Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Tipo de documento: | Tese |
Idioma: | por |
Título da fonte: | Manancial - Repositório Digital da UFSM |
Texto Completo: | http://repositorio.ufsm.br/handle/1/28657 |
Resumo: | Bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2, classified within the genus Pestivirus, family Flaviviridae, are important pathogens of cattle worldwide. Pestiviruses are enveloped viruses and contain a positive-sense, single-stranded RNA molecule of approximately 12.3 kilobases as the genome. Up to date, 21 subtypes of BVDV-1 (a-u) and 4 of BVDV-2 (a-d) have been described. Although this genetic variability, BVDV isolates/strains have been frequently subtyped by phylogenetic analysis of the partial sequence of the 5' untranslated region (5'UTR) and/or coding regions such as Npro and E2. These analyses, however, can generate erroneous results, or with low statistical support, hindering the knowledge about the real diversity and circulation of BVDV subtypes. The best alternative to circumvent this obstacle would be to subtype the viruses by analyzing the complete genome (CG), a costly and unfeasible strategy for large-scale use. Thus, the first study investigated the most suitable genomic targets for subtyping of BVDV-1 and BVDV-2, comparing subtyping based on individual gene/region analysis and that based on whole genome (GC) analysis. The study was performed with 91 (BVDV-1) and 85 (BVDV-2) GC available in the GenBank database. The viruses were subtyped by analyzing their GC as well as the coding regions of the individual genes and the untranslated regions (complete 3' and 5'UTRs and partial 5'UTRs). Also, the geodesic distance between the tree generated by GC (reference) analysis and those generated by genomic region/UTR analyses were calculated. In general, analyses based on 3'UTR and 5'UTR showed the least reliable subtyping compared to GC analysis. For BVDV1, the phylogeny based on C, Erns, E1, E2, p7, NS2, NS3, NS4B, NS5A and NS5B was equivalent to that of GC. Regarding the BVDV-2 coding region, there was at least one noncompliance compared to the GC analysis, in all targets analyzed. After calculating the geodesic distance between GC and the coding region/UTRs trees, NS4B (for BVDV-1) and NS5A (BVDV-2) showed topology and edge lengths closer to the trees generated by GC analysis. In addition, 14 sequences of BVDV-2 could not be classified as subtype a, b or c. A second, more detailed study was then performed to investigate whether these sequences would represent a distinct BVDV-2 subtype. Initially, an "equivalence test" between phylogenetic analyses based on 85 complete/near-complete genomes (CNCGs) and their respective open reading frames (ORFs) proved that ORFs can be reliably used for BVDV-2 phylogeny. This made it possible to increase the data set to 139 sequences. Among these, seven sequences that could not be classified as BVDV-2 a-d formed a distinct cluster in all the phylogenetic trees analyzed. This cluster was suggested as a new subtype, called BVDV-2e. The BVDV-2e sequences also showed 44 amino acid changes compared to BVDV-2a-c. In conclusion, it is suggested that the NS4B and NS5A regions can be used as genomic targets for subtyping BVDV-1 and BVDV-2, respectively. In addition, a cluster of BVDV-2 was identified that may represent a new subtype (BVDV-2e), which could be investigated in future epidemiological and phylogenetic studies of BVDV. |
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Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2Selection of gene targets for phylogeny of bovine viral diarrhea virus (BVDV) and identification of a novel BVDV-2 subtypeNS4BNS5ABVDV-2eFilogeniaPhylogenyCNPQ::CIENCIAS AGRARIAS::MEDICINA VETERINARIABovine viral diarrhea virus 1 (BVDV-1) and BVDV-2, classified within the genus Pestivirus, family Flaviviridae, are important pathogens of cattle worldwide. Pestiviruses are enveloped viruses and contain a positive-sense, single-stranded RNA molecule of approximately 12.3 kilobases as the genome. Up to date, 21 subtypes of BVDV-1 (a-u) and 4 of BVDV-2 (a-d) have been described. Although this genetic variability, BVDV isolates/strains have been frequently subtyped by phylogenetic analysis of the partial sequence of the 5' untranslated region (5'UTR) and/or coding regions such as Npro and E2. These analyses, however, can generate erroneous results, or with