Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage
High-throughput sequencing (HTS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care HTS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particular...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-10-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.967021/full |
| _version_ | 1798028792400183296 |
|---|---|
| author | Sandro L. Valenzuela Tomás Norambuena Verónica Morgante Francisca García Juan C. Jiménez Carlos Núñez Ignacia Fuentes Bernardo Pollak Bernardo Pollak |
| author_facet | Sandro L. Valenzuela Tomás Norambuena Verónica Morgante Francisca García Juan C. Jiménez Carlos Núñez Ignacia Fuentes Bernardo Pollak Bernardo Pollak |
| author_sort | Sandro L. Valenzuela |
| collection | DOAJ |
| description | High-throughput sequencing (HTS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care HTS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets, and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand HTS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis. |
| first_indexed | 2024-04-11T19:15:03Z |
| format | Article |
| id | doaj.art-0686782d60a742319d3a0bbbd794edaf |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T19:15:03Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-0686782d60a742319d3a0bbbd794edaf2022-12-22T04:07:27ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-10-011310.3389/fmicb.2022.967021967021Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverageSandro L. Valenzuela0Tomás Norambuena1Verónica Morgante2Francisca García3Juan C. Jiménez4Carlos Núñez5Ignacia Fuentes6Bernardo Pollak7Bernardo Pollak8Meristem SpA, Santiago, ChileMeristem SpA, Santiago, ChileMultiplex SpA, Santiago, ChileMultiplex SpA, Santiago, ChileMultiplex SpA, Santiago, ChileMeristem SpA, Santiago, ChileMeristem SpA, Santiago, ChileMeristem SpA, Santiago, ChileMultiplex SpA, Santiago, ChileHigh-throughput sequencing (HTS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care HTS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets, and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand HTS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.https://www.frontiersin.org/articles/10.3389/fmicb.2022.967021/fullViroscopeplant viral diagnosticsnext-generation sequencinggenome assembly coveragereplicase identificationphytopathology |
| spellingShingle | Sandro L. Valenzuela Tomás Norambuena Verónica Morgante Francisca García Juan C. Jiménez Carlos Núñez Ignacia Fuentes Bernardo Pollak Bernardo Pollak Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage Frontiers in Microbiology Viroscope plant viral diagnostics next-generation sequencing genome assembly coverage replicase identification phytopathology |
| title | Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage |
| title_full | Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage |
| title_fullStr | Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage |
| title_full_unstemmed | Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage |
| title_short | Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage |
| title_sort | viroscope plant viral diagnosis from high throughput sequencing data using biologically informed genome assembly coverage |
| topic | Viroscope plant viral diagnostics next-generation sequencing genome assembly coverage replicase identification phytopathology |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.967021/full |
| work_keys_str_mv | AT sandrolvalenzuela viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage AT tomasnorambuena viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage AT veronicamorgante viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage AT franciscagarcia viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage AT juancjimenez viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage AT carlosnunez viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage AT ignaciafuentes viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage AT bernardopollak viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage AT bernardopollak viroscopeplantviraldiagnosisfromhighthroughputsequencingdatausingbiologicallyinformedgenomeassemblycoverage |