Comparison of different RT‐qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins
Aims The aim of this study was to compare the performance of four RT‐qPCR assays for the detection of human and bovine group A rotaviruses and to characterize the positive samples by sequence analysis of VP4 and VP7 genes. Methods and Results RNA extracted from eight human rotavirus strains, and a p...
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| Veröffentlicht in: | Journal of applied microbiology 2013-05, Vol.114 (5), p.1435-1448 |
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| creator | Ward, P. Poitras, E. Leblanc, D. Gagnon, C.A. Brassard, J. Houde, A. |
| description | Aims
The aim of this study was to compare the performance of four RT‐qPCR assays for the detection of human and bovine group A rotaviruses and to characterize the positive samples by sequence analysis of VP4 and VP7 genes.
Methods and Results
RNA extracted from eight human rotavirus strains, and a panel of 33 human and 25 bovine faecal samples was subjected to different RT‐qPCR detection systems. Among these assays, only RT‐qPCR primers and probe systems B and C were able to detect all human rotavirus strains from cell culture solutions and faecal samples. However, the results showed that the system C was generally more sensitive by one or two logs than the other RT‐qPCR assays tested. With the bovine faecal samples, the most efficient RT‐qPCR systems were B and A with the detection in 100 and 92% of samples tested, respectively. Human group A rotavirus G1P[8] and bovine G6P[11] were the most frequently used strains identified in this study. A G3P[9] strain, closely related to a feline rotavirus isolated in the USA, was also discovered in a human rotavirus infection.
Conclusion
The RT‐qPCR system B was the only TaqMan assay evaluated in this study able to detect rotavirus RNA in all positive human and bovine faecal samples.
Significance and Impact of the Study
Utilization of only one RT‐qPCR for the detection of human and bovine group A rotaviruses and the possibility of human infection by a feline rotavirus strain. |
| doi_str_mv | 10.1111/jam.12165 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1352284838</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1352284838</sourcerecordid><originalsourceid>FETCH-LOGICAL-c5175-5ca63bc838937efba3c9e47dee93b8789db95ee171a5acbde29da823cf9b6b653</originalsourceid><addsrcrecordid>eNqN0d-K1DAUBvAiiruuXvgCEpAFvZjdJmma9nIY_MuKy7LubTlNT2cytMlsTrsyXvkIvo9v45OY6YwKgmBvUpJfvy_0JMlTnp7x-JyvoT_jgufqXnLMZa5mItfi_vSezVSqxVHyiGidplymKn-YHAmZCa7T4jj5vvD9BoIl75hvWWPbFgO6gV1d__j67fZyccWACLbEWh_YsELW4IBmsHu_GntwDFzDan9nHbJl8OOGzVnwA9zZMBLSdGxWEMAMGOwXmD6ut4zwdkRnJgHdliztIpfo4k7c9411S3ZzmU0BN5eaGdiQbdgmhqN19Dh50EJH-OSwniSfXr-6XrydXXx8824xv5gZxbWaKQO5rE0hi1JqbGuQpsRMN4ilrAtdlE1dKkSuOSgwdYOibKAQ0rRlnde5kifJi31uLI43pqHqLRnsOnDoR6q4VEIUWSz4Dyq0FnlZ7ujzv-jajyH-iKgyyUudKS6ierlXJniigG21CbaHsK14Wu2GX8XhV9Pwo312SBzrHpvf8te0Izg9ACADXRvAGUt_nBaZEFPp-d59th1u_91YvZ9_2Ff_BIuSyQU</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1431974512</pqid></control><display><type>article</type><title>Comparison of different RT‐qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins</title><source>MEDLINE</source><source>Access via Wiley Online Library</source><source>Oxford University Press Journals All Titles (1996-Current)</source><creator>Ward, P. ; Poitras, E. ; Leblanc, D. ; Gagnon, C.A. ; Brassard, J. ; Houde, A.</creator><creatorcontrib>Ward, P. ; Poitras, E. ; Leblanc, D. ; Gagnon, C.A. ; Brassard, J. ; Houde, A.</creatorcontrib><description>Aims
The aim of this study was to compare the performance of four RT‐qPCR assays for the detection of human and bovine group A rotaviruses and to characterize the positive samples by sequence analysis of VP4 and VP7 genes.
