Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2.

Journal: Viruses
PMID: 32883050

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.

Authors

  • Mohammed A Rohaim
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom.
  • Emily Clayton
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Irem Sahin
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Julianne Vilela
    Philippine Genome Center Program for Agriculture, Office of the Vice Chancellor for Research and Extension, University of the Philippines Los Baños, Philippines.
  • Manar E Khalifa
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Mohammad Q Al-Natour
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Mahmoud Bayoumi
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Aurore C Poirier
    Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom.
  • Manoharanehru Branavan
    College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom.
  • Mukunthan Tharmakulasingam
    Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom.
  • Nouman S Chaudhry
    Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom.
  • 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.
  • Peter Burkhart
    The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom.
  • Wendy Hacking
    The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK.
  • Judy Botham
    The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK.
  • Joe Boyce
    The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK.
  • Hayley Wilkinson
    The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK.
  • Craig Williams
    The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom.
  • Jayde Whittingham-Dowd
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Elisabeth Shaw
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Matt Hodges
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Lisa Butler
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Michelle D Bates
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK.
  • Roberto La Ragione
    Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK.
  • Wamadeva Balachandran
    College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom.
  • Anil Fernando
    Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom.
  • Muhammad Munir
    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom.

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