associated RNA viruses (p...
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| Veröffentlicht in: | Research in veterinary science 2020-02, Vol.128, p.286-292 |
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| creator | Chung, Hee-Chun Nguyen, Van-Giap Huynh, Thi-My-Le Do, Hai-Quynh Vo, Dinh-Chuong Park, Yong-Ho Park, Bong-Kyun |
| description | Recent results on the detection and genetic characterization of stool-associated RNA viruses from different species have increased the knowledge about the extreme genetic diversity of picornaviruses. This study aimed to investigate the presence of unclassified porcine stool-associated RNA viruses (posaviruses) in South Korea and to elucidate the molecular evolution of the viruses. By RT-PCR, posaviruses 1 and 3 were exclusively found in fecal samples and consistently detected in three consecutive years in six of eight provinces, with 148/697 (21.2%) and 33/84 (39.3%) positive samples and farms, respectively. Every age group but the older age groups (finisher, sow) had significantly higher positive rates of posavirus 1 than posavirus 3. An analysis of the RNA-dependent RNA polymerase sequences by likelihood mapping and maximum-likelihood-based phylogenetic analysis revealed that stool-associated RNA viruses formed four supergroups that were well separated from all recognized families of the order Picornavirales. Five genomes of Korean posaviruses generated in this study were phylogenetically grouped with posavirus 1 and posavirus 3 and were predicted to have the typical genome organization of picornaviruses.
•Posavirus 1 and 3 were detected in fecal samples from different age groups of pigs.•Posavirus 1 and 3 branched apart from the posavirus Ascaris RNA-like and fisavirus.•Posavirus 1 and 3 were predicted to have the genome organization of picornaviruses. |
| doi_str_mv | 10.1016/j.rvsc.2019.11.007 |
| format | Article |
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•Posavirus 1 and 3 were detected in fecal samples from different age groups of pigs.•Posavirus 1 and 3 branched apart from the posavirus Ascaris RNA-like and fisavirus.•Posavirus 1 and 3 were predicted to have the genome organization of picornaviruses.</description><identifier>ISSN: 0034-5288</identifier><identifier>EISSN: 1532-2661</identifier><identifier>DOI: 10.1016/j.rvsc.2019.11.007</identifier><identifier>PMID: 31869594</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Animals ; Biological evolution ; Cloning ; Cobalt ; Design ; Detection ; Digestive system ; DNA-directed RNA polymerase ; Farms ; Feces ; Feces - virology ; Fetuses ; Gene mapping ; Gene sequencing ; Genes, Viral ; Genetic characterization ; Genetic diversity ; Genome, Viral ; Genomes ; Hogs ; Laboratories ; Mapping ; Molecular evolution ; Pathogens ; Phylogenetics ; Phylogeny ; Picornaviridae - classification ; Picornaviridae - genetics ; Picornaviridae - isolation & purification ; Picornaviridae Infections - veterinary ; Polymerase chain reaction ; Posavirus ; Republic of Korea ; Ribonucleic acid ; RNA ; RNA polymerase ; RNA Replicase - genetics ; RNA viruses ; RNA-directed RNA polymerase ; South Korea ; Species diversity ; Swine ; Swine Diseases - virology ; Veterinary colleges ; Veterinary medicine ; Virology ; Viruses</subject><ispartof>Research in veterinary science, 2020-02, Vol.128, p.286-292</ispartof><rights>2019 Elsevier Ltd</rights><rights>Copyright © 2019 Elsevier Ltd. All rights reserved.</rights><rights>2019. Elsevier Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c384t-7a52ed8933f4cbc724d0d6f5c8a20318499d44d8fcdae1ffccdffe6aed6cdff03</citedby><cites>FETCH-LOGICAL-c384t-7a52ed8933f4cbc724d0d6f5c8a20318499d44d8fcdae1ffccdffe6aed6cdff03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0034528819301535$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31869594$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chung, Hee-Chun</creatorcontrib><creatorcontrib>Nguyen, Van-Giap</creatorcontrib><creatorcontrib>Huynh, Thi-My-Le</creatorcontrib><creatorcontrib>Do, Hai-Quynh</creatorcontrib><creatorcontrib>Vo, Dinh-Chuong</creatorcontrib><creatorcontrib>Park, Yong-Ho</creatorcontrib><creatorcontrib>Park, Bong-Kyun</creatorcontrib><title>Molecular-based investigation and genetic characterization of porcine stool-associated RNA virus (posavirus) lineages 1 to 3 in pigs in South Korea from 2017 to 2019</title><title>Research in veterinary science</title><addtitle>Res Vet Sci</addtitle><description>Recent results on the detection and genetic characterization of stool-associated RNA viruses from different species have increased the knowledge about the extreme genetic diversity of picornaviruses. This study aimed to investigate the presence of unclassified porcine stool-associated RNA viruses (posaviruses) in South Korea and to elucidate the molecular evolution of the viruses. By RT-PCR, posaviruses 1 and 3 were exclusively found in fecal samples and consistently detected in three consecutive years in six of eight provinces, with 148/697 (21.2%) and 33/84 (39.3%) positive samples and farms, respectively. Every age group but the older age groups (finisher, sow) had significantly higher positive rates of posavirus 1 than posavirus 3. An analysis of the RNA-dependent RNA polymerase sequences by likelihood mapping and maximum-likelihood-based phylogenetic analysis revealed that stool-associated RNA viruses formed four supergroups that were well separated from all recognized families of the order Picornavirales. Five genomes of Korean posaviruses generated in this study were phylogenetically grouped with posavirus 1 and posavirus 3 and were predicted to have the typical genome organization of picornaviruses.
