Phylogenetic analysis of human P[8]G9 rotavirus strains circulating in Brazil reveals the presence of a novel genetic variant
Abstract Background Group A rotavirus (RV-A) genotype P[8]G9 has emerged as one of the leading causes of gastroenteritis in children worldwide and currently is recognized as one of the five most common genotypes detected in humans. High intragenotype diversity in G9 RV-A has been observed, and nowad...
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| Veröffentlicht in: | Journal of clinical virology 2010-04, Vol.47 (4), p.345-355 |
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| creator | Tort, Luis Fernando López Volotão, Eduardo de Mello de Mendonça, Marcos César Lima da Silva, Marcelle Figueira Marques Siqueira, Alessandra A Assis, Rosane Maria Santos Moratorio, Gonzalo Cristina, Juan Leite, José Paulo G |
| description | Abstract Background Group A rotavirus (RV-A) genotype P[8]G9 has emerged as one of the leading causes of gastroenteritis in children worldwide and currently is recognized as one of the five most common genotypes detected in humans. High intragenotype diversity in G9 RV-A has been observed, and nowadays, based on the genetic variability of the VP7 gene, six different phylogenetic lineages and eleven sublineages were described. Objectives To study the degree of genetic variation and evolution of Brazilian P[8]G9 RV-A strains. Study design Phylogenetic analysis of 19 P[8]G9 RV-A strains isolated from 2004 to 2007 in five different Brazilian states was conducted using the NSP1, NSP3, NSP5, VP4 and VP7 genes. For the VP4 and VP7 genes, 3D protein structure predictions were generated to analyze the spatial distribution of amino acid substitutions observed in Brazilian strains. Results Based on the phylogenetic analyses, all Brazilian strains clustered within lineage G9-III and P[8]-3 for VP7 and VP4, respectively, and were classified as genotype A1, T1 and H1 for the NSP1, NSP3 and NSP5 genes, respectively. Interestingly, all the strains isolated in Acre State (Northern Brazil) formed a closely related cluster clearly separated from the other Brazilian and prototype strains with regard to the five genes studied. Unique amino acid substitutions were observed in Acre strains in comparison with the prototype and Brazilian strains. Conclusion Inclusion of Acre strains in the phylogenetic analysis revealed the presence of a novel genetic variant and demonstrated a diversification of P[8]G9 rotaviruses in Brazil. |
| doi_str_mv | 10.1016/j.jcv.2009.12.018 |
| format | Article |
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High intragenotype diversity in G9 RV-A has been observed, and nowadays, based on the genetic variability of the VP7 gene, six different phylogenetic lineages and eleven sublineages were described. Objectives To study the degree of genetic variation and evolution of Brazilian P[8]G9 RV-A strains. Study design Phylogenetic analysis of 19 P[8]G9 RV-A strains isolated from 2004 to 2007 in five different Brazilian states was conducted using the NSP1, NSP3, NSP5, VP4 and VP7 genes. For the VP4 and VP7 genes, 3D protein structure predictions were generated to analyze the spatial distribution of amino acid substitutions observed in Brazilian strains. Results Based on the phylogenetic analyses, all Brazilian strains clustered within lineage G9-III and P[8]-3 for VP7 and VP4, respectively, and were classified as genotype A1, T1 and H1 for the NSP1, NSP3 and NSP5 genes, respectively. Interestingly, all the strains isolated in Acre State (Northern Brazil) formed a closely related cluster clearly separated from the other Brazilian and prototype strains with regard to the five genes studied. Unique amino acid substitutions were observed in Acre strains in comparison with the prototype and Brazilian strains. Conclusion Inclusion of Acre strains in the phylogenetic analysis revealed the presence of a novel genetic variant and demonstrated a diversification of P[8]G9 rotaviruses in Brazil.