Methods and Results
RNA extracted from eight human rotavirus strains, and a panel of 33 human and 25 bovine faecal samples was subjected to different RT‐qPCR detection systems. Among these assays, only RT‐qPCR primers and probe systems B and C were able to detect all human rotavirus strains from cell culture solutions and faecal samples. However, the results showed that the system C was generally more sensitive by one or two logs than the other RT‐qPCR assays tested. With the bovine faecal samples, the most efficient RT‐qPCR systems were B and A with the detection in 100 and 92% of samples tested, respectively. Human group A rotavirus G1P[8] and bovine G6P[11] were the most frequently used strains identified in this study. A G3P[9] strain, closely related to a feline rotavirus isolated in the USA, was also discovered in a human rotavirus infection.
Conclusion
The RT‐qPCR system B was the only TaqMan assay evaluated in this study able to detect rotavirus RNA in all positive human and bovine faecal samples.
Significance and Impact of the Study
Utilization of only one RT‐qPCR for the detection of human and bovine group A rotaviruses and the possibility of human infection by a feline rotavirus strain.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/jam.12165</identifier><identifier>PMID: 23421708</identifier><identifier>CODEN: JAMIFK</identifier><language>eng</language><publisher>Oxford: Blackwell</publisher><subject>Animals ; Antigens, Viral - genetics ; Biological and medical sciences ; Bovine rotavirus ; capsid protein sequences ; Capsid Proteins - genetics ; Cattle ; Cell culture ; Child ; detection ; Diarrhea ; DNA Primers ; Feces - virology ; Fundamental and applied biological sciences. Psychology ; Genotype ; Group a rotavirus ; group A rotaviruses ; Human rotavirus ; Humans ; Microbiology ; phylogenetic analysis ; Phylogeny ; Polymerase chain reaction ; Reverse Transcriptase Polymerase Chain Reaction - methods ; RNA, Viral - isolation & purification ; Rotavirus - classification ; Rotavirus - genetics ; Rotavirus - isolation & purification ; Rotavirus Infections - diagnosis ; Rotavirus Infections - veterinary ; Rotavirus Infections - virology ; RT‐qPCR assays ; Salmonella ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Viruses</subject><ispartof>Journal of applied microbiology, 2013-05, Vol.114 (5), p.1435-1448</ispartof><rights>Her Majesty the Queen in Right of Canada [2013]. Reproduced with the permission of the Minister of Agriculture and Agri‐food Canada.</rights><rights>2014 INIST-CNRS</rights><rights>Her Majesty the Queen in Right of Canada [2013]. Reproduced with the permission of the Minister of Agriculture and Agri-food Canada.</rights><rights>Copyright © 2013 The Society for Applied Microbiology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5175-5ca63bc838937efba3c9e47dee93b8789db95ee171a5acbde29da823cf9b6b653</citedby><cites>FETCH-LOGICAL-c5175-5ca63bc838937efba3c9e47dee93b8789db95ee171a5acbde29da823cf9b6b653</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjam.12165$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjam.12165$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=27242212$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23421708$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ward, P.</creatorcontrib><creatorcontrib>Poitras, E.</creatorcontrib><creatorcontrib>Leblanc, D.</creatorcontrib><creatorcontrib>Gagnon, C.A.</creatorcontrib><creatorcontrib>Brassard, J.</creatorcontrib><creatorcontrib>Houde, A.</creatorcontrib><title>Comparison of different RT‐qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins</title><title>Journal of applied microbiology</title><addtitle>J Appl Microbiol</addtitle><description>Aims
The aim of this study was to compare the performance of four RT‐qPCR assays for the detection of human and bovine group A rotaviruses and to characterize the positive samples by sequence analysis of VP4 and VP7 genes.
Methods and Results
RNA extracted from eight human rotavirus strains, and a panel of 33 human and 25 bovine faecal samples was subjected to different RT‐qPCR detection systems. Among these assays, only RT‐qPCR primers and probe systems B and C were able to detect all human rotavirus strains from cell culture solutions and faecal samples. However, the results showed that the system C was generally more sensitive by one or two logs than the other RT‐qPCR assays tested. With the bovine faecal samples, the most efficient RT‐qPCR systems were B and A with the detection in 100 and 92% of samples tested, respectively. Human group A rotavirus G1P[8] and bovine G6P[11] were the most frequently used strains identified in this study. A G3P[9] strain, closely related to a feline rotavirus isolated in the USA, was also discovered in a human rotavirus infection.
