Publications

@article{Thompson2021-wc,

title = {Comparative effects of viral-transport-medium heat inactivation 

 upon downstream SARS-CoV-2 detection in patient samples},

author = {Jamie L Thompson and Angela Downie Ruiz Velasco and Alice Cardall and Rebecca Tarbox and Jaineeta Richardson and Gemma Clarke and Michelle Lister and Hannah C Howson-Wells and Vicki M Fleming and Manjinder Khakh and Tim Sloan and Nichola Duckworth and Sarah Walsh and Chris Denning and C Patrick McClure and Andrew V Benest and Claire H Seedhouse},

year  = {2021},

date = {2021-03-01},

journal = {J. Med. Microbiol.},

volume = {70},

number = {3},

publisher = {Microbiology Society},

abstract = {Introduction. The COVID-19 pandemic, which began in 2020 is 

 testing economic resilience and surge capacity of healthcare 

 providers worldwide. At the time of writing, positive detection 

 of the SARS-CoV-2 virus remains the only method for diagnosing 

 COVID-19 infection. Rapid upscaling of national SARS-CoV-2 

 genome testing presented challenges: (1) Unpredictable supply 

 chains of reagents and kits for virus inactivation, RNA 

 extraction and PCR-detection of viral genomes. (2) Rapid time to 

 result of \<24 h is required in order to facilitate timely 

 infection control measures.Hypothesis. Extraction-free sample 

 processing would impact commercially available SARS-CoV-2 genome 

 detection methods.Aim. We evaluated whether alternative 

 commercially available kits provided sensitivity and accuracy of 

 SARS-CoV-2 genome detection comparable to those used by regional 

 National Healthcare Services (NHS).Methodology. We tested 

 several detection methods and tested whether detection was 

 altered by heat inactivation, an approach for rapid one-step 

 viral inactivation and RNA extraction without chemicals or 

 kits.Results. Using purified RNA, we found the CerTest VIASURE 

 kit to be comparable to the Altona RealStar system currently in 

 use, and further showed that both diagnostic kits performed 

 similarly in the BioRad CFX96 and Roche LightCycler 480 II 

 machines. Additionally, both kits were comparable to a third 

 alternative using a combination of Quantabio qScript one-step 

 Quantitative Reverse Transcription Polymerase Chain Reaction 

 (qRT-PCR) mix and Centre for Disease Control and Prevention 

 (CDC)-accredited N1 and N2 primer/probes when looking 

 specifically at borderline samples. Importantly, when using the 

 kits in an extraction-free protocol, following heat 

 inactivation, we saw differing results, with the combined 

 Quantabio-CDC assay showing superior accuracy and sensitivity. 

 In particular, detection using the CDC N2 probe following the 

 extraction-free protocol was highly correlated to results 

 generated with the same probe following RNA extraction and reported clinically (n=127; R2=0.9259).Conclusion. Our results 

 demonstrate that sample treatment can greatly affect the 

 downstream performance of SARS-CoV-2 diagnostic kits, with 

 varying impact depending on the kit. We also showed that 

 one-step heat-inactivation methods could reduce time from swab 

 receipt to outcome of test result. Combined, these findings 

 present alternatives to the protocols in use and can serve to 

 alleviate any arising supply-chain issues at different points in 

 the workflow, whilst accelerating testing, and reducing cost and 

 environmental impact.},

keywords = {COVID-19, RT-qPCR testing, SARS-CoV-2, viral transport media},

pubstate = {published},

tppubtype = {article}

}