Imperial College London
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Professor Anthony Gordon

Faculty of Medicine, Department of Surgery & Cancer

Chair in Anaesthesia and Critical Care
 
 
 
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Contact

 

anthony.gordon

 
 
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Location

 

ICUQueen Elizabeth the Queen Mother Wing (QEQM)St Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Ratcliff:2021:10.1101/2021.11.01.21265384,
author = {Ratcliff, J and Al-Beidh, F and Bibi, S and Bonsall, D and Costa, Clemens SA and Estcourt, L and Evans, A and Fish, M and Folegatti, PM and Gordon, AC and Jay, C and Jennings, A and Laing, E and Lambe, T and MacIntyre-Cockett, G and Menon, D and Mouncey, PR and Nguyen, D and Pollard, AJ and Ramasamy, MN and Roberts, DJ and Rowan, KM and Rynne, J and Shankar-Hari, M and Williams, S and Harvala, H and Golubchik, T and Simmonds, P},
doi = {10.1101/2021.11.01.21265384},
title = {Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction},
url = {http://dx.doi.org/10.1101/2021.11.01.21265384},
year = {2021}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - <jats:title>Abstract</jats:title><jats:sec><jats:title>Introduction</jats:title><jats:p>Tools to detect SARS-Coronavirus-2 variants of concern and track the ongoing evolution of the virus are necessary to support public health efforts and the design and evaluation of novel COVID-19 therapeutics and vaccines. Although next-generation sequencing (NGS) has been adopted as the gold standard method for discriminating SARS-CoV-2 lineages, alternative methods may be required when processing samples with low viral loads or low RNA quality.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>An allele-specific probe polymerase chain reaction (ASP-PCR) targeting lineage-specific single nucleotide polymorphisms (SNPs) was developed and used to screen 1,082 samples from two clinical trials in the United Kingdom and Brazil. Probit regression models were developed to compare ASP-PCR performance against 1,771 NGS results for the same cohorts.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Individual SNPs were shown to readily identify specific variants of concern. ASP-PCR was shown to discriminate SARS-CoV-2 lineages with a higher likelihood than NGS over a wide range of viral loads. Comparative advantage for ASP-PCR over NGS was most pronounced in samples with Ct values between 26-30 and in samples that showed evidence of degradation. Results for samples screened by ASP-PCR and NGS showed 99% concordant results.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>ASP-PCR is well-suited to augment but not replace NGS. The method can differentiate SARS-COV-2 lineages with high accuracy and would be best deployed to screen samples with lower viral loads or that may suffer from degradation. Future work should investigate further destabilization from primer:target base mismatch through
AU  - Ratcliff,J
AU  - Al-Beidh,F
AU  - Bibi,S
AU  - Bonsall,D
AU  - Costa,Clemens SA
AU  - Estcourt,L
AU  - Evans,A
AU  - Fish,M
AU  - Folegatti,PM
AU  - Gordon,AC
AU  - Jay,C
AU  - Jennings,A
AU  - Laing,E
AU  - Lambe,T
AU  - MacIntyre-Cockett,G
AU  - Menon,D
AU  - Mouncey,PR
AU  - Nguyen,D
AU  - Pollard,AJ
AU  - Ramasamy,MN
AU  - Roberts,DJ
AU  - Rowan,KM
AU  - Rynne,J
AU  - Shankar-Hari,M
AU  - Williams,S
AU  - Harvala,H
AU  - Golubchik,T
AU  - Simmonds,P
DO  - 10.1101/2021.11.01.21265384
PY  - 2021///
TI  - Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction
UR  - http://dx.doi.org/10.1101/2021.11.01.21265384
ER  -
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