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Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China
A total of 127 porcine samples were collected from 48 farms in six provinces in south China. The positive rate of porcine epidemic diarrhea virus (PEDV) was 43.0 % (55/127), and the co-infection rate of PEDV and transmissible gastroenteritis virus (TGEV) was 12.0 % (15/127). The partial S gene and c...
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| Published in: | Virus genes 2012-08, Vol.45 (1), p.181-185 |
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| creator | Li, Zhi-Li Zhu, Ling Ma, Jing-Yun Zhou, Qing-Feng Song, Yan-Hua Sun, Bao-Li Chen, Rui-Ai Xie, Qing-Mei Bee, Ying-Zuo |
| description | A total of 127 porcine samples were collected from 48 farms in six provinces in south China. The positive rate of porcine epidemic diarrhea virus (PEDV) was 43.0 % (55/127), and the co-infection rate of PEDV and transmissible gastroenteritis virus (TGEV) was 12.0 % (15/127). The partial S gene and complete M gene were amplified from PEDV-positive strains by RT-PCR, cloned, sequenced and compared with each other, as well as with the reference strains in GenBank. Sequence homology results of the partial S gene and complete M gene showed that all south China field PEDV strains had nucleotide (deduced amino acid) sequence identities of 86.7–98.7 % (83.2–99.3 %) and 96.1–100 % (95.0–100%), respectively, with the foreign reference strains reported in GenBank. Phylogenetic analysis of the partial S gene showed that all the south China PEDV strains and two Thailand strains (08UB01 and 08RB07) belong to the same group and differ genetically from European strains and early domestic strains. Phylogenetic analysis of the complete M gene showed that all south China PEDV strains have a close relationship with most of the strains in Korea and Thailand, but differ genetically from the vaccine strain (CV777). |
| doi_str_mv | 10.1007/s11262-012-0735-8 |
| format | article |
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The positive rate of porcine epidemic diarrhea virus (PEDV) was 43.0 % (55/127), and the co-infection rate of PEDV and transmissible gastroenteritis virus (TGEV) was 12.0 % (15/127). The partial S gene and complete M gene were amplified from PEDV-positive strains by RT-PCR, cloned, sequenced and compared with each other, as well as with the reference strains in GenBank. Sequence homology results of the partial S gene and complete M gene showed that all south China field PEDV strains had nucleotide (deduced amino acid) sequence identities of 86.7–98.7 % (83.2–99.3 %) and 96.1–100 % (95.0–100%), respectively, with the foreign reference strains reported in GenBank. Phylogenetic analysis of the partial S gene showed that all the south China PEDV strains and two Thailand strains (08UB01 and 08RB07) belong to the same group and differ genetically from European strains and early domestic strains. Phylogenetic analysis of the complete M gene showed that all south China PEDV strains have a close relationship with most of the strains in Korea and Thailand, but differ genetically from the vaccine strain (CV777).</description><identifier>ISSN: 0920-8569</identifier><identifier>EISSN: 1572-994X</identifier><identifier>DOI: 10.1007/s11262-012-0735-8</identifier><identifier>PMID: 22528639</identifier><language>eng</language><publisher>Boston: Springer-Verlag</publisher><subject>Amino acid sequence ; Animals ; Biomedical and Life Sciences ; Biomedicine ; China - epidemiology ; Coronavirus Infections - epidemiology ; Coronavirus Infections - veterinary ; Coronavirus Infections - virology ; Farms ; genes ; Homology ; M gene ; Medical Microbiology ; Membrane Glycoproteins - genetics ; Nucleotide sequence ; Phylogeny ; Plant Sciences ; Polymerase chain reaction ; Porcine epidemic diarrhea virus ; Porcine epidemic diarrhea virus - classification ; Porcine epidemic diarrhea virus - genetics ; Porcine epidemic diarrhea virus - isolation & purification ; Reverse Transcriptase Polymerase Chain Reaction ; S gene ; Sequence Analysis, DNA ; sequence homology ; Spike Glycoprotein, Coronavirus ; swine ; Swine - virology ; Swine Diseases - epidemiology ; Swine Diseases - virology ; Transmissible gastroenteritis ; Transmissible gastroenteritis virus ; Vaccines ; Viral Envelope Proteins - genetics ; Viral Matrix Proteins - genetics ; Virology</subject><ispartof>Virus genes, 2012-08, Vol.45 (1), p.181-185</ispartof><rights>Springer Science+Business Media, LLC 2012</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c519t-d4c8259bbad1ebcce1c0ed1d74b4df5f4c53f3d5adf5410c993a47539927a7c83</citedby><cites>FETCH-LOGICAL-c519t-d4c8259bbad1ebcce1c0ed1d74b4df5f4c53f3d5adf5410c993a47539927a7c83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22528639$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Zhi-Li</creatorcontrib><creatorcontrib>Zhu, Ling</creatorcontrib><creatorcontrib>Ma, Jing-Yun</creatorcontrib><creatorcontrib>Zhou, Qing-Feng</creatorcontrib><creatorcontrib>Song, Yan-Hua</creatorcontrib><creatorcontrib>Sun, Bao-Li</creatorcontrib><creatorcontrib>Chen, Rui-Ai</creatorcontrib><creatorcontrib>Xie, Qing-Mei</creatorcontrib><creatorcontrib>Bee, Ying-Zuo</creatorcontrib><title>Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China</title><title>Virus genes</title><addtitle>Virus Genes</addtitle><addtitle>Virus Genes</addtitle><description>A total of 127 porcine samples were collected from 48 farms in six provinces in south China. The positive rate of porcine epidemic diarrhea virus (PEDV) was 43.0 % (55/127), and the co-infection rate of PEDV and transmissible gastroenteritis virus (TGEV) was 12.0 % (15/127). The partial S gene and complete M gene were amplified from PEDV-positive strains by RT-PCR, cloned, sequenced and compared with each other, as well as with the reference strains in GenBank. Sequence homology results of the partial S gene and complete M gene showed that all south China field PEDV strains had nucleotide (deduced amino acid) sequence identities of 86.7–98.7 % (83.2–99.3 %) and 96.1–100 % (95.0–100%), respectively, with the foreign reference strains reported in GenBank. Phylogenetic analysis of the partial S gene showed that all the south China PEDV strains and two Thailand strains (08UB01 and 08RB07) belong to the same group and differ genetically from European strains and early domestic strains. Phylogenetic analysis of the complete M gene showed that all south China PEDV strains have a close relationship with most of the strains in Korea and Thailand, but differ genetically from the vaccine strain (CV777).</description><subject>Amino acid sequence</subject><subject>Animals</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>China - epidemiology</subject><subject>Coronavirus Infections - epidemiology</subject><subject>Coronavirus Infections - veterinary</subject><subject>Coronavirus Infections - virology</subject><subject>Farms</subject><subject>genes</subject><subject>Homology</subject><subject>M gene</subject><subject>Medical Microbiology</subject><subject>Membrane Glycoproteins - genetics</subject><subject>Nucleotide sequence</subject><subject>Phylogeny</subject><subject>Plant Sciences</subject><subject>Polymerase chain reaction</subject><subject>Porcine epidemic diarrhea virus</subject><subject>Porcine epidemic diarrhea virus - classification</subject><subject>Porcine epidemic diarrhea virus - genetics</subject><subject>Porcine epidemic diarrhea virus - isolation & purification</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>S gene</subject><subject>Sequence Analysis, DNA</subject><subject>sequence homology</subject><subject>Spike Glycoprotein, Coronavirus</subject><subject>swine</subject><subject>Swine - virology</subject><subject>Swine Diseases - epidemiology</subject><subject>Swine Diseases - virology</subject><subject>Transmissible gastroenteritis</subject><subject>Transmissible gastroenteritis virus</subject><subject>Vaccines</subject><subject>Viral Envelope Proteins - genetics</subject><subject>Viral Matrix Proteins - genetics</subject><subject>Virology</subject><issn>0920-8569</issn><issn>1572-994X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><recordid>eNqNkt2LFSEYhyWK9rT1B3RTQjfbxZSfo17GafuAjYLa6E4cdc64zNFZnQlO_fN5mC0iKLoQ0fd5fy_4CMBDjJ5hhMTzgjFpSYNwXYLyRt4CG8wFaZRiX26DDVIENZK36gTcK-UKISQlYXfBCSGcyJaqDfj-Lo3eLqPJ0A4mGzv7HL6ZOaQITXRwGg5j2vno52DrhRkPJRSYejilbEP00E_B-X0tumByHryBX0NeCjz7cP7y81PYBz86WOZsQiwwRFjSMg9wO4Ro7oM7vRmLf3Czn4LLV-eftm-ai_ev325fXDSWYzU3jllJuOo647DvrPXYIu-wE6xjruc9s5z21HFTDwwjqxQ1THCqFBFGWElPwdmaO-V0vfgy630o1o-jiT4tRWNEJKK4leJ_UMaEJO0x9ckf6FVacn2hlSKIS8wqhVfK5lRK9r2ectibfKiQPkrUq0RdJeqjRH1MfnSTvHR77351_LRWAbICpZbizuffR_899fHa1JukzS6Hoi8_EoRZ_RaUC4T_SWDBWkJ_ABCbuk4</recordid><startdate>20120801</startdate><enddate>20120801</enddate><creator>Li, Zhi-Li</creator><creator>Zhu, Ling</creator><creator>Ma, Jing-Yun</creator><creator>Zhou, Qing-Feng</creator><creator>Song, Yan-Hua</creator><creator>Sun, Bao-Li</creator><creator>Chen, Rui-Ai</creator><creator>Xie, Qing-Mei</creator><creator>Bee, Ying-Zuo</creator><general>Springer-Verlag</general><general>Springer US</general><general>Springer Nature B.V</general><scope>FBQ</scope><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>3V.