Conclusion
The RT‐qPCR system B was the only TaqMan assay evaluated in this study able to detect rotavirus RNA in all positive human and bovine faecal samples.
Significance and Impact of the Study
Utilization of only one RT‐qPCR for the detection of human and bovine group A rotaviruses and the possibility of human infection by a feline rotavirus strain.</description><subject>Animals</subject><subject>Antigens, Viral - genetics</subject><subject>Biological and medical sciences</subject><subject>Bovine rotavirus</subject><subject>capsid protein sequences</subject><subject>Capsid Proteins - genetics</subject><subject>Cattle</subject><subject>Cell culture</subject><subject>Child</subject><subject>detection</subject><subject>Diarrhea</subject><subject>DNA Primers</subject><subject>Feces - virology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genotype</subject><subject>Group a rotavirus</subject><subject>group A rotaviruses</subject><subject>Human rotavirus</subject><subject>Humans</subject><subject>Microbiology</subject><subject>phylogenetic analysis</subject><subject>Phylogeny</subject><subject>Polymerase chain reaction</subject><subject>Reverse Transcriptase Polymerase Chain Reaction - methods</subject><subject>RNA, Viral - isolation & purification</subject><subject>Rotavirus - classification</subject><subject>Rotavirus - genetics</subject><subject>Rotavirus - isolation & purification</subject><subject>Rotavirus Infections - diagnosis</subject><subject>Rotavirus Infections - veterinary</subject><subject>Rotavirus Infections - virology</subject><subject>RT‐qPCR assays</subject><subject>Salmonella</subject><subject>Sensitivity and Specificity</subject><subject>Sequence Analysis, DNA</subject><subject>Viruses</subject><issn>1364-5072</issn><issn>1365-2672</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqN0d-K1DAUBvAiiruuXvgCEpAFvZjdJmma9nIY_MuKy7LubTlNT2cytMlsTrsyXvkIvo9v45OY6YwKgmBvUpJfvy_0JMlTnp7x-JyvoT_jgufqXnLMZa5mItfi_vSezVSqxVHyiGidplymKn-YHAmZCa7T4jj5vvD9BoIl75hvWWPbFgO6gV1d__j67fZyccWACLbEWh_YsELW4IBmsHu_GntwDFzDan9nHbJl8OOGzVnwA9zZMBLSdGxWEMAMGOwXmD6ut4zwdkRnJgHdliztIpfo4k7c9411S3ZzmU0BN5eaGdiQbdgmhqN19Dh50EJH-OSwniSfXr-6XrydXXx8824xv5gZxbWaKQO5rE0hi1JqbGuQpsRMN4ilrAtdlE1dKkSuOSgwdYOibKAQ0rRlnde5kifJi31uLI43pqHqLRnsOnDoR6q4VEIUWSz4Dyq0FnlZ7ujzv-jajyH-iKgyyUudKS6ierlXJniigG21CbaHsK14Wu2GX8XhV9Pwo312SBzrHpvf8te0Izg9ACADXRvAGUt_nBaZEFPp-d59th1u_91YvZ9_2Ff_BIuSyQU</recordid><startdate>201305</startdate><enddate>201305</enddate><creator>Ward, P.</creator><creator>Poitras, E.</creator><creator>Leblanc, D.</creator><creator>Gagnon, C.A.</creator><creator>Brassard, J.</creator><creator>Houde, A.</creator><general>Blackwell</general><general>Oxford University Press</general><scope>IQODW</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>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7TM</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7U9</scope><scope>H94</scope></search><sort><creationdate>201305</creationdate><title>Comparison of different RT‐qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins</title><author>Ward, P. ; Poitras, E. ; Leblanc, D. ; Gagnon, C.A. ; Brassard, J. ; Houde, A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5175-5ca63bc838937efba3c9e47dee93b8789db95ee171a5acbde29da823cf9b6b653</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Animals</topic><topic>Antigens, Viral - genetics</topic><topic>Biological and medical sciences</topic><topic>Bovine rotavirus</topic><topic>capsid protein sequences</topic><topic>Capsid Proteins - genetics</topic><topic>Cattle</topic><topic>Cell culture</topic><topic>Child</topic><topic>detection</topic><topic>Diarrhea</topic><topic>DNA Primers</topic><topic>Feces - virology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genotype</topic><topic>Group a rotavirus</topic><topic>group A rotaviruses</topic><topic>Human rotavirus</topic><topic>Humans</topic><topic>Microbiology</topic><topic>phylogenetic analysis</topic><topic>Phylogeny</topic><topic>Polymerase chain reaction</topic><topic>Reverse Transcriptase Polymerase Chain Reaction - methods</topic><topic>RNA, Viral - isolation & purification</topic><topic>Rotavirus - classification</topic><topic>Rotavirus - genetics</topic><topic>Rotavirus - isolation & purification</topic><topic>Rotavirus Infections - diagnosis</topic><topic>Rotavirus Infections - veterinary</topic><topic>Rotavirus Infections - virology</topic><topic>RT‐qPCR assays</topic><topic>Salmonella</topic><topic>Sensitivity and Specificity</topic><topic>Sequence Analysis, DNA</topic><topic>Viruses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ward, P.