A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics.
Betacoronavirus
/ genetics
Biological Assay
COVID-19
COVID-19 Testing
CRISPR-Cas Systems
Clinical Laboratory Techniques
/ instrumentation
Coronavirus Infections
/ diagnosis
Humans
Molecular Diagnostic Techniques
/ methods
Nucleic Acid Amplification Techniques
/ methods
Pandemics
Pneumonia, Viral
/ diagnosis
RNA, Viral
/ analysis
Real-Time Polymerase Chain Reaction
SARS-CoV-2
Sensitivity and Specificity
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
08 09 2020
08 09 2020
Historique:
received:
05
05
2020
accepted:
05
08
2020
entrez:
9
9
2020
pubmed:
10
9
2020
medline:
24
9
2020
Statut:
epublish
Résumé
The SARS-CoV-2 pandemic has shown how a rapid rise in demand for patient and community sample testing can quickly overwhelm testing capability globally. With most diagnostic infrastructure dependent on specialized instruments, their exclusive reagent supplies quickly become bottlenecks, creating an urgent need for approaches to boost testing capacity. We address this challenge by refocusing the London Biofoundry onto the development of alternative testing pipelines. Here, we present a reagent-agnostic automated SARS-CoV-2 testing platform that can be quickly deployed and scaled. Using an in-house-generated, open-source, MS2-virus-like particle (VLP) SARS-CoV-2 standard, we validate RNA extraction and RT-qPCR workflows as well as two detection assays based on CRISPR-Cas13a and RT-loop-mediated isothermal amplification (RT-LAMP). In collaboration with an NHS diagnostic testing lab, we report the performance of the overall workflow and detection of SARS-CoV-2 in patient samples using RT-qPCR, CRISPR-Cas13a, and RT-LAMP. The validated RNA extraction and RT-qPCR platform has been installed in NHS diagnostic labs, increasing testing capacity by 1000 samples per day.
Identifiants
pubmed: 32900994
doi: 10.1038/s41467-020-18130-3
pii: 10.1038/s41467-020-18130-3
pmc: PMC7479142
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4464Subventions
Organisme : Department of Health
ID : NIHR-RP-011-048
Pays : United Kingdom
Commentaires et corrections
Type : ErratumIn
Références
World Health Organisation. Coronavirus disease 2019 (Covid-19) situation report 51. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200311-sitrep-51-covid-19.pdf?sfvrsn=1ba62e57_10 . Accessed 4 Feb 2020.
Gorbalenya, A. E. et al. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5. https://doi.org/10.1038/s41564-020-0695-z (2020).
Dong, E., Du, H. & Gardner, L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect. Dis. https://doi.org/10.1016/S1473-3099(20)30120-1 (2020).
Freemont, P. S. Synthetic biology industry: data-driven design is creating new opportunities in biotechnology. Emerg. Top. Life Sci. 3, 651–657 (2019).
doi: 10.1042/ETLS20190040
pmcid: 7289019
Pasloske, B. L., Walkerpeach, C. R., Dawn Obermoeller, R., Winkler, M. & DuBois, D. B. Armored RNA technology for production of ribonuclease-resistant viral RNA controls and standards. J. Clin. Microbiol. 36, 3590–3594 (1998).
doi: 10.1128/JCM.36.12.3590-3594.1998
pubmed: 9817878
pmcid: 105245
Cheng, Y., Niu, J., Zhang, Y., Huang, J. & Li, Q. Preparation of his-tagged armored RNA phage particles as a control for real-time reverse transcription-PCR detection of severe acute respiratory syndrome coronavirus. J. Clin. Microbiol. 44, 3557–3561 (2006).
doi: 10.1128/JCM.00713-06
pubmed: 17021082
pmcid: 1594775
Yu, X. F., Pan, J. C., Ye, R., Xiang, H. Q., Kou, Y. & Huang, Z. C. Preparation of armored RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza virus and severe acute respiratory syndrome coronavirus. J. Clin. Microbiol. 46, 837–841 (2008).
doi: 10.1128/JCM.01904-07
pubmed: 18160451
Jung, Y. J. et al. Comparative analysis of primer-probe sets for the laboratory confirmation of SARS-CoV-2. Preprint at https://doi.org/10.1101/2020.02.25.964775 (2020).
Centers for Disease Control and Prevention Division of Viral Diseases. 2019-Novel Coronavirus (2019-nCoV) Real-time Rt-PCR Panel Primers and Probes (Centers for Disease Control and Prevention Division of Viral Diseases) (2020).
