Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing
Abstract Background Newcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease viruses (NDV), the causative agent of ND. However, these diagnostics are hindered by th...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-11-01
|
| Series: | Virology Journal |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12985-018-1077-5 |
| _version_ | 1818505949008101376 |
|---|---|
| author | Salman L. Butt Tonya L. Taylor Jeremy D. Volkening Kiril M. Dimitrov Dawn Williams-Coplin Kevin K. Lahmers Patti J. Miller Asif M. Rana David L. Suarez Claudio L. Afonso James B. Stanton |
| author_facet | Salman L. Butt Tonya L. Taylor Jeremy D. Volkening Kiril M. Dimitrov Dawn Williams-Coplin Kevin K. Lahmers Patti J. Miller Asif M. Rana David L. Suarez Claudio L. Afonso James B. Stanton |
| author_sort | Salman L. Butt |
| collection | DOAJ |
| description | Abstract Background Newcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease viruses (NDV), the causative agent of ND. However, these diagnostics are hindered by the genetic diversity and rapid evolution of NDVs. Methods An amplicon sequencing (AmpSeq) workflow for virulence and genotype prediction of NDV samples using a third-generation, real-time DNA sequencing platform is described here. 1D MinION sequencing of barcoded NDV amplicons was performed using 33 egg-grown isolates, (15 NDV genotypes), and 15 clinical swab samples collected from field outbreaks. Assembly-based data analysis was performed in a customized, Galaxy-based AmpSeq workflow. MinION-based results were compared to previously published sequences and to sequences obtained using a previously published Illumina MiSeq workflow. Results For all egg-grown isolates, NDV was detected and virulence and genotype were accurately predicted. For clinical samples, NDV was detected in ten of eleven NDV samples. Six of the clinical samples contained two mixed genotypes as determined by MiSeq, of which the MinION method detected both genotypes in four samples. Additionally, testing a dilution series of one NDV isolate resulted in NDV detection in a dilution as low as 101 50% egg infectious dose per milliliter. This was accomplished in as little as 7 min of sequencing time, with a 98.37% sequence identity compared to the expected consensus obtained by MiSeq. Conclusion The depth of sequencing, fast sequencing capabilities, accuracy of the consensus sequences, and the low cost of multiplexing allowed for effective virulence prediction and genotype identification of NDVs currently circulating worldwide. The sensitivity of this protocol was preliminary tested using only one genotype. After more extensive evaluation of the sensitivity and specificity, this protocol will likely be applicable to the detection and characterization of NDV. |
| first_indexed | 2024-12-10T21:57:48Z |
| format | Article |
| id | doaj.art-c602e1844c5b4cd7868d1c060e9ea952 |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-12-10T21:57:48Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-c602e1844c5b4cd7868d1c060e9ea9522022-12-22T01:31:59ZengBMCVirology Journal1743-422X2018-11-0115111410.1186/s12985-018-1077-5Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencingSalman L. Butt0Tonya L. Taylor1Jeremy D. Volkening2Kiril M. Dimitrov3Dawn Williams-Coplin4Kevin K. Lahmers5Patti J. Miller6Asif M. Rana7David L. Suarez8Claudio L. Afonso9James B. Stanton10Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDASoutheast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDABASE2BIOSoutheast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDASoutheast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDADepartment of Biomedical Sciences & Pathobiology,VA-MD College of Veterinary Medicine, Virginia TechSoutheast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDAHivet Animal Health BusinessSoutheast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDASoutheast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDADepartment of Pathology, College of Veterinary Medicine, University of GeorgiaAbstract Background Newcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease viruses (NDV), the causative agent of ND. However, these diagnostics are hindered by the genetic diversity and rapid evolution of NDVs. Methods An amplicon sequencing (AmpSeq) workflow for virulence and genotype prediction of NDV samples using a third-generation, real-time DNA sequencing platform is described here. 1D MinION sequencing of barcoded NDV amplicons was performed using 33 egg-grown isolates, (15 NDV genotypes), and 15 clinical swab samples collected from field outbreaks. Assembly-based data analysis was performed in a customized, Galaxy-based AmpSeq workflow. MinION-based results were compared to previously published sequences and to sequences obtained using a previously published Illumina MiSeq workflow. Results For all egg-grown isolates, NDV was detected and virulence and genotype were accurately predicted. For clinical samples, NDV was detected in ten of eleven NDV samples. Six of the clinical samples contained two mixed genotypes as determined by MiSeq, of which the MinION method detected both genotypes in four samples. Additionally, testing a dilution series of one NDV isolate resulted in NDV detection in a dilution as low as 101 50% egg infectious dose per milliliter. This was accomplished in as little as 7 min of sequencing time, with a 98.37% sequence identity compared to the expected consensus obtained by MiSeq. Conclusion The depth of sequencing, fast sequencing capabilities, accuracy of the consensus sequences, and the low cost of multiplexing allowed for effective virulence prediction and genotype identification of NDVs currently circulating worldwide. The sensitivity of this protocol was preliminary tested using only one genotype. After more extensive evaluation of the sensitivity and specificity, this protocol will likely be applicable to the detection and characterization of NDV.http://link.springer.com/article/10.1186/s12985-018-1077-5Newcastle disease virusRNAGenotypeNanopore sequencingRapid sequencingMinION |
| spellingShingle | Salman L. Butt Tonya L. Taylor Jeremy D. Volkening Kiril M. Dimitrov Dawn Williams-Coplin Kevin K. Lahmers Patti J. Miller Asif M. Rana David L. Suarez Claudio L. Afonso James B. Stanton Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing Virology Journal Newcastle disease virus RNA Genotype Nanopore sequencing Rapid sequencing MinION |
| title | Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing |
| title_full | Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing |
| title_fullStr | Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing |
| title_full_unstemmed | Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing |
| title_short | Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing |
| title_sort | rapid virulence prediction and identification of newcastle disease virus genotypes using third generation sequencing |
| topic | Newcastle disease virus RNA Genotype Nanopore sequencing Rapid sequencing MinION |
| url | http://link.springer.com/article/10.1186/s12985-018-1077-5 |
| work_keys_str_mv | AT salmanlbutt rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT tonyaltaylor rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT jeremydvolkening rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT kirilmdimitrov rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT dawnwilliamscoplin rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT kevinklahmers rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT pattijmiller rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT asifmrana rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT davidlsuarez rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT claudiolafonso rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing AT jamesbstanton rapidvirulencepredictionandidentificationofnewcastlediseasevirusgenotypesusingthirdgenerationsequencing |