Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil

Detalhes bibliográficos
Ano de defesa: 2015
Autor(a) principal: Chamorro, Claudia Carranza
Orientador(a): Não Informado pela instituição
Banca de defesa: Não Informado pela instituição
Tipo de documento: Dissertação
Tipo de acesso: Acesso aberto
Idioma: eng
Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
Programa de Pós-Graduação: Não Informado pela instituição
Departamento: Não Informado pela instituição
País: Não Informado pela instituição
Palavras-chave em Português:
Link de acesso: http://www.teses.usp.br/teses/disponiveis/10/10134/tde-04032016-154921/
Resumo: Infectious bronchitis virus (IBV) is the causative agent of an economically important disease of poultry. In Brazil this disease causes respiratory, renal and reproductive problems in birds of all ages, despite constant vaccination with the Massachusetts strain H120. This lack of immunological protection is known to be due the genetic variation in the spike glycoprotein of IBV, which is involved in host cell attachment, neutralization and the induction of protective immunity. Brazilian IBV variants resulting of this genetic variation are present since the 80s and this study aimed to epidemiologicaly analyze and molecularly characterize the existing variants during 2010-2015 and perform a bioinformatics analysis of the available sequences of IBV variants in a 40 year period. Of the 453 samples tested, 61.4% were positive for IBV and 75.9% of them were considered variants and were detected in birds of all ages, distributed in all five Brazilian regions. A fragment of 559-566 bp was obtained from 12 isolates, where BR-I was the predominant variant while only one isolate belonged to the BR-II genotype. Bioinformatics analysis of the sequences of 40 years of Brazilian IBV variants was performed and the ratio of non-synonymous substitutions per non-synonymous site (dn) to synonymous substitutions per synonymous site (ds) dN/dS was calculated. It revealed a predominance of codons with non-synonymous substitutions in the first third of the S1 gene and a dN/dS ratio of 0.6757, indicating that this portion of the gene was under negative selection. Additionally prediction of N-glycosilation sites showed that most of the BR-I variants (from 2003 to early 2014) present an extra site at animoacid position 20, while the newest ones lack this feature.Together these results suggest that IBV Brazilian variants had probably suffered drastic mutations in some points between the years 1983 to 2003 and after achieving an antigenic structure effective enough for invasion and replication in their hosts, the selection processes became silent.
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spelling Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in BrazilDiversidade genética do vírus da bronquite infecciosa isolado de aves de produção no BrasilBR-IBR-IBR-IIBR-IIdN/dSdN/dSGlicoproteína da espículan-glicosilaçãon-glycosilationSpike glycoproteinInfectious bronchitis virus (IBV) is the causative agent of an economically important disease of poultry. In Brazil this disease causes respiratory, renal and reproductive problems in birds of all ages, despite constant vaccination with the Massachusetts strain H120. This lack of immunological protection is known to be due the genetic variation in the spike glycoprotein of IBV, which is involved in host cell attachment, neutralization and the induction of protective immunity. Brazilian IBV variants resulting of this genetic variation are present since the 80s and this study aimed to epidemiologicaly analyze and molecularly characterize the existing variants during 2010-2015 and perform a bioinformatics analysis of the available sequences of IBV variants in a 40 year period. Of the 453 samples tested, 61.4% were positive for IBV and 75.9% of them were considered variants and were detected in birds of all ages, distributed in all five Brazilian regions. A fragment of 559-566 bp was obtained from 12 isolates, where BR-I was the predominant variant while only one isolate belonged to the BR-II genotype. Bioinformatics analysis of the sequences of 40 years of Brazilian IBV variants was performed and the ratio of non-synonymous substitutions per non-synonymous site (dn) to synonymous substitutions per synonymous site (ds) dN/dS was calculated. It revealed a predominance of codons with non-synonymous substitutions in the first third of the S1 gene and a dN/dS ratio of 0.6757, indicating that this portion of the gene was under negative selection. Additionally prediction of N-glycosilation sites showed that most of the BR-I variants (from 2003 to early 2014) present an extra site at animoacid position 20, while the newest ones lack this feature.Together these results suggest that IBV Brazilian variants had probably suffered drastic mutations in some points between the years 1983 to 2003 and after achieving an antigenic structure effective enough for invasion and replication in their hosts, the selection processes became silent.O vírus da bronquite infecciosa das galinhas (IBV) é o agente causador de uma doença aviária economicamente importante. No Brasil, esta doença ocasiona problemas respiratórios, renais e reprodutivos em aves de todas as idades, apesar da vacinação constante com a cepa Massachusetts H120. Esta falha na proteção conferida pela vacina é ocasionada por mutações nos nucleotídeos do gene da glicoproteína da espícula, a qual está envolvida no processo de interação comas células do hospedeiro, a neutralização e a indução de imunidade protetora. As variantes brasileiras resultantes dessa mutação genética estão presentes desde os anos 80 e este estudo teve como objetivo analisar epidemiologicamente e caracterizar molecularmente os vírus variantes existentes durante 2010-2015 e realizar uma análise bioinformática das sequências disponíveis no GenBank em um período de 40 anos. Das 453 amostras analisadas, 61,4% foram positivas para IBV e 75,9% delas foram consideradas variantes e foram detectados em aves de todas as idades, distribuídos em todas as 5 regiões do Brasil. Um fragmento de 559-566 pb foi obtido a partir de 