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Rohaim MA, Clayton E, Sahin I, Vilela J, Khalifa ME, Al-Natour MQ, Bayoumi M, Poirier AC, Branavan M, Tharmakulasingam M, Chaudhry NS, Sodi R, Brown A, Burkhart P, Hacking W, Botham J, Boyce J, Wilkinson H, Williams C, Whittingham-Dowd J, Shaw E, Hodges M, Butler L, Bates MD, La Ragione R, Balachandran W, Fernando A, Munir M. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2. Viruses 2020; 12:v12090972. [PMID: 32883050 PMCID: PMC7552048 DOI: 10.3390/v12090972] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 01/13/2023] Open
Abstract
Until vaccines and effective therapeutics become available, the practical solution to transit safely out of the current coronavirus disease 19 (CoVID-19) lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of results, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ~200 coronavirus disease (CoVID-19)-suspected NHS patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. Therefore, this system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.
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Affiliation(s)
- Mohammed A. Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Emily Clayton
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Irem Sahin
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Julianne Vilela
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Manar E. Khalifa
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Mohammad Q. Al-Natour
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Aurore C. Poirier
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK; (A.C.P.); (R.L.R.)
| | - Manoharanehru Branavan
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (M.B.); (W.B.)
| | - Mukunthan Tharmakulasingam
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford GU2 7XH, UK; (M.T.); (N.S.C.); (A.F.)
| | - Nouman S. Chaudhry
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford GU2 7XH, UK; (M.T.); (N.S.C.); (A.F.)
| | - Ravinder Sodi
- Department of Biochemistry, Poole & Bournemouth Hospitals NHS Trust, Longfleet Road, Poole BH15 2JB, UK;
| | - Amy Brown
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Peter Burkhart
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Wendy Hacking
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Judy Botham
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Joe Boyce
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Hayley Wilkinson
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Craig Williams
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Jayde Whittingham-Dowd
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Elisabeth Shaw
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Matt Hodges
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Lisa Butler
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Michelle D. Bates
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Roberto La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK; (A.C.P.); (R.L.R.)
| | - Wamadeva Balachandran
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (M.B.); (W.B.)
| | - Anil Fernando
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford GU2 7XH, UK; (M.T.); (N.S.C.); (A.F.)
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
- Correspondence:
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