Analysis of amino acid variation in the P2 domain of the GII-4 norovirus VP1 protein reveals putative variant-specific epitopes
Human noroviruses are a highly diverse group of viruses classified into three of the five currently recognised Norovirus genogroups, and contain numerous genotypes or genetic clusters. Noroviruses are the major aetiological agent of endemic gastroenteritis in all age groups, as well as the cause of...
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| description | Human noroviruses are a highly diverse group of viruses classified into three of the five currently recognised Norovirus genogroups, and contain numerous genotypes or genetic clusters. Noroviruses are the major aetiological agent of endemic gastroenteritis in all age groups, as well as the cause of periodic epidemic gastroenteritis. The noroviruses most commonly associated with outbreaks of gastroenteritis are genogroup II genotype 4 (GII-4) strains. The relationship between genotypes of noroviruses with their phenotypes and antigenic profile remains poorly understood through an inability to culture these viruses and the lack of a suitable animal model.
Here we describe a study of the diversity of amino acid sequences of the highly variable P2 region in the major capsid protein, VP1, of the GII-4 human noroviruses strains using sequence analysis and homology modelling techniques.
Our data identifies two sites in this region, which show significant amino acid substitutions associated with the appearance of variant strains responsible for epidemics with major public health impact. Homology modelling studies revealed the exposed nature of these sites on the capsid surface, providing supportive structural data that these two sites are likely to be associated with putative variant-specific epitopes. Furthermore, the patterns in the evolution of these viruses at these sites suggests that noroviruses follow a neutral network pattern of evolution. |
| doi_str_mv | 10.1371/journal.pone.0001485 |
| format | Article |
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Here we describe a study of the diversity of amino acid sequences of the highly variable P2 region in the major capsid protein, VP1, of the GII-4 human noroviruses strains using sequence analysis and homology modelling techniques.
Our data identifies two sites in this region, which show significant amino acid substitutions associated with the appearance of variant strains responsible for epidemics with major public health impact. Homology modelling studies revealed the exposed nature of these sites on the capsid surface, providing supportive structural data that these two sites are likely to be associated with putative variant-specific epitopes. Furthermore, the patterns in the evolution of these viruses at these sites suggests that noroviruses follow a neutral network pattern of evolution.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0001485</identifier><identifier>PMID: 18213393</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acids ; Amino Acid Sequence ; Amino Acid Substitution ; Amino acids ; Analysis ; Antigenic determinants ; Antigens ; Base Sequence ; Biosynthesis ; Blood groups ; Capsid protein ; Capsid Proteins - chemistry ; Disease ; DNA Primers ; Epidemics ; Epitopes ; Epitopes - chemistry ; Evolution ; Gastroenteritis ; Genotypes ; Homology ; Infections ; Influenza ; Modelling ; Molecular Sequence Data ; Mutation ; Norovirus - chemistry ; Outbreaks ; Polymerase Chain Reaction ; Proteins ; Public health ; Sequence Homology, Amino Acid ; Strains (organisms) ; Thermal cycling ; Viral proteins ; Virology ; Virology/Virus Evolution and Symbiosis ; Viruses ; VP1 protein ; Winter</subject><ispartof>PloS one, 2008-01, Vol.3 (1), p.e1485</ispartof><rights>COPYRIGHT 2008 Public Library of Science</rights><rights>2008 Allen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Allen et al. 2008</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c728t-c095d175995ad4859d4187920f3ea589adc683c16474488206288e4e4f344bcb3</citedby><cites>FETCH-LOGICAL-c728t-c095d175995ad4859d4187920f3ea589adc683c16474488206288e4e4f344bcb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2194622/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2194622/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18213393$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Allen, David J</creatorcontrib><creatorcontrib>Gray, Jim J</creatorcontrib><creatorcontrib>Gallimore, Chris I</creatorcontrib><creatorcontrib>Xerry, Jacqueline</creatorcontrib><creatorcontrib>Iturriza-Gómara, Miren</creatorcontrib><title>Analysis of amino acid variation in the P2 domain of the GII-4 norovirus VP1 protein reveals putative variant-specific epitopes</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Human noroviruses are a highly diverse group of viruses classified into three of the five currently recognised Norovirus genogroups, and contain numerous genotypes or genetic clusters. Noroviruses are the major aetiological agent of endemic gastroenteritis in all age groups, as well as the cause of periodic epidemic gastroenteritis. The noroviruses most commonly associated with outbreaks of gastroenteritis are genogroup II genotype 4 (GII-4) strains. The relationship between genotypes of noroviruses with their phenotypes and antigenic profile remains poorly understood through an inability to culture these viruses and the lack of a suitable animal model.
Here we describe a study of the diversity of amino acid sequences of the highly variable P2 region in the major capsid protein, VP1, of the GII-4 human noroviruses strains using sequence analysis and homology modelling techniques.
