Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study

Describing PRRSV whole-genome viral diversity data over time within the host and within-farm is crucial for a better understanding of viral evolution and its implications. A cohort study was conducted at one naïve farrow-to-wean farm reporting a PRRSV outbreak. All piglets 3-5 days of age (DOA) born...

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Autores: Kikuti, Mariana, Vilalta, Carles|||0000-0002-9220-8620, Sanhueza, Juan|||0000-0003-4320-3839, Pamornchainavakul, Nakarin|||0000-0003-0378-0316, Kevill, Jessica, Yang, My, Paploski, Igor A. D., Lenskaia, Tatiana, Odogwu, Nkechi M.|||0000-0001-7824-0096, Kiehne, Ross, VanderWaal, Kimberly|||0000-0002-5764-6430, Schroeder, Declan|||0000-0001-5991-2838, Corzo, Cesar A.|||0000-0002-2749-3496
Tipo de recurso: artículo
Fecha de publicación:2023
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:284273
Acceso en línea:https://ddd.uab.cat/record/284273
https://dx.doi.org/urn:doi:10.3390/v15091837
Access Level:acceso abierto
Palabra clave:Porcine reproductive and respiratory syndrome
Genetic variation
Whole-genome sequencing
Molecular epidemiology
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spelling Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort StudyKikuti, MarianaVilalta, Carles|||0000-0002-9220-8620Sanhueza, Juan|||0000-0003-4320-3839Pamornchainavakul, Nakarin|||0000-0003-0378-0316Kevill, JessicaYang, MyPaploski, Igor A. D.Lenskaia, TatianaOdogwu, Nkechi M.|||0000-0001-7824-0096Kiehne, RossVanderWaal, Kimberly|||0000-0002-5764-6430Schroeder, Declan|||0000-0001-5991-2838Corzo, Cesar A.|||0000-0002-2749-3496Porcine reproductive and respiratory syndromeGenetic variationWhole-genome sequencingMolecular epidemiologyDescribing PRRSV whole-genome viral diversity data over time within the host and within-farm is crucial for a better understanding of viral evolution and its implications. A cohort study was conducted at one naïve farrow-to-wean farm reporting a PRRSV outbreak. All piglets 3-5 days of age (DOA) born to mass-exposed sows through live virus inoculation with the recently introduced wild-type virus two weeks prior were sampled and followed up at 17-19 DOA. Samples from 127 piglets were individually tested for PRRSV by RT-PCR and 100 sequences were generated using Oxford Nanopore Technologies chemistry. Female piglets had significantly higher median Ct values than males (15.5 vs. 13.7, Kruskal-Wallis p < 0.001) at 3-5 DOA. A 52.8% mortality between sampling points was found, and the odds of dying by 17-19 DOA decreased with every one unit increase in Ct values at 3-5 DOA (OR = 0.76, 95% CI 0.61-0.94, p = 0.01). Although the within-pig percent nucleotide identity was overall high (99.7%) between 3-5 DOA and 17-19 DOA samples, ORFs 4 and 5a showed much lower identities (97.26% and 98.53%, respectively). When looking solely at ORF5, 62% of the sequences were identical to the 3-5 DOA consensus. Ten and eight regions showed increased nucleotide and amino acid genetic diversity, respectively, all found throughout ORFs 2a/2b, 4, 5a/5, 6, and 7. 22023-01-0120232023-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/284273https://dx.doi.org/urn:doi:10.3390/v15091837reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2842732026-06-06T12:50:31Z
dc.title.none.fl_str_mv Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study
title Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study
spellingShingle Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study
Kikuti, Mariana
Porcine reproductive and respiratory syndrome
Genetic variation
Whole-genome sequencing
Molecular epidemiology
title_short Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study
title_full Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study
title_fullStr Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study
title_full_unstemmed Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study
title_sort Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study
dc.creator.none.fl_str_mv Kikuti, Mariana
Vilalta, Carles|||0000-0002-9220-8620
Sanhueza, Juan|||0000-0003-4320-3839
Pamornchainavakul, Nakarin|||0000-0003-0378-0316
Kevill, Jessica
Yang, My
Paploski, Igor A. D.
Lenskaia, Tatiana
Odogwu, Nkechi M.|||0000-0001-7824-0096
Kiehne, Ross
VanderWaal, Kimberly|||0000-0002-5764-6430
Schroeder, Declan|||0000-0001-5991-2838
Corzo, Cesar A.|||0000-0002-2749-3496
author Kikuti, Mariana
author_facet Kikuti, Mariana
Vilalta, Carles|||0000-0002-9220-8620
Sanhueza, Juan|||0000-0003-4320-3839
Pamornchainavakul, Nakarin|||0000-0003-0378-0316
Kevill, Jessica
Yang, My
Paploski, Igor A. D.
Lenskaia, Tatiana
Odogwu, Nkechi M.|||0000-0001-7824-0096
Kiehne, Ross
VanderWaal, Kimberly|||0000-0002-5764-6430
Schroeder, Declan|||0000-0001-5991-2838
Corzo, Cesar A.|||0000-0002-2749-3496
author_role author
author2 Vilalta, Carles|||0000-0002-9220-8620
Sanhueza, Juan|||0000-0003-4320-3839
Pamornchainavakul, Nakarin|||0000-0003-0378-0316
Kevill, Jessica
Yang, My
Paploski, Igor A. D.
Lenskaia, Tatiana
Odogwu, Nkechi M.|||0000-0001-7824-0096
Kiehne, Ross
VanderWaal, Kimberly|||0000-0002-5764-6430
Schroeder, Declan|||0000-0001-5991-2838
Corzo, Cesar A.|||0000-0002-2749-3496
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Porcine reproductive and respiratory syndrome
Genetic variation
Whole-genome sequencing
Molecular epidemiology
topic Porcine reproductive and respiratory syndrome
Genetic variation
Whole-genome sequencing
Molecular epidemiology
description Describing PRRSV whole-genome viral diversity data over time within the host and within-farm is crucial for a better understanding of viral evolution and its implications. A cohort study was conducted at one naïve farrow-to-wean farm reporting a PRRSV outbreak. All piglets 3-5 days of age (DOA) born to mass-exposed sows through live virus inoculation with the recently introduced wild-type virus two weeks prior were sampled and followed up at 17-19 DOA. Samples from 127 piglets were individually tested for PRRSV by RT-PCR and 100 sequences were generated using Oxford Nanopore Technologies chemistry. Female piglets had significantly higher median Ct values than males (15.5 vs. 13.7, Kruskal-Wallis p < 0.001) at 3-5 DOA. A 52.8% mortality between sampling points was found, and the odds of dying by 17-19 DOA decreased with every one unit increase in Ct values at 3-5 DOA (OR = 0.76, 95% CI 0.61-0.94, p = 0.01). Although the within-pig percent nucleotide identity was overall high (99.7%) between 3-5 DOA and 17-19 DOA samples, ORFs 4 and 5a showed much lower identities (97.26% and 98.53%, respectively). When looking solely at ORF5, 62% of the sequences were identical to the 3-5 DOA consensus. Ten and eight regions showed increased nucleotide and amino acid genetic diversity, respectively, all found throughout ORFs 2a/2b, 4, 5a/5, 6, and 7.
publishDate 2023
dc.date.none.fl_str_mv 2
2023-01-01
2023
2023-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/284273
https://dx.doi.org/urn:doi:10.3390/v15091837
url https://ddd.uab.cat/record/284273
https://dx.doi.org/urn:doi:10.3390/v15091837
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
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