</description><identifier>ISSN: 1386-6532</identifier><identifier>EISSN: 1873-5967</identifier><identifier>DOI: 10.1016/j.jcv.2009.12.018</identifier><identifier>PMID: 20133185</identifier><language>eng</language><publisher>Amsterdam: Elsevier B.V</publisher><subject>Allergy and Immunology ; Amino acid substitution ; Biological and medical sciences ; Brazil ; Child, Preschool ; Cluster Analysis ; Fundamental and applied biological sciences. Psychology ; Genetics ; Genotype ; Genotype PG9 ; Group a rotavirus ; Human viral diseases ; Humans ; Infant ; Infant, Newborn ; Infectious Disease ; Infectious diseases ; Medical sciences ; Microbiology ; Miscellaneous ; Molecular Sequence Data ; Phylogenetic analysis ; Phylogeny ; Polymorphism, Genetic ; RNA, Viral - genetics ; Rotavirus - classification ; Rotavirus - genetics ; Rotavirus - isolation & purification ; Rotavirus A ; Rotavirus Infections - virology ; Sequence Analysis, DNA ; Structural and non-structural genes ; Viral diseases ; Viral Proteins - genetics ; Virology</subject><ispartof>Journal of clinical virology, 2010-04, Vol.47 (4), p.345-355</ispartof><rights>Elsevier B.V.</rights><rights>2010 Elsevier B.V.</rights><rights>2015 INIST-CNRS</rights><rights>Copyright 2010 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c512t-4a3dde1ada709a448d43d8c65d53b9d3151c1af5f32fa9a088fbb770859e7bad3</citedby><cites>FETCH-LOGICAL-c512t-4a3dde1ada709a448d43d8c65d53b9d3151c1af5f32fa9a088fbb770859e7bad3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S1386653210000028$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65534</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22567058$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20133185$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tort, Luis Fernando López</creatorcontrib><creatorcontrib>Volotão, Eduardo de Mello</creatorcontrib><creatorcontrib>de Mendonça, Marcos César Lima</creatorcontrib><creatorcontrib>da Silva, Marcelle Figueira Marques</creatorcontrib><creatorcontrib>Siqueira, Alessandra A</creatorcontrib><creatorcontrib>Assis, Rosane Maria Santos</creatorcontrib><creatorcontrib>Moratorio, Gonzalo</creatorcontrib><creatorcontrib>Cristina, Juan</creatorcontrib><creatorcontrib>Leite, José Paulo G</creatorcontrib><title>Phylogenetic analysis of human P[8]G9 rotavirus strains circulating in Brazil reveals the presence of a novel genetic variant</title><title>Journal of clinical virology</title><addtitle>J Clin Virol</addtitle><description>Abstract Background Group A rotavirus (RV-A) genotype P[8]G9 has emerged as one of the leading causes of gastroenteritis in children worldwide and currently is recognized as one of the five most common genotypes detected in humans. High intragenotype diversity in G9 RV-A has been observed, and nowadays, based on the genetic variability of the VP7 gene, six different phylogenetic lineages and eleven sublineages were described. Objectives To study the degree of genetic variation and evolution of Brazilian P[8]G9 RV-A strains. Study design Phylogenetic analysis of 19 P[8]G9 RV-A strains isolated from 2004 to 2007 in five different Brazilian states was conducted using the NSP1, NSP3, NSP5, VP4 and VP7 genes. For the VP4 and VP7 genes, 3D protein structure predictions were generated to analyze the spatial distribution of amino acid substitutions observed in Brazilian strains. Results Based on the phylogenetic analyses, all Brazilian strains clustered within lineage G9-III and P[8]-3 for VP7 and VP4, respectively, and were classified as genotype A1, T1 and H1 for the NSP1, NSP3 and NSP5 genes, respectively. Interestingly, all the strains isolated in Acre State (Northern Brazil) formed a closely related cluster clearly separated from the other Brazilian and prototype strains with regard to the five genes studied. Unique amino acid substitutions were observed in Acre strains in comparison with the prototype and Brazilian strains. Conclusion Inclusion of Acre strains in the phylogenetic analysis revealed the presence of a novel genetic variant and demonstrated a diversification of P[8]G9 rotaviruses in Brazil.