The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein

There are a wide variety of porcine parvoviruses (PPVs) referred to as PPV1 to PPV7. The latter was discovered in 2016 and later reported in some countries in America, Asia, and Europe. PPV7 as a pathogenic agent or coinfection with other pathogens causing disease has not yet been determined. In the...

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Autores:
Vargas Bermúdez, Diana
Rendón Marín, Santiago
Ruiz Sáenz, Julián
Mogollón, José
Jaime, Jairo
Tipo de recurso:
Article of investigation
Fecha de publicación:
2021
Institución:
Universidad Cooperativa de Colombia
Repositorio:
Repositorio UCC
Idioma:
OAI Identifier:
oai:repository.ucc.edu.co:20.500.12494/43972
Acceso en línea:
https://hdl.handle.net/20.500.12494/43972
Palabra clave:
Capsids
Swine
Phylogenetic analysis
B cells
Nucleotide sequencing
Parvoviruses
Colombia
Structural proteins
Rights
openAccess
License
Atribución – No comercial – Compartir igual
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oai_identifier_str oai:repository.ucc.edu.co:20.500.12494/43972
network_acronym_str COOPER2
network_name_str Repositorio UCC
repository_id_str
dc.title.spa.fl_str_mv The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein
title The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein
spellingShingle The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein
Capsids
Swine
Phylogenetic analysis
B cells
Nucleotide sequencing
Parvoviruses
Colombia
Structural proteins
title_short The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein
title_full The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein
title_fullStr The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein
title_full_unstemmed The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein
title_sort The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein
dc.creator.fl_str_mv Vargas Bermúdez, Diana
Rendón Marín, Santiago
Ruiz Sáenz, Julián
Mogollón, José
Jaime, Jairo
dc.contributor.author.none.fl_str_mv Vargas Bermúdez, Diana
Rendón Marín, Santiago
Ruiz Sáenz, Julián
Mogollón, José
Jaime, Jairo
dc.subject.spa.fl_str_mv Capsids
Swine
Phylogenetic analysis
B cells
Nucleotide sequencing
Parvoviruses
Colombia
Structural proteins
topic Capsids
Swine
Phylogenetic analysis
B cells
Nucleotide sequencing
Parvoviruses
Colombia
Structural proteins
description There are a wide variety of porcine parvoviruses (PPVs) referred to as PPV1 to PPV7. The latter was discovered in 2016 and later reported in some countries in America, Asia, and Europe. PPV7 as a pathogenic agent or coinfection with other pathogens causing disease has not yet been determined. In the present study, we report the identification of PPV7 for the first time in Colombia, where it was found retrospectively since 2015 in 40% of the provinces that make up the country (13/32), and the virus was ratified for 2018 in 4/5 provinces evaluated. Additionally, partial sequencing (nucleotides 380 to 4000) was performed of four Colombian strains completely covering the VP2 and NS1 viral genes. A sequence identity greater than 99% was found when comparing them with reference strains from the USA and China. In three of the four Colombian strains, an insertion of 15 nucleotides (five amino acids) was found in the PPV7-VP2 capsid protein (540–5554 nt; 180–184 aa). Based on this insertion, the VP2 phylogenetic analysis exhibited two well-differentiated evolutionarily related groups. To evaluate the impact of this insertion on the structure of the PPV7-VP2 capsid protein, the secondary structure of two different Colombian strains was predicted, and it was determined that the insertion is located in the coil region and not involved in significant changes in the structure of the protein. The 3D structure of the PPV7-VP2 capsid protein was determined by threading and homology modeling, and it was shown that the insertion did not imply a change in the shape of the protein. Additionally, it was determined that the insertion is not involved in suppressing a potential B cell epitope, although the increase in length of the epitope could affect the interaction with molecules that allow a specific immune response.
publishDate 2021
dc.date.issued.none.fl_str_mv 2021-12
dc.date.accessioned.none.fl_str_mv 2022-02-15T20:20:49Z
dc.date.available.none.fl_str_mv 2022-02-15T20:20:49Z
dc.type.none.fl_str_mv Artículos Científicos
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dc.identifier.issn.spa.fl_str_mv 1932-6203
dc.identifier.uri.spa.fl_str_mv 10.1371/journal.pone.0258311
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12494/43972
dc.identifier.bibliographicCitation.spa.fl_str_mv Vargas-Bermudez DS, Rendon-Marin S, Ruiz-Saenz J, Mogollón D, Jaime J (2021) The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein. PLOS ONE 16(12): e0258311. https://doi.org/10.1371/journal.pone.0258311
identifier_str_mv 1932-6203
10.1371/journal.pone.0258311
Vargas-Bermudez DS, Rendon-Marin S, Ruiz-Saenz J, Mogollón D, Jaime J (2021) The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein. PLOS ONE 16(12): e0258311. https://doi.org/10.1371/journal.pone.0258311
url https://hdl.handle.net/20.500.12494/43972
dc.relation.isversionof.spa.fl_str_mv https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0258311
dc.relation.ispartofjournal.spa.fl_str_mv PLOS ONE
dc.relation.references.spa.fl_str_mv Ranz AI, Manclús JJ, Díaz-Aroca E, Casal JI. Porcine parvovirus: DNA sequence and genome organization. J Gen Virol. 1989;70 (Pt 10): 2541–2553. pmid:2794971