•Posavirus 1 and 3 were detected in fecal samples from different age groups of pigs.•Posavirus 1 and 3 branched apart from the posavirus Ascaris RNA-like and fisavirus.•Posavirus 1 and 3 were predicted to have the genome organization of picornaviruses.</description><subject>Animals</subject><subject>Biological evolution</subject><subject>Cloning</subject><subject>Cobalt</subject><subject>Design</subject><subject>Detection</subject><subject>Digestive system</subject><subject>DNA-directed RNA polymerase</subject><subject>Farms</subject><subject>Feces</subject><subject>Feces - virology</subject><subject>Fetuses</subject><subject>Gene mapping</subject><subject>Gene sequencing</subject><subject>Genes, Viral</subject><subject>Genetic characterization</subject><subject>Genetic diversity</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>Hogs</subject><subject>Laboratories</subject><subject>Mapping</subject><subject>Molecular evolution</subject><subject>Pathogens</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Picornaviridae - classification</subject><subject>Picornaviridae - genetics</subject><subject>Picornaviridae - isolation & purification</subject><subject>Picornaviridae Infections - veterinary</subject><subject>Polymerase chain reaction</subject><subject>Posavirus</subject><subject>Republic of Korea</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA polymerase</subject><subject>RNA Replicase - genetics</subject><subject>RNA viruses</subject><subject>RNA-directed RNA polymerase</subject><subject>South Korea</subject><subject>Species diversity</subject><subject>Swine</subject><subject>Swine Diseases - virology</subject><subject>Veterinary colleges</subject><subject>Veterinary medicine</subject><subject>Virology</subject><subject>Viruses</subject><issn>0034-5288</issn><issn>1532-2661</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kctuFDEQRS0EIkPgB1ggS2zCohu_-iWxiSJeIoDEY215yuWJRz3txnaPBP_Df-JmAgsWrKokn7quW5eQx5zVnPH2-b6OxwS1YHyoOa8Z6-6QDW-kqETb8rtkw5hUVSP6_ow8SGnPGFOcd_fJmeR9OzSD2pCf78OIsIwmVluT0FI_HTFlvzPZh4maydIdTpg9ULgx0UDG6H-cHoOjc4jgJ6QphzBWJqUA3uQi8-nDJT36uCR6MYdkfrfP6FhYs8NEOc2ByvIZnf0urfVzWPINfRciGupiONBiq1up1d5Dcs-ZMeGj23pOvr56-eXqTXX98fXbq8vrCmSvctWZRqDtBymdgi10QllmW9dAbwQrntUwWKVs78Aa5M4BWOewNWjbtWPynFycdOcYvi3lDvrgE-A4mgnDkrSQkknRl7MW9Ok_6D4scSrbrZQcWMPaoVDiREEMKUV0eo7-YOJ3zZleQ9R7vYaoV5eac11CLENPbqWX7QHt35E_qRXgxQnAcoujx6gTeJwArY8IWdvg_6f_C02Lr5E</recordid><startdate>202002</startdate><enddate>202002</enddate><creator>Chung, Hee-Chun</creator><creator>Nguyen, Van-Giap</creator><creator>Huynh, Thi-My-Le</creator><creator>Do, Hai-Quynh</creator><creator>Vo, Dinh-Chuong</creator><creator>Park, Yong-Ho</creator><creator>Park, Bong-Kyun</creator><general>Elsevier Ltd</general><general>Elsevier Limited</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QP</scope><scope>7QR</scope><scope>7T5</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U7</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>202002</creationdate><title>Molecular-based investigation and genetic characterization of porcine stool-associated RNA virus (posavirus) lineages 1 to 3 in pigs in South Korea from 2017 to 2019</title><author>Chung, Hee-Chun ; Nguyen, Van-Giap ; Huynh, Thi-My-Le ; Do, Hai-Quynh ; Vo, Dinh-Chuong ; Park, Yong-Ho ; Park, Bong-Kyun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c384t-7a52ed8933f4cbc724d0d6f5c8a20318499d44d8fcdae1ffccdffe6aed6cdff03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Animals</topic><topic>Biological evolution</topic><topic>Cloning</topic><topic>Cobalt</topic><topic>Design</topic><topic>Detection</topic><topic>Digestive system</topic><topic>DNA-directed RNA polymerase</topic><topic>Farms</topic><topic>Feces</topic><topic>Feces - virology</topic><topic>Fetuses</topic><topic>Gene mapping</topic><topic>Gene sequencing</topic><topic>Genes, Viral</topic><topic>Genetic characterization</topic><topic>Genetic diversity</topic><topic>Genome, Viral</topic><topic>Genomes</topic><topic>Hogs</topic><topic>Laboratories</topic><topic>Mapping</topic><topic>Molecular evolution</topic><topic>Pathogens</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Picornaviridae - classification</topic><topic>Picornaviridae - genetics</topic><topic>Picornaviridae - isolation & purification</topic><topic>Picornaviridae Infections - veterinary</topic><topic>Polymerase chain