Metsky, H. C., Freije, C. A., Kosoko-Thoroddsen, T.-S. F., Sabeti, P. C. & Myhrvold, C. CRISPR-based COVID-19 surveillance using a genomically-comprehensive machine learning approach. Preprint at https://doi.org/10.1101/2020.02.26.967026 (2020).
Zhang, Y. et al. Rapid molecular detection of SARS-CoV-2 (COVID-19) virus RNA using colorimetric LAMP. Preprint at https://doi.org/10.1101/2020.02.26.20028373 (2020).
Department of Health and Social Care and Public Health England. Coronavirus cases in the UK: daily updated statistics–GOV.UK. https://www.gov.uk/guidance/coronavirus-covid-19-information-for-the-public . Accessed 8 July 2020.
de Martín Garrido, N., Crone, M. A., Ramlaul, K., Simpson, P. A., Freemont, P. S. & Aylett, C. H. S. Bacteriophage MS2 displays unreported capsid variability assembling T = 4 and mixed capsids. Mol. Microbiol. 113, 143–152 (2020).
doi: 10.1111/mmi.14406
pubmed: 31618483
Mikel, P., Vasickova, P. & Kralik, P. One-plasmid double-expression His-tag system for rapid production and easy purification of MS2 phage-like particles. Sci. Rep. 7, 1–12 (2017).
doi: 10.1038/s41598-017-17951-5
Vogels, C. B. F. et al. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets. Nat. Microbiol. (2020).
Gootenberg, J. S., Abudayyeh, O. O., Kellner, M. J., Joung, J., Collins, J. J. & Zhang, F. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360, 439–444 (2018).
doi: 10.1126/science.aaq0179
pubmed: 29449508
pmcid: 5961727
Tanner, N. A., Zhang, Y. & Evans, T. C. Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes. Biotechniques 58, 59–68 (2015).
doi: 10.2144/000114253
pubmed: 25652028
Pan, Y., Zhang, D., Yang, P., Poon, L. L. M. & Wang, Q. Viral load of SARS-CoV-2 in clinical samples. Lancet Infect. Dis. 20, 411–412 (2020).
doi: 10.1016/S1473-3099(20)30113-4
pubmed: 32105638
pmcid: 7128099
Joung, J. et al. Point-of-care testing for COVID-19 using SHERLOCK diagnostics. Preprint at https://doi.org/10.1101/2020.05.04.20091231 (2020).
Foundation for Innovative New Diagnostics. Covid-19 diagnostics. https://www.finddx.org/covid-19/ . Accessed 2 April 2020.
Sheridan, C. Fast, portable tests come online to curb coronavirus pandemic. Nat. Biotechnol. https://doi.org/10.1038/d41587-020-00010-2 (2020).
Xie, Q. et al. Effect of large-scale testing platform in prevention and control of the COVID-19 pandemic: an empirical study with a novel numerical model. Preprint at https://doi.org/10.1101/2020.03.15.20036624 (2020).
Open Wet Ware. SPRI bead mix. https://openwetware.org/wiki/SPRI_bead_mix#Example_with_RNA_standard . Accessed 2 April 2020.
Aitken, J. et al. Scalable and robust SARS-CoV-2 testing in an academic center. Nat. Biotechnol. 38, 927–931 (2020).
doi: 10.1038/s41587-020-0588-y
pubmed: 32555528
Broughton, J. P. et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 38, 870–874 (2020).
doi: 10.1038/s41587-020-0513-4
pubmed: 32300245
Ackerman, C. M. et al. Massively multiplexed nucleic acid detection using Cas13. Nature https://doi.org/10.1038/s41586-020-2279-8 (2020).
Mohon, A. N. et al. Development and validation of direct RT-LAMP for SARS-CoV-2. Clin. Sect. Microbiol. 78, 1–26 (2020).
Metz, S. W. et al. Dengue virus-like particles mimic the antigenic properties of the infectious dengue virus envelope. Virol. J. 15, 1. https://doi.org/10.1186/s12985-018-0970-2 (2018).
Stevenson, J., Hymas, W. & Hillyard, D. The use of armored RNA as a multi-purpose internal control for RT-PCR. J. Virol. Methods 150, 73–76 (2008).
doi: 10.1016/j.jviromet.2008.02.007
pubmed: 18395804
pmcid: 7119664
Hillson, N. et al. Building a global alliance of biofoundries. Nat. Commun. 10, 1. https://doi.org/10.1038/s41467-019-10079-2 (2019).
Der, B. S. et al. DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data. ACS Synthetic Biology 6, 1115–1119 (2017).
doi: 10.1021/acssynbio.6b00252
pubmed: 27744689