low statistical support, hindering the knowledge about the real diversity and circulation of BVDV subtypes. The best alternative to circumvent this obstacle would be to subtype the viruses by analyzing the complete genome (CG), a costly and unfeasible strategy for large-scale use. Thus, the first study investigated the most suitable genomic targets for subtyping of BVDV-1 and BVDV-2, comparing subtyping based on individual gene/region analysis and that based on whole genome (GC) analysis. The study was performed with 91 (BVDV-1) and 85 (BVDV-2) GC available in the GenBank database. The viruses were subtyped by analyzing their GC as well as the coding regions of the individual genes and the untranslated regions (complete 3' and 5'UTRs and partial 5'UTRs). Also, the geodesic distance between the tree generated by GC (reference) analysis and those generated by genomic region/UTR analyses were calculated. In general, analyses based on 3'UTR and 5'UTR showed the least reliable subtyping compared to GC analysis. For BVDV1, the phylogeny based on C, Erns, E1, E2, p7, NS2, NS3, NS4B, NS5A and NS5B was equivalent to that of GC. Regarding the BVDV-2 coding region, there was at least one noncompliance compared to the GC analysis, in all targets analyzed. After calculating the geodesic distance between GC and the coding region/UTRs trees, NS4B (for BVDV-1) and NS5A (BVDV-2) showed topology and edge lengths closer to the trees generated by GC analysis. In addition, 14 sequences of BVDV-2 could not be classified as subtype a, b or c. A second, more detailed study was then performed to investigate whether these sequences would represent a distinct BVDV-2 subtype. Initially, an "equivalence test" between phylogenetic analyses based on 85 complete/near-complete genomes (CNCGs) and their respective open reading frames (ORFs) proved that ORFs can be reliably used for BVDV-2 phylogeny. This made it possible to increase the data set to 139 sequences. Among these, seven sequences that could not be classified as BVDV-2 a-d formed a distinct cluster in all the phylogenetic trees analyzed. This cluster was suggested as a new subtype, called BVDV-2e. The BVDV-2e sequences also showed 44 amino acid changes compared to BVDV-2a-c. In conclusion, it is suggested that the NS4B and NS5A regions can be used as genomic targets for subtyping BVDV-1 and BVDV-2, respectively. In addition, a cluster of BVDV-2 was identified that may represent a new subtype (BVDV-2e), which could be investigated in future epidemiological and phylogenetic studies of BVDV.Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPqOs vírus da diarreia viral bovina 1 (Bovine viral diarrhea virus, BVDV-1) e BVDV-2, classificados no gênero Pestivirus, família Flaviviridae, são importantes patógenos de distribuição mundial. Os pestivírus são vírus envelopados e contêm uma molécula de RNA de sentido positivo com aproximadamente 2.3 quilobases (kb) como genoma. Até o presente, foram descritos 21 subtipos de BVDV-1 (a-u) e 4 de BVDV-2 (a-d). Apesar dessa variabilidade genética, isolados e cepas de BVDV têm sido frequentemente subtipados pela análise filogenética da sequência parcial da região não-traduzida 5' (5'UTR) e/ou de regiões codificantes, como de Npro e E2. Essas análises, no entanto, podem gerar resultados equivocados ou de baixo suporte estatístico, dificultando o conhecimento sobre a real diversidade e circulação dos subtipos de BVDV. A melhor alternativa para contornar esses obstáculos seria a subtipagem dos vírus a partir da análise do genoma completo. Essa estratégia, no entanto, apresenta custo alto, além de ser inviável para uso em larga escala. Assim, o primeiro estudo investigou os alvos genômicos mais adequados para a subtipagem de BVDV-1 e BVDV-2, comparando-se a subtipagem baseada em análise de genes/regiões individuais com aquela baseada na análise do genoma completo (GC). O estudo foi realizado com 91 (BVDV-1) e 85 (BVDV-2) GC disponíveis no banco de dados GenBank. Os vírus foram subtipados analisando-se seu GC, bem como as regiões codificantes dos genes individuais e as regiões não-traduzidas (3' e 5' UTRs completas e 5' UTRs parciais). A distância geodésica entre a árvore gerada pela análise do GC (referência) e aquelas geradas pelas análises das regiões genômicas/UTRs também foi calculada. Em geral, as análises baseadas em 3'UTR e 5'UTR apresentaram as subtipagens menos confiáveis, comparando-se