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Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing

African swine fever virus (ASFV), classical swine fever virus (CSFV), and foot-and-mouth disease virus (FMDV) cause important transboundary animal diseases (TADs) that have a significant economic impact. The rapid and unequivocal identification of these pathogens and distinction from other animal di...

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Autores principales: Bold, Dashzeveg, Souza-Neto, Jayme A., Gombo-Ochir, Delgerzul, Gaudreault, Natasha N., Meekins, David A., McDowell, Chester D., Zayat, Batsukh, Richt, Juergen A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10140976/
https://www.ncbi.nlm.nih.gov/pubmed/37111419
http://dx.doi.org/10.3390/pathogens12040533
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author Bold, Dashzeveg
Souza-Neto, Jayme A.
Gombo-Ochir, Delgerzul
Gaudreault, Natasha N.
Meekins, David A.
McDowell, Chester D.
Zayat, Batsukh
Richt, Juergen A.
author_facet Bold, Dashzeveg
Souza-Neto, Jayme A.
Gombo-Ochir, Delgerzul
Gaudreault, Natasha N.
Meekins, David A.
McDowell, Chester D.
Zayat, Batsukh
Richt, Juergen A.
author_sort Bold, Dashzeveg
collection PubMed
description African swine fever virus (ASFV), classical swine fever virus (CSFV), and foot-and-mouth disease virus (FMDV) cause important transboundary animal diseases (TADs) that have a significant economic impact. The rapid and unequivocal identification of these pathogens and distinction from other animal diseases based on clinical symptoms in the field is difficult. Nevertheless, early pathogen detection is critical in limiting their spread and impact as is the availability of a reliable, rapid, and cost-effective diagnostic test. The purpose of this study was to evaluate the feasibility to identify ASFV, CSFV, and FMDV in field samples using next generation sequencing of short PCR products as a point-of-care diagnostic. We isolated nucleic acids from tissue samples of animals in Mongolia that were infected with ASFV (2019), CSFV (2015), or FMDV (2018), and performed conventional (RT-) PCR using primers recommended by the Terrestrial Animal Health Code of the World Organization for Animal Health (WOAH). The (RT-) PCR products were then sequenced in Mongolia using the MinION nanopore portable sequencer. The resulting sequencing reads successfully identified the respective pathogens that exhibited 91–100% nucleic acid similarity to the reference strains. Phylogenetic analyses suggest that the Mongolian virus isolates are closely related to other isolates circulating in the same geographic region. Based on our results, sequencing short fragments derived by conventional (RT-) PCR is a reliable approach for rapid point-of-care diagnostics for ASFV, CSFV, and FMDV even in low-resource countries.
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spelling pubmed-101409762023-04-29 Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing Bold, Dashzeveg Souza-Neto, Jayme A. Gombo-Ochir, Delgerzul Gaudreault, Natasha N. Meekins, David A. McDowell, Chester D. Zayat, Batsukh Richt, Juergen A. Pathogens Brief Report African swine fever virus (ASFV), classical swine fever virus (CSFV), and foot-and-mouth disease virus (FMDV) cause important transboundary animal diseases (TADs) that have a significant economic impact. The rapid and unequivocal identification of these pathogens and distinction from other animal diseases based on clinical symptoms in the field is difficult. Nevertheless, early pathogen detection is critical in limiting their spread and impact as is the availability of a reliable, rapid, and cost-effective diagnostic test. The purpose of this study was to evaluate the feasibility to identify ASFV, CSFV, and FMDV in field samples using next generation sequencing of short PCR products as a point-of-care diagnostic. We isolated nucleic acids from tissue samples of animals in Mongolia that were infected with ASFV (2019), CSFV (2015), or FMDV (2018), and performed conventional (RT-) PCR using primers recommended by the Terrestrial Animal Health Code of the World Organization for Animal Health (WOAH). The (RT-) PCR products were then sequenced in Mongolia using the MinION nanopore portable sequencer. The resulting sequencing reads successfully identified the respective pathogens that exhibited 91–100% nucleic acid similarity to the reference strains. Phylogenetic analyses suggest that the Mongolian virus isolates are closely related to other isolates circulating in the same geographic region. Based on our results, sequencing short fragments derived by conventional (RT-) PCR is a reliable approach for rapid point-of-care diagnostics for ASFV, CSFV, and FMDV even in low-resource countries. MDPI 2023-03-29 /pmc/articles/PMC10140976/ /pubmed/37111419 http://dx.doi.org/10.3390/pathogens12040533 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Brief Report
Bold, Dashzeveg
Souza-Neto, Jayme A.
Gombo-Ochir, Delgerzul
Gaudreault, Natasha N.
Meekins, David A.
McDowell, Chester D.
Zayat, Batsukh
Richt, Juergen A.
Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing
title Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing
title_full Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing
title_fullStr Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing
title_full_unstemmed Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing
title_short Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing
title_sort rapid identification of asfv, csfv and fmdv from mongolian outbreaks with minion short amplicon sequencing
topic Brief Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10140976/
https://www.ncbi.nlm.nih.gov/pubmed/37111419
http://dx.doi.org/10.3390/pathogens12040533
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