MSACL 2023 Abstract

Rapid Translation of a SARS-CoV-2 Targeted Peptide Immunoaffinity LC-MS Test from Research into Routine Clinical Use

Jenny Hällqvist (1,2), Dan Lane (3,4), Andrew Shapanis (5,6), Kayleigh Davis (7), Wendy E Heywood (1), Ivan Doykov (1), Justyna Śpiewak (1), Nana Ghansah (8), Brian Keevil (9), Pankaj Gupta (3,10), Rebekah Jukes-Jones (3,11), Raj Singh (11), Dominic Foley (12,13), Johannes P C Vissers (12,13), Rebecca Pattison (12,13), Samantha Ferries (12,13), Robert Wardle (12,13), Amy Bartlett (12,13), Lisa J Calton (12,13), Leigh Anderson (14,15), Morteza Razavi (14,15), Terry Pearson (14,15), Matt Pope (14,15), Richard Yip (14,15), Leong L Ng (10,11), Benjamin I Nicholas (5), Alistair Bailey (5), Dan Noel (6), R Neil Dalton (16), Simon Heales (8), Christopher Hopley (17), Andrew R Pitt (18), Perdita Barran (18), Donald J L Jones (11), Kevin Mills (1), Paul Skipp (5,6), Rachel S Carling (7,19)
(1) UCL Translational Mass Spectrometry Research Group Unit, London, UK (2) UCL Queen Square Institute of Neurology, London, UK (3) The Department of Chemical Pathology and Metabolic Diseases, Leicester, UK (4) Leicester Diabetes Centre, Leicester, UK (5) Centre for Proteomic Research, Southampton, UK (6) Biological Sciences, Southampton, UK (7) Synnovis, London, UK (8) Neurometabolic Unit National Hospital, London, UK (9) Department of Biochemistry, Manchester, UK (10) Department of Cardiovascular Sciences, Leicester, UK (11) van Geest MS-OMICS Facility, Leicester, UK (12) Waters Corporation, Wilmslow, UK (13) Waters Corporation, Milford, MA, USA (14) SISCAPA Assay Technologies, Inc., Washington, DC (15) SISCAPA Assay Technologies, Inc., Victoria, BC, Canada (16) Evelina London Children's Hospital, London, UK (17) LGC Teddington, Teddington, UK (18) Manchester Institute of Biotechnology, Manchester, UK (19) GKT School Medical Education, Kings College London, London, UK.

Hans Vissers, PhD (Presenter) Waters Corporation

Relevant Financial Disclosures (within past 24 months, reported on Jan 16, 2024) Honorarium/Expenses EMBL-EBI Stock/Bonds Waters Corporation Salary Waters Corporation Royalty / IP / Other Income EMBL-EBI Conflict mitigation NOT REQUIRED.

OBJECTIVES: During 2020, the Department of Health and Social Care (DHSC) of the United Kingdom established the Moonshot programme to fund various diagnostic approaches for the detection of SARS-CoV-2, the pathogen behind the COVID-19 pandemic. Mass spectrometry was one of the technologies proposed to increase testing capacity.

METHODS: Moonshot funded a multi-phase development programme, bringing together experts from academia, industry and the NHS to develop a state-of-the-art targeted protein assay utilising enrichment and liquid chromatography tandem mass spectrometry (LC-MS/MS) to capture and detect low levels of tryptic peptides derived from SARS-CoV-2 virus. The assay relies on detection of target peptides, ADETQALPQRK and AYNVTQAFGR, derived from the nucleocapsid protein of SARS-CoV-2, measurement of which allowed the specific, sensitive, and robust detection of the virus from nasopharyngeal (NP) swabs. The diagnostic sensitivity and specificity of LC-MS/MS was compared with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) via a prospective study.

RESULTS: Analysis of NP swabs (n=361) with a median RT-qPCR quantification cycle (Cq) of 27 (range 16.7-39.1) demonstrated diagnostic sensitivity of 92.4% (87.4-95.5), specificity of 97.4% (94.0-98.9) and near total concordance with RT-qPCR (Cohen's Kappa 0.90). Excluding Cq>32 samples, sensitivity was 97.9% (94.1-99.3), specificity 97.4% (94.0-98.9) and Cohen's Kappa 0.95.

CONCLUSION: This unique collaboration between academia, industry and the NHS enabled development, translation, and validation of a SARS-CoV-2 method in NP swabs to be achieved in 5 months. This pilot provides a model and pipeline for future accelerated development and implementation of LC-MS/MS protein/peptide assays into the routine clinical laboratory.