com análise de GC. Para o BVDV-1, a filogenia baseada em C, Erns, E1, E2, p7, NS2, NS3, NS4B, NS5A e NS5B foi equivalente à do GC. Em relação à região codificante de BVDV-2, houve pelo menos uma não conformidade em comparação com a análise do GC, em todos os alvos analisados. Após calcular a distância geodésica entre as árvores de GC e da região codificante/UTRs, observou-se que a NS4B (para BVDV-1) e NS5A (BVDV-2) apresentaram topologia e extensão de haste mais próximos às árvores geradas pela análise de GC. Além desses resultados, também observou-se que 14 sequências de BVDV-2 não puderam ser classificadas como subtipos a, b ou c. Então, realizou-se um segundo estudo mais detalhado para verificar se essas sequências poderiam representar um subtipo distinto de BVDV-2. Inicialmente, realizou-se uma “prova de equivalência” entre as análises filogenéticas baseadas em 85 genomas completos/quase completos (GCQCs) e suas respectivas fases abertas de leitura (open reading frames, ORFs), o que comprovou que as ORFs podem ser utilizadas de forma confiável para a filogenia de BVDV-2. Isso possibilitou aumentar o conjunto de dados para 139 sequências. Dentre essas, sete sequências, que não puderam ser classificadas como BVDV-2 a-d, formaram um agrupamento distinto em todas as árvores filogenéticas analisadas. Esse agrupamento foi então sugerido como um novo subtipo, denominado BVDV2e. As sequências de BVDV-2e também apresentaram 44 alterações de aminoácidos em comparação com o BVDV-2a-c. Em conclusão, sugere-se que as regiões de NS4B e NS5A podem ser utilizadas como alvos genômicos para a subtipagem de BVDV-1 e BVDV-2, respectivamente. Além disso, identificou-se um grupo de BVDV-2 que pode constituir um novo subtipo (BVDV-2e), e que poderia ser investigado em futuros estudos epidemiológicos e filogenéticos de BVDV.Universidade Federal de Santa MariaBrasilMedicina VeterináriaUFSMPrograma de Pós-Graduação em Medicina VeterináriaCentro de Ciências RuraisFlores, Eduardo Furtadohttp://lattes.cnpq.br/0446078331070694Silva Jr, José Valter JoaquimWeiblen, RudiAraújo, Daniel ArdissonMonteiro, Francielle LizStreck, AndréOliveira, Pablo Sebastian Britto de2023-04-12T17:38:03Z2023-04-12T17:38:03Z2023-02-03info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisapplication/pdfhttp://repositorio.ufsm.br/handle/1/28657porAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessreponame:Manancial - Repositório Digital da UFSMinstname:Universidade Federal de Santa Maria (UFSM)instacron:UFSM2023-04-12T17:38:03Zoai:repositorio.ufsm.br:1/28657Biblioteca Digital de Teses e Dissertaçõeshttps://repositorio.ufsm.br/ONGhttps://repositorio.ufsm.br/oai/requestatendimento.sib@ufsm.br||tedebc@gmail.comopendoar:2023-04-12T17:38:03Manancial - Repositório Digital da UFSM - Universidade Federal de Santa Maria (UFSM)false |
dc.title.none.fl_str_mv |
Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2 Selection of gene targets for phylogeny of bovine viral diarrhea virus (BVDV) and identification of a novel BVDV-2 subtype |
title |
Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2 |
spellingShingle |
Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2 Oliveira, Pablo Sebastian Britto de NS4B NS5A BVDV-2e Filogenia Phylogeny CNPQ::CIENCIAS AGRARIAS::MEDICINA VETERINARIA |
title_short |
Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2 |
title_full |
Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2 |
title_fullStr |
Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2 |
title_full_unstemmed |
Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2 |
title_sort |
Seleção de alvos genômicos para a filogenia de vírus da diarreia viral bovina (BVDV) e identificação de novo subtipo de BVDV-2 |
author |
Oliveira, Pablo Sebastian Britto de |
author_facet |
Oliveira, Pablo Sebastian Britto de |
author_role |
author |
dc.contributor.none.fl_str_mv |
Flores, Eduardo Furtado http://lattes.cnpq.br/0446078331070694 Silva Jr, José Valter Joaquim Weiblen, Rudi Araújo, Daniel Ardisson Monteiro, Francielle Liz Streck, André |
dc.contributor.author.fl_str_mv |
Oliveira, Pablo Sebastian Britto de |
dc.subject.por.fl_str_mv |
NS4B NS5A BVDV-2e Filogenia Phylogeny CNPQ::CIENCIAS AGRARIAS::MEDICINA VETERINARIA |
topic |
NS4B NS5A BVDV-2e Filogenia Phylogeny CNPQ::CIENCIAS AGRARIAS::MEDICINA VETERINARIA |
description |
Bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2, classified within the genus Pestivirus, family Flaviviridae, are important pathogens of cattle worldwide. Pestiviruses are enveloped viruses and contain a positive-sense, single-stranded RNA molecule of approximately 12.3 kilobases as the genome. Up to date, 21 subtypes of BVDV-1 (a-u) and 4 of BVDV-2 (a-d) have been described. Although this genetic variability, BVDV isolates/strains have been frequently subtyped by phylogenetic analysis of the partial sequence of the 5' untranslated region (5'UTR) and/or coding regions such as Npro and E2. These analyses, however, can generate erroneous results, or with low statistical support, hindering the knowledge about the real diversity and circulation of BVDV subtypes. The best alternative to circumvent this obstacle would be to subtype the viruses by analyzing the complete genome (CG), a costly and unfeasible strategy for large-scale use. Thus, the first study investigated the most suitable genomic targets for subtyping of BVDV-1 and BVDV-2, comparing subtyping based on individual gene/region analysis and that based on whole genome (GC) analysis. The study was performed with 91 (BVDV-1) and 85 (BVDV-2) GC available in the GenBank database. The viruses were subtyped by analyzing their GC as well as the coding regions of the individual genes and the untranslated regions (complete 3' and 5'UTRs and partial 5'UTRs). Also, the geodesic distance between the tree generated by GC (reference) analysis and those generated by genomic region/UTR analyses were calculated. In general, analyses based on 3'UTR and 5'UTR showed the least reliable subtyping compared to GC analysis. For BVDV1, the phylogeny based on C, Erns, E1, E2, p7, NS2, NS3, NS4B, NS5A and NS5B was equivalent to that of GC. Regarding the BVDV-2 coding region, there was at least one noncompliance compared to the GC analysis, in all targets analyzed. After calculating the geodesic distance between GC and the coding region/UTRs trees, NS4B (for BVDV-1) and NS5A (BVDV-2) showed topology and edge lengths closer to the trees generated by GC analysis. In addition, 14 sequences of BVDV-2 could not be classified as subtype a, b or c. A second, more detailed study was then performed to investigate whether these sequences would represent a distinct BVDV-2 subtype. Initially, an "equivalence test" between phylogenetic analyses based on 85 complete/near-complete genomes (CNCGs) and their respective open reading frames (ORFs) proved that ORFs can be reliably used for BVDV-2 phylogeny. This made it possible to increase the data set to 139 sequences. Among these, seven sequences that could not be classified as BVDV-2 a-d formed a distinct cluster in all the phylogenetic trees analyzed. This cluster was suggested as a new subtype, called BVDV-2e. The BVDV-2e sequences also showed 44 amino acid changes compared to BVDV-2a-c. In conclusion, it is suggested that the NS4B and NS5A regions can be used as genomic targets for subtyping BVDV-1 and BVDV-2, respectively. In addition, a cluster of BVDV-2 was identified that may represent a new subtype (BVDV-2e), which could be investigated in future epidemiological and phylogenetic studies of BVDV. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-04-12T17:38:03Z 2023-04-12T17:38:03Z 2023-02-03 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://repositorio.ufsm.br/handle/1/28657 |
url |
http://repositorio.ufsm.br/handle/1/28657 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.rights.driver.fl_str_mv |
Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Universidade Federal de Santa Maria Brasil Medicina Veterinária UFSM Programa de Pós-Graduação em Medicina Veterinária Centro de Ciências Rurais |
publisher.none.fl_str_mv |
Universidade Federal de Santa Maria Brasil Medicina Veterinária UFSM Programa de Pós-Graduação em Medicina Veterinária Centro de Ciências Rurais |
dc.source.none.fl_str_mv |
reponame:Manancial - Repositório Digital da UFSM instname:Universidade Federal de Santa Maria (UFSM) instacron:UFSM |
instname_str |
Universidade Federal de Santa Maria (UFSM) |
instacron_str |
UFSM |
institution |
UFSM |
reponame_str |
Manancial - Repositório Digital da UFSM |
collection |
Manancial - Repositório Digital da UFSM |
repository.name.fl_str_mv |
Manancial - Repositório Digital da UFSM - Universidade Federal de Santa Maria (UFSM) |
repository.mail.fl_str_mv |
atendimento.sib@ufsm.br||tedebc@gmail.com |
_version_ |
1805922178250571776 |