12 isolados, onde BR-I foi a variante predominante ao contrario que apenas um isolado pertencia ao genótipo BR-II. Análise bioinformática de 40 anos de variantes do IBV brasileiros revelou uma predominância de codões com as substituições não sinónimos no primeiro terço do gene S1 e uma relação dN / dS de 0,6757, indicando que esta porção do gene estava sob selecção negativa. Além disso a previsão de pontos de de N-glicosilação mostrou que a maioria das amostras variantes BR-I (entre o 2003 e início de 2014) apresentam um ponto adicional na posição 20, enquanto as variantes mais novas não apresentam esse ponto de nglicosilação. Estes resultados sugerem que as variantes brasileiras teriam sofrido mutações provavelmente drásticas em alguns pontos do genoma, entre os anos de 1983 a 2003 e depois de atingir uma estrutura antigênica eficaz o suficiente para a invasão e replicação em seus hospedeiros, o processo de seleção mudou para seleção negativa.Biblioteca Digitais de Teses e Dissertações da USPFerreira, Antônio José PiantinoChamorro, Claudia Carranza2015-12-10info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://www.teses.usp.br/teses/disponiveis/10/10134/tde-04032016-154921/reponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USPLiberar o conteúdo para acesso público.info:eu-repo/semantics/openAccesseng2024-10-09T13:16:04Zoai:teses.usp.br:tde-04032016-154921Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212024-10-09T13:16:04Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false
dc.title.none.fl_str_mv Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil
Diversidade genética do vírus da bronquite infecciosa isolado de aves de produção no Brasil
title Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil
spellingShingle Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil
Chamorro, Claudia Carranza
BR-I
BR-I
BR-II
BR-II
dN/dS
dN/dS
Glicoproteína da espícula
n-glicosilação
n-glycosilation
Spike glycoprotein
title_short Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil
title_full Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil
title_fullStr Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil
title_full_unstemmed Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil
title_sort Genetic diversity of avian coronavirus infectious bronchitis detected from commercial poultry in Brazil
author Chamorro, Claudia Carranza
author_facet Chamorro, Claudia Carranza
author_role author
dc.contributor.none.fl_str_mv Ferreira, Antônio José Piantino
dc.contributor.author.fl_str_mv Chamorro, Claudia Carranza
dc.subject.por.fl_str_mv BR-I
BR-I
BR-II
BR-II
dN/dS
dN/dS
Glicoproteína da espícula
n-glicosilação
n-glycosilation
Spike glycoprotein
topic BR-I
BR-I
BR-II
BR-II
dN/dS
dN/dS
Glicoproteína da espícula
n-glicosilação
n-glycosilation
Spike glycoprotein
description Infectious bronchitis virus (IBV) is the causative agent of an economically important disease of poultry. In Brazil this disease causes respiratory, renal and reproductive problems in birds of all ages, despite constant vaccination with the Massachusetts strain H120. This lack of immunological protection is known to be due the genetic variation in the spike glycoprotein of IBV, which is involved in host cell attachment, neutralization and the induction of protective immunity. Brazilian IBV variants resulting of this genetic variation are present since the 80s and this study aimed to epidemiologicaly analyze and molecularly characterize the existing variants during 2010-2015 and perform a bioinformatics analysis of the available sequences of IBV variants in a 40 year period. Of the 453 samples tested, 61.4% were positive for IBV and 75.9% of them were considered variants and were detected in birds of all ages, distributed in all five Brazilian regions. A fragment of 559-566 bp was obtained from 12 isolates, where BR-I was the predominant variant while only one isolate belonged to the BR-II genotype. Bioinformatics analysis of the sequences of 40 years of Brazilian IBV variants was performed and the ratio of non-synonymous substitutions per non-synonymous site (dn) to synonymous substitutions per synonymous site (ds) dN/dS was calculated. It revealed a predominance of codons with non-synonymous substitutions in the first third of the S1 gene and a dN/dS ratio of 0.6757, indicating that this portion of the gene was under negative selection. Additionally prediction of N-glycosilation sites showed that most of the BR-I variants (from 2003 to early 2014) present an extra site at animoacid position 20, while the newest ones lack this feature.Together these results suggest that IBV Brazilian variants had probably suffered drastic mutations in some points between the years 1983 to 2003 and after achieving an antigenic structure effective enough for invasion and replication in their hosts, the selection processes became silent.
publishDate 2015
dc.date.none.fl_str_mv 2015-12-10
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://www.teses.usp.br/teses/disponiveis/10/10134/tde-04032016-154921/
url http://www.teses.usp.br/teses/disponiveis/10/10134/tde-04032016-154921/
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv
dc.rights.driver.fl_str_mv Liberar o conteúdo para acesso público.
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Liberar o conteúdo para acesso público.
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
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dc.publisher.none.fl_str_mv Biblioteca Digitais de Teses e Dissertações da USP
publisher.none.fl_str_mv Biblioteca Digitais de Teses e Dissertações da USP
dc.source.none.fl_str_mv
reponame:Biblioteca Digital de Teses e Dissertações da USP
instname:Universidade de São Paulo (USP)
instacron:USP
instname_str Universidade de São Paulo (USP)
instacron_str USP
institution USP
reponame_str Biblioteca Digital de Teses e Dissertações da USP
collection Biblioteca Digital de Teses e Dissertações da USP
repository.name.fl_str_mv Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)
repository.mail.fl_str_mv virginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.br
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