Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges

doi:10.3389/fpls.2018.01082

. 2018 Aug 27:9:1082.

doi: 10.3389/fpls.2018.01082. eCollection 2018.

Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges

Hans J Maree^{1

2}, Adrian Fox³, Maher Al Rwahnih⁴, Neil Boonham⁵, Thierry Candresse⁶

Affiliations

¹ Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
² Agricultural Research Council, Infruitec-Nietvoorbij, The Fruit, Vine and Wine Institute, Stellenbosch, South Africa.
³ Department of Plant Protection, Fera Science Ltd., York, United Kingdom.
⁴ Department of Plant Pathology, University of California, Davis, Davis, CA, United States.
⁵ School of Natural and Environmental Sciences, University of Newcastle, Newcastle Upon Tyne, United Kingdom.
⁶ UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, Bordeaux, France.

PMID: 30210506
PMCID: PMC6119710
DOI: 10.3389/fpls.2018.01082

Free PMC article

Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges

Hans J Maree et al. Front Plant Sci. 2018.

Free PMC article

. 2018 Aug 27:9:1082.

doi: 10.3389/fpls.2018.01082. eCollection 2018.

Authors

Hans J Maree^{1

2}, Adrian Fox³, Maher Al Rwahnih⁴, Neil Boonham⁵, Thierry Candresse⁶

Affiliations

¹ Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
² Agricultural Research Council, Infruitec-Nietvoorbij, The Fruit, Vine and Wine Institute, Stellenbosch, South Africa.
³ Department of Plant Protection, Fera Science Ltd., York, United Kingdom.
⁴ Department of Plant Pathology, University of California, Davis, Davis, CA, United States.
⁵ School of Natural and Environmental Sciences, University of Newcastle, Newcastle Upon Tyne, United Kingdom.
⁶ UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, Bordeaux, France.

PMID: 30210506
PMCID: PMC6119710
DOI: 10.3389/fpls.2018.01082

No abstract available

Keywords: HTS for virus detection; considerations for HTS detection assays; high-throughput sequencing; next generation sequencing (NGS); plant virus detection; validation of diagnostic tool.

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References

1. Al Rwahnih M., Daubert S., Golino D., Islas C., Rowhani A. (2015). Comparison of next-generation sequencing versus biological indexing for the optimal detection of viral pathogens in grapevine. Phytopathology 105, 758–763. 10.1094/PHYTO-06-14-0165-R - DOI - PubMed
1. Bukowska-Ośko I., Perlejewski K., Nakamura S., Motooka D., Stokowy T., Kosinska J., et al. . (2017). Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: the confounding effect of background contamination, in Respiratory Treatment and Prevention, ed. Pokorski M. (Cham: Springer International Publishing; ), 53–62. - PubMed
1. Dickins B., Rebolledo-Jaramillo B., Su M. S., Paul I. M., Blankenberg D., Stoler N., et al. . (2014). Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. BioTechniques 56, 134–141. 10.2144/000114146 - DOI - PMC - PubMed
1. Golino D. A., Fuchs M., Rwahnih M. A., Farrar K., Schmidt A., Martelli G. P. (2017). Regulatory aspects of grape viruses and virus diseases: certification, quarantine, and harmonization, in Grapevine Viruses: Molecular Biology, Diagnostics and Management (Cham, Springer; ), 581–598.
1. Hagen C., Frizzi A., Gabriels S., Huang M., Salati R., Gabor B., et al. . (2012). Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification. Arch. Virol. 157, 907–915. 10.1007/s00705-012-1253-7 - DOI - PubMed

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[1] Al Rwahnih M., Daubert S., Golino D., Islas C., Rowhani A. (2015). Comparison of next-generation sequencing versus biological indexing for the optimal detection of viral pathogens in grapevine. Phytopathology 105, 758–763. 10.1094/PHYTO-06-14-0165-R - DOI - PubMed

[2] Al Rwahnih M., Daubert S., Golino D., Islas C., Rowhani A. (2015). Comparison of next-generation sequencing versus biological indexing for the optimal detection of viral pathogens in grapevine. Phytopathology 105, 758–763. 10.1094/PHYTO-06-14-0165-R - DOI - PubMed

[3] Bukowska-Ośko I., Perlejewski K., Nakamura S., Motooka D., Stokowy T., Kosinska J., et al. . (2017). Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: the confounding effect of background contamination, in Respiratory Treatment and Prevention, ed. Pokorski M. (Cham: Springer International Publishing; ), 53–62. - PubMed

[4] Bukowska-Ośko I., Perlejewski K., Nakamura S., Motooka D., Stokowy T., Kosinska J., et al. . (2017). Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: the confounding effect of background contamination, in Respiratory Treatment and Prevention, ed. Pokorski M. (Cham: Springer International Publishing; ), 53–62. - PubMed

[5] Dickins B., Rebolledo-Jaramillo B., Su M. S., Paul I. M., Blankenberg D., Stoler N., et al. . (2014). Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. BioTechniques 56, 134–141. 10.2144/000114146 - DOI - PMC - PubMed

[6] Dickins B., Rebolledo-Jaramillo B., Su M. S., Paul I. M., Blankenberg D., Stoler N., et al. . (2014). Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. BioTechniques 56, 134–141. 10.2144/000114146 - DOI - PMC - PubMed

[7] Golino D. A., Fuchs M., Rwahnih M. A., Farrar K., Schmidt A., Martelli G. P. (2017). Regulatory aspects of grape viruses and virus diseases: certification, quarantine, and harmonization, in Grapevine Viruses: Molecular Biology, Diagnostics and Management (Cham, Springer; ), 581–598.

[8] Golino D. A., Fuchs M., Rwahnih M. A., Farrar K., Schmidt A., Martelli G. P. (2017). Regulatory aspects of grape viruses and virus diseases: certification, quarantine, and harmonization, in Grapevine Viruses: Molecular Biology, Diagnostics and Management (Cham, Springer; ), 581–598.

[9] Hagen C., Frizzi A., Gabriels S., Huang M., Salati R., Gabor B., et al. . (2012). Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification. Arch. Virol. 157, 907–915. 10.1007/s00705-012-1253-7 - DOI - PubMed

[10] Hagen C., Frizzi A., Gabriels S., Huang M., Salati R., Gabor B., et al. . (2012). Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification. Arch. Virol. 157, 907–915. 10.1007/s00705-012-1253-7 - DOI - PubMed

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Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges

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Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges

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References

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