reaction</topic><topic>Posavirus</topic><topic>Republic of Korea</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA polymerase</topic><topic>RNA Replicase - genetics</topic><topic>RNA viruses</topic><topic>RNA-directed RNA polymerase</topic><topic>South Korea</topic><topic>Species diversity</topic><topic>Swine</topic><topic>Swine Diseases - virology</topic><topic>Veterinary colleges</topic><topic>Veterinary medicine</topic><topic>Virology</topic><topic>Viruses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chung, Hee-Chun</creatorcontrib><creatorcontrib>Nguyen, Van-Giap</creatorcontrib><creatorcontrib>Huynh, Thi-My-Le</creatorcontrib><creatorcontrib>Do, Hai-Quynh</creatorcontrib><creatorcontrib>Vo, Dinh-Chuong</creatorcontrib><creatorcontrib>Park, Yong-Ho</creatorcontrib><creatorcontrib>Park, Bong-Kyun</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Animal Behavior Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Immunology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Research in veterinary science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chung, Hee-Chun</au><au>Nguyen, Van-Giap</au><au>Huynh, Thi-My-Le</au><au>Do, Hai-Quynh</au><au>Vo, Dinh-Chuong</au><au>Park, Yong-Ho</au><au>Park, Bong-Kyun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Molecular-based investigation and genetic characterization of porcine stool-associated RNA virus (posavirus) lineages 1 to 3 in pigs in South Korea from 2017 to 2019</atitle><jtitle>Research in veterinary science</jtitle><addtitle>Res Vet Sci</addtitle><date>2020-02</date><risdate>2020</risdate><volume>128</volume><spage>286</spage><epage>292</epage><pages>286-292</pages><issn>0034-5288</issn><eissn>1532-2661</eissn><abstract>Recent results on the detection and genetic characterization of stool-associated RNA viruses from different species have increased the knowledge about the extreme genetic diversity of picornaviruses. This study aimed to investigate the presence of unclassified porcine stool-associated RNA viruses (posaviruses) in South Korea and to elucidate the molecular evolution of the viruses. By RT-PCR, posaviruses 1 and 3 were exclusively found in fecal samples and consistently detected in three consecutive years in six of eight provinces, with 148/697 (21.2%) and 33/84 (39.3%) positive samples and farms, respectively. Every age group but the older age groups (finisher, sow) had significantly higher positive rates of posavirus 1 than posavirus 3. An analysis of the RNA-dependent RNA polymerase sequences by likelihood mapping and maximum-likelihood-based phylogenetic analysis revealed that stool-associated RNA viruses formed four supergroups that were well separated from all recognized families of the order Picornavirales. Five genomes of Korean posaviruses generated in this study were phylogenetically grouped with posavirus 1 and posavirus 3 and were predicted to have the typical genome organization of picornaviruses.
•Posavirus 1 and 3 were detected in fecal samples from different age groups of pigs.•Posavirus 1 and 3 branched apart from the posavirus Ascaris RNA-like and fisavirus.•Posavirus 1 and 3 were predicted to have the genome organization of picornaviruses.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>31869594</pmid><doi>10.1016/j.rvsc.2019.11.007</doi><tpages>7</tpages></addata></record> |
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| subjects | Animals Biological evolution Cloning Cobalt Design Detection Digestive system DNA-directed RNA polymerase Farms Feces Feces - virology Fetuses Gene mapping Gene sequencing Genes, Viral Genetic characterization Genetic diversity Genome, Viral Genomes Hogs Laboratories Mapping Molecular evolution Pathogens Phylogenetics Phylogeny Picornaviridae - classification Picornaviridae - genetics Picornaviridae - isolation & purification Picornaviridae Infections - veterinary Polymerase chain reaction Posavirus Republic of Korea Ribonucleic acid RNA RNA polymerase RNA Replicase - genetics RNA viruses RNA-directed RNA polymerase South Korea Species diversity Swine Swine Diseases - virology Veterinary colleges Veterinary medicine Virology Viruses |
| title | Molecular-based investigation and genetic characterization of porcine stool-associated RNA virus (posavirus) lineages 1 to 3 in pigs in South Korea from 2017 to 2019 |
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