Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence
High-throughput sequencing (HTS) technologies and bioinformatic analyses are of growing interest to be used as a routine diagnostic tool in the field of plant viruses. The reliability of HTS workflows from sample preparation to data analysis and results interpretation for plant virus detection and i...
| Autores principales: | , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2021
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/115074 |
| _version_ | 1855532840379219968 |
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| author | Gaafar, Y.Z.A. Westenberg, M. Botermans, M. László, K. Jonghe, K. Foucart, Y. Ferretti, L. Kutnjak, D. Pecman, A. Mehle, N. Kreuze, Jan F. Muller, G. Vakirlis, N. Beris, D. Varveri, C. Ziebell, H. |
| author_browse | Beris, D. Botermans, M. Ferretti, L. Foucart, Y. Gaafar, Y.Z.A. Jonghe, K. Kreuze, Jan F. Kutnjak, D. László, K. Mehle, N. Muller, G. Pecman, A. Vakirlis, N. Varveri, C. Westenberg, M. Ziebell, H. |
| author_facet | Gaafar, Y.Z.A. Westenberg, M. Botermans, M. László, K. Jonghe, K. Foucart, Y. Ferretti, L. Kutnjak, D. Pecman, A. Mehle, N. Kreuze, Jan F. Muller, G. Vakirlis, N. Beris, D. Varveri, C. Ziebell, H. |
| author_sort | Gaafar, Y.Z.A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | High-throughput sequencing (HTS) technologies and bioinformatic analyses are of growing interest to be used as a routine diagnostic tool in the field of plant viruses. The reliability of HTS workflows from sample preparation to data analysis and results interpretation for plant virus detection and identification must be evaluated (verified and validated) to approve this tool for diagnostics. Many different extraction methods, library preparation protocols, and sequence and bioinformatic pipelines are available for virus sequence detection. To assess the performance of plant virology diagnostic laboratories in using the HTS of ribosomal RNA depleted total RNA (ribodepleted totRNA) as a diagnostic tool, we carried out an interlaboratory comparison study in which eight participants were required to use the same samples, (RNA) extraction kit, ribosomal RNA depletion kit, and commercial sequencing provider, but also their own bioinformatics pipeline, for analysis. The accuracy of virus detection ranged from 65% to 100%. The false-positive detection rate was very low and was related to the misinterpretation of results as well as to possible cross-contaminations in the lab or sequencing provider. The bioinformatic pipeline used by each laboratory influenced the correct detection of the viruses of this study. The main difficulty was the detection of a novel virus as its sequence was not available in a publicly accessible database at the time. The raw data were reanalysed using Virtool to assess its ability for virus detection. All virus sequences were detected using Virtool in the different pools. This study revealed that the ribodepletion target enrichment for sample preparation is a reliable approach for the detection of plant viruses with different genomes. A significant level of virology expertise is needed to correctly interpret the results. It is also important to improve and complete the reference data. |
| format | Journal Article |
| id | CGSpace115074 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1150742025-12-08T09:54:28Z Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence Gaafar, Y.Z.A. Westenberg, M. Botermans, M. László, K. Jonghe, K. Foucart, Y. Ferretti, L. Kutnjak, D. Pecman, A. Mehle, N. Kreuze, Jan F. Muller, G. Vakirlis, N. Beris, D. Varveri, C. Ziebell, H. rna plant viruses bioinformatics High-throughput sequencing (HTS) technologies and bioinformatic analyses are of growing interest to be used as a routine diagnostic tool in the field of plant viruses. The reliability of HTS workflows from sample preparation to data analysis and results interpretation for plant virus detection and identification must be evaluated (verified and validated) to approve this tool for diagnostics. Many different extraction methods, library preparation protocols, and sequence and bioinformatic pipelines are available for virus sequence detection. To assess the performance of plant virology diagnostic laboratories in using the HTS of ribosomal RNA depleted total RNA (ribodepleted totRNA) as a diagnostic tool, we carried out an interlaboratory comparison study in which eight participants were required to use the same samples, (RNA) extraction kit, ribosomal RNA depletion kit, and commercial sequencing provider, but also their own bioinformatics pipeline, for analysis. The accuracy of virus detection ranged from 65% to 100%. The false-positive detection rate was very low and was related to the misinterpretation of results as well as to possible cross-contaminations in the lab or sequencing provider. The bioinformatic pipeline used by each laboratory influenced the correct detection of the viruses of this study. The main difficulty was the detection of a novel virus as its sequence was not available in a publicly accessible database at the time. The raw data were reanalysed using Virtool to assess its ability for virus detection. All virus sequences were detected using Virtool in the different pools. This study revealed that the ribodepletion target enrichment for sample preparation is a reliable approach for the detection of plant viruses with different genomes. A significant level of virology expertise is needed to correctly interpret the results. It is also important to improve and complete the reference data. 2021-09-12 2021-09-21T15:18:58Z 2021-09-21T15:18:58Z Journal Article https://hdl.handle.net/10568/115074 en Open Access MDPI Gaafar, Y. Z. A., Westenberg, M., Botermans, M., László, K., de Jonghe, K., Foucart, Y., Ferretti, L., Kutnjak, D., Pecman, A., Mehle, N., Kreuze, J., Muller, G., Vakirlis, N., Beris, D., Varveri, C., & Ziebell, H. (2021). Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence. Pathogens. ISSN 2076-0817. 10(9). 16 p. |
| spellingShingle | rna plant viruses bioinformatics Gaafar, Y.Z.A. Westenberg, M. Botermans, M. László, K. Jonghe, K. Foucart, Y. Ferretti, L. Kutnjak, D. Pecman, A. Mehle, N. Kreuze, Jan F. Muller, G. Vakirlis, N. Beris, D. Varveri, C. Ziebell, H. Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence |
| title | Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence |
| title_full | Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence |
| title_fullStr | Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence |
| title_full_unstemmed | Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence |
| title_short | Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence |
| title_sort | interlaboratory comparison study on ribodepleted total rna high throughput sequencing for plant virus diagnostics and bioinformatic competence |
| topic | rna plant viruses bioinformatics |
| url | https://hdl.handle.net/10568/115074 |
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