VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance

Nan, Xinsheng ORCID: https://orcid.org/0000-0002-0865-7934, Hardinge, Patrick ORCID: https://orcid.org/0000-0002-6292-5186, Hoehn, Sven, Dighe, Shrinivas Nivrutti ORCID: https://orcid.org/0000-0002-2826-8733, Ukeri, John, Pease, Darius F., Griffin, Joshua, Warrington, Jessica I., Saud, Zack, Hottinger, Emma, Webster, Gordon ORCID: https://orcid.org/0000-0002-9530-7835, Jones, Davey, Kille, Peter ORCID: https://orcid.org/0000-0001-6023-5221, Weightman, Andrew ORCID: https://orcid.org/0000-0002-6671-2209, Stanton, Richard ORCID: https://orcid.org/0000-0002-6799-1182, Castell, Oliver K. ORCID: https://orcid.org/0000-0002-6059-8062, Murray, James A. H. ORCID: https://orcid.org/0000-0002-2282-3839 and Jurkowski, Tomasz P. ORCID: https://orcid.org/0000-0002-2012-0240 2023. VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance. Scientific Reports 13 (1) , 20832. 10.1038/s41598-023-47289-0

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Abstract

The COVID-19 pandemic demonstrated the need for rapid molecular diagnostics. Vaccination programs can provide protection and facilitate the opening of society, but newly emergent and existing viral variants capable of evading the immune system endanger their efficacy. Effective surveillance for Variants of Concern (VOC) is therefore important. Rapid and specific molecular diagnostics can provide speed and coverage advantages compared to genomic sequencing alone, benefitting the public health response and facilitating VOC containment. Here we expand the recently developed SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) to provide rapid and sensitive discrimination of SARS-CoV-2 VOCs that can be used at point of care, implemented in the pipelines of small or large testing facilities, and even determine the proportion of VOCs in pooled population-level wastewater samples. This technology complements sequencing efforts to allow facile and rapid identification of individuals infected with VOCs to help break infection chains. We show the optimisation of our VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validation with samples from the Cardiff University Testing Service. We also show the applicability of VarLOCK to national wastewater surveillance of SARS-CoV-2 variants and the rapid adaptability of the technique for new and emerging VOCs.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Medicine Biosciences Systems Immunity Research Institute (SIURI)
Publisher:	Nature Research
ISSN:	2045-2322
Funders:	BBSRC, MRC, Wellcome Trust
Date of First Compliant Deposit:	29 November 2023
Date of Acceptance:	11 November 2023
Last Modified:	03 Jan 2024 17:42
URI:	https://orca.cardiff.ac.uk/id/eprint/164429

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