Our data identifies two sites in this region, which show significant amino acid substitutions associated with the appearance of variant strains responsible for epidemics with major public health impact. Homology modelling studies revealed the exposed nature of these sites on the capsid surface, providing supportive structural data that these two sites are likely to be associated with putative variant-specific epitopes. Furthermore, the patterns in the evolution of these viruses at these sites suggests that noroviruses follow a neutral network pattern of evolution.</description><subject>Acids</subject><subject>Amino Acid Sequence</subject><subject>Amino Acid Substitution</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Antigenic determinants</subject><subject>Antigens</subject><subject>Base Sequence</subject><subject>Biosynthesis</subject><subject>Blood groups</subject><subject>Capsid protein</subject><subject>Capsid Proteins - chemistry</subject><subject>Disease</subject><subject>DNA Primers</subject><subject>Epidemics</subject><subject>Epitopes</subject><subject>Epitopes - chemistry</subject><subject>Evolution</subject><subject>Gastroenteritis</subject><subject>Genotypes</subject><subject>Homology</subject><subject>Infections</subject><subject>Influenza</subject><subject>Modelling</subject><subject>Molecular Sequence Data</subject><subject>Mutation</subject><subject>Norovirus - chemistry</subject><subject>Outbreaks</subject><subject>Polymerase Chain Reaction</subject><subject>Proteins</subject><subject>Public health</subject><subject>Sequence Homology, Amino Acid</subject><subject>Strains (organisms)</subject><subject>Thermal cycling</subject><subject>Viral proteins</subject><subject>Virology</subject><subject>Virology/Virus Evolution and Symbiosis</subject><subject>Viruses</subject><subject>VP1 protein</subject><subject>Winter</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNkluLEzEYhgdR3HX1H4gGBMGLqTlNDjdCWXQtLOziYW9DmmTalOlkTDLFvfKvm9pR2wtBcpHJl-d9k3zzVtVzBGeIcPR2E8bY6242hN7NIISIiuZBdY4kwTXDkDw8-j6rnqS0gbAhgrHH1RkSGBEiyXn1Y1487pNPILRAb30fgDbegp2OXmcfeuB7kNcO3GJgw1aXVQH3havFoqagDzHsfBwTuLtFYIghu4JEt3O6S2AYczHZuYNdn-s0OONbb4AbfA6DS0-rR20h3bNpvqi-fnj_5fJjfX1ztbicX9eGY5FrA2VjEW-kbLQtD5WWIsElhi1xuhFSW8MEMYhRTqkQGDIshKOOtoTSpVmSi-rlwXfoQlJT75JCBGEkypCFWBwIG_RGDdFvdbxXQXv1qxDiSumYvemckkXEOCLYYEwbqkVDreGEEW6IMJYXr3fTaeNy66xxfY66OzE93en9Wq3CTmEkKcO4GLyaDGL4NrqU_3Hl2YFa6XIr37ehmJkyrNt6U3LR-lKfU44ZawhnRfDmRFCY7L7nlR5TUovPn_6fvbk7ZV8fsevy7_M6hW7cByidgvQAmhhSiq790xME1T7Wv9-p9rFWU6yL7MVxP_-KphyTn_cc8jU</recordid><startdate>20080123</startdate><enddate>20080123</enddate><creator>Allen, David J</creator><creator>Gray, Jim J</creator><creator>Gallimore, Chris I</creator><creator>Xerry, Jacqueline</creator><creator>Iturriza-Gómara, Miren</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</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>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20080123</creationdate><title>Analysis of amino acid variation in the P2 domain of the GII-4 norovirus VP1 protein reveals putative variant-specific epitopes</title><author>Allen, David J ; Gray, Jim J ; Gallimore, Chris I ; Xerry, Jacqueline ; Iturriza-Gómara, Miren</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c728t-c095d175995ad4859d4187920f3ea589adc683c16474488206288e4e4f344bcb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Acids</topic><topic>Amino Acid Sequence</topic><topic>Amino Acid Substitution</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Antigenic determinants</topic><topic>Antigens</topic><topic>Base Sequence</topic><topic>Biosynthesis</topic><topic>Blood groups</topic><topic>Capsid protein</topic><topic>Capsid Proteins - 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Noroviruses are the major aetiological agent of endemic gastroenteritis in all age groups, as well as the cause of periodic epidemic gastroenteritis. The noroviruses most commonly associated with outbreaks of gastroenteritis are genogroup II genotype 4 (GII-4) strains. The relationship between genotypes of noroviruses with their phenotypes and antigenic profile remains poorly understood through an inability to culture these viruses and the lack of a suitable animal model.
Here we describe a study of the diversity of amino acid sequences of the highly variable P2 region in the major capsid protein, VP1, of the GII-4 human noroviruses strains using sequence analysis and homology modelling techniques.
Our data identifies two sites in this region, which show significant amino acid substitutions associated with the appearance of variant strains responsible for epidemics with major public health impact. Homology modelling studies revealed the exposed nature of these sites on the capsid surface, providing supportive structural data that these two sites are likely to be associated with putative variant-specific epitopes. Furthermore, the patterns in the evolution of these viruses at these sites suggests that noroviruses follow a neutral network pattern of evolution.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>18213393</pmid><doi>10.1371/journal.pone.0001485</doi><tpages>e1485</tpages><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry; EZB Electronic Journals Library |
| subjects | Acids Amino Acid Sequence Amino Acid Substitution Amino acids Analysis Antigenic determinants Antigens Base Sequence Biosynthesis Blood groups Capsid protein Capsid Proteins - chemistry Disease DNA Primers Epidemics Epitopes Epitopes - chemistry Evolution Gastroenteritis Genotypes Homology Infections Influenza Modelling Molecular Sequence Data Mutation Norovirus - chemistry Outbreaks Polymerase Chain Reaction Proteins Public health Sequence Homology, Amino Acid Strains (organisms) Thermal cycling Viral proteins Virology Virology/Virus Evolution and Symbiosis Viruses VP1 protein Winter |
| title | Analysis of amino acid variation in the P2 domain of the GII-4 norovirus VP1 protein reveals putative variant-specific epitopes |
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