Rapid Molecular Diagnostics For New&Emerging SARS-CoV-2 Variants of Concern-Protecting Vaccine Efficacy

Lead Research Organisation: CARDIFF UNIVERSITY
Department Name: School of Biosciences


Despite the successful development of several efficacious vaccines, the COVID-19 pandemic continues to threaten the UK and global populations. Whilst vaccinations efforts have been hugely successful and provide the basis to facilitate opening up of society and a return to normality, the emergence of SARS-CoV-2 variants capable of evading the immune response endanger the efficacy of the vaccination strategy. To preserve the efficacy of SARS-CoV-2 vaccination in the UK population, aggressive and rapid surveillance for known and emerging SARS-CoV-2 variants of concern (VoCs) is required. Rapid and specific molecular diagnostics can provide speed and coverage advantages compared to genomic sequencing alone, benefitting the public health response to facilitate containment.

In this project, we expand our recently developed SARS-CoV-2 variant-specific detection technology to allow rapid discrimination of variants of concern. This approach can be implemented directly and immediately on positive samples in the pipelines of large testing facilities or developed for Point of Care (PoC) use. This technology will complement the current genomic sequencing efforts that allow identification of new and existing VoCs and facilitate lineage tracking, with rapid molecular diagnostics able to assist the public health response by identifying key variants without the delay and sub-sampling associated with genomic sequencing, therefore allowing a rapid and agile response to aid breaking chains of transmission and facilitate containment before widespread community transmission occurs.
Description In this work, we have established an improved CRISPR-based diagnostic method that is capable of efficiently and rapidly identifying SARS-CoV-2 variants of concern (VOC). We have established 16 assays to discriminate and quantify mutations found in COVID-19 VOCs and used them to identify COVID-19 variants in positive saliva samples of Cardiff University students and staff (it is now a routine part of the testing service). In addition, we apply our method for VOC quantification in wastewater samples that are collected throughout Wales. The collected results are reported to Welsh Government weekly.

For other aims, we have successfully tested and established storage conditions (lyophylisation) for the testing reagents as well as identified direct methods for detection without the need for RNA isolation.
We have met all the objectives of the award
Exploitation Route As follow up, together with Llusern Ltd (Molecular diagnostics company), we are translating our assays and findings to be used on the Point-Of-Care device manufactured by Llusern Ltd, in order to offer rapid VOC testing to the public. For this part we have received funding from CALIN project.
Sectors Environment



including Industrial Biotechology

Description The technology that we developed in this project has been applied in: 1) it is used for SARS-CoV-2 variant of concern (VOC) detection as part of the now routine testing for COVID19 infections at Cardiff University 2) Wastewater COVID-19 testing and quantification of VOCs (Welsh Government project) 3) translation of the technology to commercial point-of-care testing devices (Llusern Ltd) to offer the rapid VOC detection to the public (translational project supported by CALIN - The Celtic Advanced Life Science Innovation Network)
First Year Of Impact 2022
Sector Environment,Healthcare,Manufacturing, including Industrial Biotechology
Impact Types Economic

Title Sensitive CRISPR diagnostics for SNP detection 
Description We have developed a rapid, sequencing-independent, CRISPR based molecular diagnostics tools for sensitive detection and discrimination of genetic variants. Our established method is versatile - it can be applied for any nucleic acid-based pathogen detection, sensitive - as low as 10 genome copies are required for detection, specific - capable of discriminating single nucleotide exchanges, rapidly adaptable - provides a very short TAT for assay development 
Type Of Material Technology assay or reagent 
Year Produced 2022 
Provided To Others? Yes  
Impact This technology is applied for SARS-CoV-2 variant identification as a standard process at the Cardiff University COVID-19 testing centre. It is also used for SARS-CoV-2 VOC quantification for pan-Wales wastewater samples. 
Description Innovation guidance Welsh Gov group 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Advising the Welsh Government on the Innovation for Molecular Diagnostics (SARS-CoV-2 and beyond)
Year(s) Of Engagement Activity 2021,2022