</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20120801</creationdate><title>Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China</title><author>Li, Zhi-Li ; Zhu, Ling ; Ma, Jing-Yun ; Zhou, Qing-Feng ; Song, Yan-Hua ; Sun, Bao-Li ; Chen, Rui-Ai ; Xie, Qing-Mei ; Bee, Ying-Zuo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c519t-d4c8259bbad1ebcce1c0ed1d74b4df5f4c53f3d5adf5410c993a47539927a7c83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Amino acid sequence</topic><topic>Animals</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>China - 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Academic</collection><jtitle>Virus genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Zhi-Li</au><au>Zhu, Ling</au><au>Ma, Jing-Yun</au><au>Zhou, Qing-Feng</au><au>Song, Yan-Hua</au><au>Sun, Bao-Li</au><au>Chen, Rui-Ai</au><au>Xie, Qing-Mei</au><au>Bee, Ying-Zuo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China</atitle><jtitle>Virus genes</jtitle><stitle>Virus Genes</stitle><addtitle>Virus Genes</addtitle><date>2012-08-01</date><risdate>2012</risdate><volume>45</volume><issue>1</issue><spage>181</spage><epage>185</epage><pages>181-185</pages><issn>0920-8569</issn><eissn>1572-994X</eissn><notes>http://dx.doi.org/10.1007/s11262-012-0735-8</notes><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><notes>ObjectType-Article-2</notes><notes>ObjectType-Feature-1</notes><abstract>A total of 127 porcine samples were collected from 48 farms in six provinces in south China. The positive rate of porcine epidemic diarrhea virus (PEDV) was 43.0 % (55/127), and the co-infection rate of PEDV and transmissible gastroenteritis virus (TGEV) was 12.0 % (15/127). The partial S gene and complete M gene were amplified from PEDV-positive strains by RT-PCR, cloned, sequenced and compared with each other, as well as with the reference strains in GenBank. Sequence homology results of the partial S gene and complete M gene showed that all south China field PEDV strains had nucleotide (deduced amino acid) sequence identities of 86.7–98.7 % (83.2–99.3 %) and 96.1–100 % (95.0–100%), respectively, with the foreign reference strains reported in GenBank. Phylogenetic analysis of the partial S gene showed that all the south China PEDV strains and two Thailand strains (08UB01 and 08RB07) belong to the same group and differ genetically from European strains and early domestic strains. Phylogenetic analysis of the complete M gene showed that all south China PEDV strains have a close relationship with most of the strains in Korea and Thailand, but differ genetically from the vaccine strain (CV777).</abstract><cop>Boston</cop><pub>Springer-Verlag</pub><pmid>22528639</pmid><doi>10.1007/s11262-012-0735-8</doi><tpages>5</tpages></addata></record> |
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| subjects | Amino acid sequence Animals Biomedical and Life Sciences Biomedicine China - epidemiology Coronavirus Infections - epidemiology Coronavirus Infections - veterinary Coronavirus Infections - virology Farms genes Homology M gene Medical Microbiology Membrane Glycoproteins - genetics Nucleotide sequence Phylogeny Plant Sciences Polymerase chain reaction Porcine epidemic diarrhea virus Porcine epidemic diarrhea virus - classification Porcine epidemic diarrhea virus - genetics Porcine epidemic diarrhea virus - isolation & purification Reverse Transcriptase Polymerase Chain Reaction S gene Sequence Analysis, DNA sequence homology Spike Glycoprotein, Coronavirus swine Swine - virology Swine Diseases - epidemiology Swine Diseases - virology Transmissible gastroenteritis Transmissible gastroenteritis virus Vaccines Viral Envelope Proteins - genetics Viral Matrix Proteins - genetics Virology |
| title | Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China |
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