Operation Moonshot: rapid translation of a SARS-CoV-2 targeted peptide immunoaffinity liquid chromatography-tandem mass spectrometry test from research into routine clinical use
Jenny Hällqvist, Dan Lane, Andrew Shapanis, Kayleigh Davis, Wendy Heywood, Ivan Doykov, Justyna Śpiewak, Nana Ghansah, Brian Keevil, Pankaj Gupta, Rebekah Jukes‐Jones, Raj Kumar Singh, Dominic Foley, Johannes P.C. Vissers, Rebecca Pattison, Samantha Ferries, R. Wardle, Amy Bartlett, Lisa Calton, Leigh C. Anderson, Morteza Razavi, Terry W. Pearson, Matt Pope, Richard Yip, Leong L. Ng, Ben Nicholas, A.G. Bailey, Daniel J. Noel, R. Neil Dalton, Simon Heales, Christopher Hopley, Andrew R. Pitt, Perdita E. Barran, Donald J. L. Jones, Kevin Mills, Paul Skipp, Rachel S. Carling
Abstract
OBJECTIVES: During 2020, the UK's Department of Health and Social Care (DHSC) 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 (ADE) and AYNVTQAFGR (AYN), 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. CONCLUSIONS: 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.