Evaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflow
Respiratory viral infections are a major global clinical problem, and rapid, cheap, scalable and agnostic diagnostic tests that capture genome-level information on viral variation are urgently needed. Metagenomic approaches would be ideal, but remain currently limited in that much of the genetic con...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
Microbiology Society
2023
|
| _version_ | 1797111197524295680 |
|---|---|
| author | Kapel, N Kalimeris, E Lumley, S Decano, A Rodger, G Alves, ML Dingle, K Oakley, S Barrett, L Barnett, S Crook, D Eyre, D Matthews, P Street, T Stoesser, NE |
| author_facet | Kapel, N Kalimeris, E Lumley, S Decano, A Rodger, G Alves, ML Dingle, K Oakley, S Barrett, L Barnett, S Crook, D Eyre, D Matthews, P Street, T Stoesser, NE |
| author_sort | Kapel, N |
| collection | OXFORD |
| description | Respiratory viral infections are a major global clinical problem, and rapid, cheap, scalable and agnostic diagnostic tests that capture genome-level information on viral variation are urgently needed. Metagenomic approaches would be ideal, but remain currently limited in that much of the genetic content in respiratory samples is human, and amplifying and sequencing the viral/pathogen component in an unbiased manner is challenging. PCR-based tests, including those which detect multiple pathogens, are already widely used, but do not capture information on strain-level variation; tests with larger viral repertoires are also expensive on a per-test basis. One intermediate approach is the use of large panels of viral probes or ‘baits’, which target or ‘capture’ sequences representing complete genomes amongst several different common viral pathogens; these are then amplified, sequenced and analysed with a sequence analysis workflow. Here we evaluate one such commercial bait capture method (the Twist Bioscience Respiratory Virus Research Panel) and sequence analysis workflow (OneCodex), using control (simulated) and patient samples head-to-head with a validated multiplex PCR clinical diagnostic test (BioFire FilmArray). We highlight the limited sensitivity and specificity of the joint Twist Bioscience/OneCodex approach, which are further reduced by shortening workflow times and increasing sample throughput to reduce per-sample costs. These issues with performance may be driven by aspects of both the laboratory (e.g. capacity to enrich for viruses present in low numbers), bioinformatics methods used (e.g. a limited viral reference database) and thresholds adopted for calling a virus as present or absent. As a result, this workflow would require further optimization prior to any implementation for respiratory virus characterization in a routine diagnostic healthcare setting. |
| first_indexed | 2024-03-07T08:05:25Z |
| format | Journal article |
| id | oxford-uuid:9b52e3c2-9965-41cd-8153-ed8bd8a8ef1b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T08:05:25Z |
| publishDate | 2023 |
| publisher | Microbiology Society |
| record_format | dspace |
| spelling | oxford-uuid:9b52e3c2-9965-41cd-8153-ed8bd8a8ef1b2023-10-27T16:26:31ZEvaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflowJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:9b52e3c2-9965-41cd-8153-ed8bd8a8ef1bEnglishSymplectic ElementsMicrobiology Society2023Kapel, NKalimeris, ELumley, SDecano, ARodger, GAlves, MLDingle, KOakley, SBarrett, LBarnett, SCrook, DEyre, DMatthews, PStreet, TStoesser, NERespiratory viral infections are a major global clinical problem, and rapid, cheap, scalable and agnostic diagnostic tests that capture genome-level information on viral variation are urgently needed. Metagenomic approaches would be ideal, but remain currently limited in that much of the genetic content in respiratory samples is human, and amplifying and sequencing the viral/pathogen component in an unbiased manner is challenging. PCR-based tests, including those which detect multiple pathogens, are already widely used, but do not capture information on strain-level variation; tests with larger viral repertoires are also expensive on a per-test basis. One intermediate approach is the use of large panels of viral probes or ‘baits’, which target or ‘capture’ sequences representing complete genomes amongst several different common viral pathogens; these are then amplified, sequenced and analysed with a sequence analysis workflow. Here we evaluate one such commercial bait capture method (the Twist Bioscience Respiratory Virus Research Panel) and sequence analysis workflow (OneCodex), using control (simulated) and patient samples head-to-head with a validated multiplex PCR clinical diagnostic test (BioFire FilmArray). We highlight the limited sensitivity and specificity of the joint Twist Bioscience/OneCodex approach, which are further reduced by shortening workflow times and increasing sample throughput to reduce per-sample costs. These issues with performance may be driven by aspects of both the laboratory (e.g. capacity to enrich for viruses present in low numbers), bioinformatics methods used (e.g. a limited viral reference database) and thresholds adopted for calling a virus as present or absent. As a result, this workflow would require further optimization prior to any implementation for respiratory virus characterization in a routine diagnostic healthcare setting. |
| spellingShingle | Kapel, N Kalimeris, E Lumley, S Decano, A Rodger, G Alves, ML Dingle, K Oakley, S Barrett, L Barnett, S Crook, D Eyre, D Matthews, P Street, T Stoesser, NE Evaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflow |
| title | Evaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflow |
| title_full | Evaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflow |
| title_fullStr | Evaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflow |
| title_full_unstemmed | Evaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflow |
| title_short | Evaluation of sequence hybridisation for respiratory viruses using the Twist Biosciences Respiratory panel and the OneCodex Respiratory Virus sequence analysis workflow |
| title_sort | evaluation of sequence hybridisation for respiratory viruses using the twist biosciences respiratory panel and the onecodex respiratory virus sequence analysis workflow |
| work_keys_str_mv | AT kapeln evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT kalimerise evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT lumleys evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT decanoa evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT rodgerg evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT alvesml evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT dinglek evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT oakleys evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT barrettl evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT barnetts evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT crookd evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT eyred evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT matthewsp evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT streett evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow AT stoesserne evaluationofsequencehybridisationforrespiratoryvirusesusingthetwistbiosciencesrespiratorypanelandtheonecodexrespiratoryvirussequenceanalysisworkflow |