</creatorcontrib><creatorcontrib>Poitras, E.</creatorcontrib><creatorcontrib>Leblanc, D.</creatorcontrib><creatorcontrib>Gagnon, C.A.</creatorcontrib><creatorcontrib>Brassard, J.</creatorcontrib><creatorcontrib>Houde, A.</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><jtitle>Journal of applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ward, P.</au><au>Poitras, E.</au><au>Leblanc, D.</au><au>Gagnon, C.A.</au><au>Brassard, J.</au><au>Houde, A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of different RT‐qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins</atitle><jtitle>Journal of applied microbiology</jtitle><addtitle>J Appl Microbiol</addtitle><date>2013-05</date><risdate>2013</risdate><volume>114</volume><issue>5</issue><spage>1435</spage><epage>1448</epage><pages>1435-1448</pages><issn>1364-5072</issn><eissn>1365-2672</eissn><coden>JAMIFK</coden><abstract>Aims
The aim of this study was to compare the performance of four RT‐qPCR assays for the detection of human and bovine group A rotaviruses and to characterize the positive samples by sequence analysis of VP4 and VP7 genes.
Methods and Results
RNA extracted from eight human rotavirus strains, and a panel of 33 human and 25 bovine faecal samples was subjected to different RT‐qPCR detection systems. Among these assays, only RT‐qPCR primers and probe systems B and C were able to detect all human rotavirus strains from cell culture solutions and faecal samples. However, the results showed that the system C was generally more sensitive by one or two logs than the other RT‐qPCR assays tested. With the bovine faecal samples, the most efficient RT‐qPCR systems were B and A with the detection in 100 and 92% of samples tested, respectively. Human group A rotavirus G1P[8] and bovine G6P[11] were the most frequently used strains identified in this study. A G3P[9] strain, closely related to a feline rotavirus isolated in the USA, was also discovered in a human rotavirus infection.
Conclusion
The RT‐qPCR system B was the only TaqMan assay evaluated in this study able to detect rotavirus RNA in all positive human and bovine faecal samples.
Significance and Impact of the Study
Utilization of only one RT‐qPCR for the detection of human and bovine group A rotaviruses and the possibility of human infection by a feline rotavirus strain.</abstract><cop>Oxford</cop><pub>Blackwell</pub><pmid>23421708</pmid><doi>10.1111/jam.12165</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Access via Wiley Online Library; Oxford University Press Journals All Titles (1996-Current) |
| subjects | Animals Antigens, Viral - genetics Biological and medical sciences Bovine rotavirus capsid protein sequences Capsid Proteins - genetics Cattle Cell culture Child detection Diarrhea DNA Primers Feces - virology Fundamental and applied biological sciences. Psychology Genotype Group a rotavirus group A rotaviruses Human rotavirus Humans Microbiology phylogenetic analysis Phylogeny Polymerase chain reaction Reverse Transcriptase Polymerase Chain Reaction - methods RNA, Viral - isolation & purification Rotavirus - classification Rotavirus - genetics Rotavirus - isolation & purification Rotavirus Infections - diagnosis Rotavirus Infections - veterinary Rotavirus Infections - virology RT‐qPCR assays Salmonella Sensitivity and Specificity Sequence Analysis, DNA Viruses |
| title | Comparison of different RT‐qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins |
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