</description><subject>Allergy and Immunology</subject><subject>Amino acid substitution</subject><subject>Biological and medical sciences</subject><subject>Brazil</subject><subject>Child, Preschool</subject><subject>Cluster Analysis</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genetics</subject><subject>Genotype</subject><subject>Genotype PG9</subject><subject>Group a rotavirus</subject><subject>Human viral diseases</subject><subject>Humans</subject><subject>Infant</subject><subject>Infant, Newborn</subject><subject>Infectious Disease</subject><subject>Infectious diseases</subject><subject>Medical sciences</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Molecular Sequence Data</subject><subject>Phylogenetic analysis</subject><subject>Phylogeny</subject><subject>Polymorphism, Genetic</subject><subject>RNA, Viral - genetics</subject><subject>Rotavirus - classification</subject><subject>Rotavirus - genetics</subject><subject>Rotavirus - isolation & purification</subject><subject>Rotavirus A</subject><subject>Rotavirus Infections - virology</subject><subject>Sequence Analysis, DNA</subject><subject>Structural and non-structural genes</subject><subject>Viral diseases</subject><subject>Viral Proteins - genetics</subject><subject>Virology</subject><issn>1386-6532</issn><issn>1873-5967</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkkGLFDEQhRtR3HX1B3iRXMTTjKmk051GEHRxV2HBBfUkEmqS6p2MPekx6W6YBf-7aWZWwYPmkhy-9yq8V0XxFPgSOFQvN8uNnZaC82YJYslB3ytOQddyoZqqvp_fUleLSklxUjxKacM5KFnWD4sTwUFK0Oq0-Hm93nf9DQUavGUYsNsnn1jfsvW4xcCuv-pvlw2L_YCTj2NiaYjoQ2LWRzt2OPhww3xgbyPe-o5Fmgi7xIY1sV2kRMHSbIYs9BN17G7QhNFjGB4XD9qM05PjfVZ8uXj3-fz94urj5YfzN1cLq0AMixKlcwTosOYNlqV2pXTaVsopuWqcBAUWsFWtFC02yLVuV6u65lo1VK_QybPixcF3F_sfI6XBbH2y1HUYqB-TqUvVCC1k9X8y5wY1KJFJOJA29ilFas0u-i3GvQFu5nrMxuR6zFyPAWFyPVnz7Og-rrbkfivu-sjA8yOAyWLXRgzWpz-cUFXN1Wz06sBRTm3yFE2yfg7b-Uh2MK73__zG67_UtvPB54HfaU9p048xL0IyYFIWmE_zHs1rBHw-QstfAC7DrA</recordid><startdate>20100401</startdate><enddate>20100401</enddate><creator>Tort, Luis Fernando López</creator><creator>Volotão, Eduardo de Mello</creator><creator>de Mendonça, Marcos César Lima</creator><creator>da Silva, Marcelle Figueira Marques</creator><creator>Siqueira, Alessandra A</creator><creator>Assis, Rosane Maria Santos</creator><creator>Moratorio, Gonzalo</creator><creator>Cristina, Juan</creator><creator>Leite, José Paulo G</creator><general>Elsevier B.V</general><general>Elsevier</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>7X8</scope><scope>7U9</scope><scope>H94</scope></search><sort><creationdate>20100401</creationdate><title>Phylogenetic analysis of human P[8]G9 rotavirus strains circulating in Brazil reveals the presence of a novel genetic variant</title><author>Tort, Luis Fernando López ; Volotão, Eduardo de Mello ; de Mendonça, Marcos César Lima ; da Silva, Marcelle Figueira Marques ; Siqueira, Alessandra A ; Assis, Rosane Maria Santos ; Moratorio, Gonzalo ; Cristina, Juan ; Leite, José Paulo G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c512t-4a3dde1ada709a448d43d8c65d53b9d3151c1af5f32fa9a088fbb770859e7bad3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Allergy and Immunology</topic><topic>Amino acid substitution</topic><topic>Biological and medical sciences</topic><topic>Brazil</topic><topic>Child, Preschool</topic><topic>Cluster Analysis</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genetics</topic><topic>Genotype</topic><topic>Genotype PG9</topic><topic>Group a rotavirus</topic><topic>Human viral diseases</topic><topic>Humans</topic><topic>Infant</topic><topic>Infant, Newborn</topic><topic>Infectious Disease</topic><topic>Infectious diseases</topic><topic>Medical sciences</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Molecular Sequence Data</topic><topic>Phylogenetic analysis</topic><topic>Phylogeny</topic><topic>Polymorphism, Genetic</topic><topic>RNA, Viral - genetics</topic><topic>Rotavirus - classification</topic><topic>Rotavirus - genetics</topic><topic>Rotavirus - isolation & purification</topic><topic>Rotavirus A</topic><topic>Rotavirus Infections - virology</topic><topic>Sequence Analysis, DNA</topic><topic>Structural and non-structural genes</topic><topic>Viral diseases</topic><topic>Viral Proteins - genetics</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tort, Luis