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Yang S, Liu Z, Wang Y, Li W, Fu X, Lin Y, et al. A novel rodent Chapparvovirus in feces of wild rats. Virol J. 2016;13: 133. pmid:27473724
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Souza WM de Romeiro MF, Fumagalli MJ, Modha S, de Araujo J, Queiroz LH, et al. Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution. J Gen Virol. 2017;98: 225–229. pmid:28284244
Palinski RM, Mitra N, Hause BM. Discovery of a novel Parvovirinae virus, porcine parvovirus 7, by metagenomic sequencing of porcine rectal swabs. Virus Genes. 2016;52: 564–567. pmid:26995221
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spelling Vargas Bermúdez, DianaRendón Marín, SantiagoRuiz Sáenz, JuliánMogollón, JoséJaime, Jairo162022-02-15T20:20:49Z2022-02-15T20:20:49Z2021-121932-620310.1371/journal.pone.0258311https://hdl.handle.net/20.500.12494/43972Vargas-Bermudez DS, Rendon-Marin S, Ruiz-Saenz J, Mogollón D, Jaime J (2021) The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein. PLOS ONE 16(12): e0258311. https://doi.org/10.1371/journal.pone.0258311There are a wide variety of porcine parvoviruses (PPVs) referred to as PPV1 to PPV7. The latter was discovered in 2016 and later reported in some countries in America, Asia, and Europe. PPV7 as a pathogenic agent or coinfection with other pathogens causing disease has not yet been determined. In the present study, we report the identification of PPV7 for the first time in Colombia, where it was found retrospectively since 2015 in 40% of the provinces that make up the country (13/32), and the virus was ratified for 2018 in 4/5 provinces evaluated. Additionally, partial sequencing (nucleotides 380 to 4000) was performed of four Colombian strains completely covering the VP2 and NS1 viral genes. A sequence identity greater than 99% was found when comparing them with reference strains from the USA and China. In three of the four Colombian strains, an insertion of 15 nucleotides (five amino acids) was found in the PPV7-VP2 capsid protein (540–5554 nt; 180–184 aa). Based on this insertion, the VP2 phylogenetic analysis exhibited two well-differentiated evolutionarily related groups. To evaluate the impact of this insertion on the structure of the PPV7-VP2 capsid protein, the secondary structure of two different Colombian strains was predicted, and it was determined that the insertion is located in the coil region and not involved in significant changes in the structure of the protein. The 3D structure of the PPV7-VP2 capsid protein was determined by threading and homology modeling, and it was shown that the insertion did not imply a change in the shape of the protein. Additionally, it was determined that the insertion is not involved in suppressing a potential B cell epitope, although the increase in length of the epitope could affect the interaction with molecules that allow a specific immune response.http://scienti.colciencias.gov.co:8081/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000153095https://orcid.org/0000-0002-1447-1458https://scienti.minciencias.gov.co/gruplac/jsp/visualiza/visualizagr.jsp?nro=00000000000695julian.ruizs@campusucc.edu.cohttps://scholar.google.com/citations?user=o3Y7mZwAAAAJ&hl=ese0258311Universidad Cooperativa de Colombia, Facultad de Ciencias de la Salud, Medicina Veterinaría y Zootecnia, BucaramangaPLOSMedicina veterinaria y zootecniaBucaramangahttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0258311PLOS ONERanz AI, Manclús JJ, Díaz-Aroca E, Casal JI. Porcine parvovirus: DNA sequence and genome organization. J Gen Virol. 1989;70 (Pt 10): 2541–2553. pmid:2794971Pénzes JJ, Söderlund-Venermo M, Canuti M, Eis-Hübinger AM, Hughes J, Cotmore SF, et al. Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association. Arch Virol. 2020; pmid:32533329Yang S, Liu Z, Wang Y, Li W, Fu X, Lin Y, et al. A novel rodent Chapparvovirus in feces of wild rats. Virol J. 2016;13: 133. pmid:27473724Williams SH, Che X, Garcia JA, Klena JD, Lee B, Muller D, et al. Viral diversity of house mice in new york city. MBio. 2018;9. pmid:29666290Fahsbender E, Altan E, Seguin MA, Young P, Estrada M, Leutenegger C, et al. Chapparvovirus DNA Found in 4% of Dogs with Diarrhea. Viruses. 2019;11. pmid:31035625Reuter G, Boros Á, Delwart E, Pankovics P. Novel circular single-stranded DNA virus from turkey faeces. Arch Virol. 2014;159: 2161–2164. pmid:24562429Lima DA, Cibulski SP, Tochetto C, Varela APM, Finkler F, Teixeira TF, et al. The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics. Virus Res. 2019;261: 9–20. pmid:30543873Souza WM de Romeiro MF, Fumagalli MJ, Modha S, de Araujo J, Queiroz LH, et al. Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution. J Gen Virol. 2017;98: 225–229. pmid:28284244Palinski RM, Mitra N, Hause BM. Discovery of a novel Parvovirinae virus, porcine parvovirus 7, by metagenomic sequencing of porcine rectal swabs. Virus Genes. 2016;52: 564–567. pmid:26995221Xing X, Zhou H, Tong L, Chen Y, Sun Y, Wang H, et al. First identification of porcine parvovirus 7 in China. Arch Virol. 2018;163: 209–213. pmid:29022179Wang Y, Yang K-K, Wang J, Wang X-P, Zhao L, Sun P, et al. Detection and molecular characterization of novel porcine parvovirus 7 in Anhui province from Central-Eastern China. Infect Genet Evol. 2019;71: 31–35. pmid:30876889Wang W, Cao L, Sun W, Xin J, Zheng M, Tian M, et al. 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Universidad Cooperativa de 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