Fernando López</creatorcontrib><creatorcontrib>Volotão, Eduardo de Mello</creatorcontrib><creatorcontrib>de Mendonça, Marcos César Lima</creatorcontrib><creatorcontrib>da Silva, Marcelle Figueira Marques</creatorcontrib><creatorcontrib>Siqueira, Alessandra A</creatorcontrib><creatorcontrib>Assis, Rosane Maria Santos</creatorcontrib><creatorcontrib>Moratorio, Gonzalo</creatorcontrib><creatorcontrib>Cristina, Juan</creatorcontrib><creatorcontrib>Leite, José Paulo G</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>MEDLINE - Academic</collection><collection>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><jtitle>Journal of clinical virology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tort, Luis Fernando López</au><au>Volotão, Eduardo de Mello</au><au>de Mendonça, Marcos César Lima</au><au>da Silva, Marcelle Figueira Marques</au><au>Siqueira, Alessandra A</au><au>Assis, Rosane Maria Santos</au><au>Moratorio, Gonzalo</au><au>Cristina, Juan</au><au>Leite, José Paulo G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phylogenetic analysis of human P[8]G9 rotavirus strains circulating in Brazil reveals the presence of a novel genetic variant</atitle><jtitle>Journal of clinical virology</jtitle><addtitle>J Clin Virol</addtitle><date>2010-04-01</date><risdate>2010</risdate><volume>47</volume><issue>4</issue><spage>345</spage><epage>355</epage><pages>345-355</pages><issn>1386-6532</issn><eissn>1873-5967</eissn><abstract>Abstract Background Group A rotavirus (RV-A) genotype P[8]G9 has emerged as one of the leading causes of gastroenteritis in children worldwide and currently is recognized as one of the five most common genotypes detected in humans. High intragenotype diversity in G9 RV-A has been observed, and nowadays, based on the genetic variability of the VP7 gene, six different phylogenetic lineages and eleven sublineages were described. Objectives To study the degree of genetic variation and evolution of Brazilian P[8]G9 RV-A strains. Study design Phylogenetic analysis of 19 P[8]G9 RV-A strains isolated from 2004 to 2007 in five different Brazilian states was conducted using the NSP1, NSP3, NSP5, VP4 and VP7 genes. For the VP4 and VP7 genes, 3D protein structure predictions were generated to analyze the spatial distribution of amino acid substitutions observed in Brazilian strains. Results Based on the phylogenetic analyses, all Brazilian strains clustered within lineage G9-III and P[8]-3 for VP7 and VP4, respectively, and were classified as genotype A1, T1 and H1 for the NSP1, NSP3 and NSP5 genes, respectively. Interestingly, all the strains isolated in Acre State (Northern Brazil) formed a closely related cluster clearly separated from the other Brazilian and prototype strains with regard to the five genes studied. Unique amino acid substitutions were observed in Acre strains in comparison with the prototype and Brazilian strains. Conclusion Inclusion of Acre strains in the phylogenetic analysis revealed the presence of a novel genetic variant and demonstrated a diversification of P[8]G9 rotaviruses in Brazil.</abstract><cop>Amsterdam</cop><pub>Elsevier B.V</pub><pmid>20133185</pmid><doi>10.1016/j.jcv.2009.12.018</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Allergy and Immunology Amino acid substitution Biological and medical sciences Brazil Child, Preschool Cluster Analysis Fundamental and applied biological sciences. Psychology Genetics Genotype Genotype PG9 Group a rotavirus Human viral diseases Humans Infant Infant, Newborn Infectious Disease Infectious diseases Medical sciences Microbiology Miscellaneous Molecular Sequence Data Phylogenetic analysis Phylogeny Polymorphism, Genetic RNA, Viral - genetics Rotavirus - classification Rotavirus - genetics Rotavirus - isolation & purification Rotavirus A Rotavirus Infections - virology Sequence Analysis, DNA Structural and non-structural genes Viral diseases Viral Proteins - genetics Virology |
| title | Phylogenetic analysis of human P[8]G9 rotavirus strains circulating in Brazil reveals the presence of a novel genetic variant |
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