Show simple item record

dc.contributor.authorRatcliff, Jeremy
dc.contributor.authorAl-Beidh, Farah
dc.contributor.authorBibi, Sagida
dc.contributor.authorBonsall, David
dc.contributor.authorCosta Clemens, Sue Ann
dc.contributor.authorEstcourt, Lise
dc.contributor.authorEvans, Amy
dc.contributor.authorFish, Matthew
dc.contributor.authorFolegatti, Pedro M
dc.contributor.authorGordon, Anthony C
dc.contributor.authorJay, Cecilia
dc.contributor.authorJennings, Aislinn
dc.contributor.authorLaing, Emma
dc.contributor.authorLambe, Teresa
dc.contributor.authorMacIntyre-Cockett, George
dc.contributor.authorMenon, David
dc.contributor.authorMouncey, Paul R
dc.contributor.authorNguyen, Dung
dc.contributor.authorPollard, Andrew J
dc.contributor.authorRamasamy, Maheshi N
dc.contributor.authorRoberts, David J
dc.contributor.authorRowan, Kathryn M
dc.contributor.authorRynne, Jennifer
dc.contributor.authorShankar-Hari, Manu
dc.contributor.authorWilliams, Sarah
dc.contributor.authorHarvala, Heli
dc.contributor.authorGolubchik, Tanya
dc.contributor.authorSimmonds, Peter
dc.contributor.authorAMPHEUS Project, REMAP-CAP Immunoglobulin Domain UK Investigators, and Oxford COVID-19 Vaccine Trial Group
dc.date.accessioned2022-04-25T01:03:06Z
dc.date.available2022-04-25T01:03:06Z
dc.date.issued2022-04-20
dc.identifier.issn0095-1137
dc.identifier.other35321556
dc.identifier.otherPMC9020347
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/336409
dc.description.abstractTools to detect SARS-CoV-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. To this aim, an allele-specific probe PCR (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. 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. The comparative advantage for ASP-PCR over NGS was most pronounced in samples with cycle threshold (CT) values between 26 and 30 and in samples that showed evidence of degradation. Results for samples screened by ASP-PCR and NGS showed 99% concordant results. 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 altered oligonucleotide chemistry or chemical additives.
dc.languageeng
dc.publisherAmerican Society for Microbiology
dc.sourcenlmid: 7505564
dc.sourceessn: 1098-660X
dc.subjectDiagnostics
dc.subjectNext-generation Sequencing
dc.subjectVariant Identification
dc.subjectSars-cov-2
dc.subjectVariants Of Concern
dc.subjectAllele-specific Probe Pcr
dc.titleHighly Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe PCR.
dc.typeArticle
dc.date.updated2022-04-25T01:03:05Z
prism.issueIdentifier4
prism.publicationNameJ Clin Microbiol
prism.volume60
dc.identifier.doi10.17863/CAM.83826
rioxxterms.versionofrecord10.1128/jcm.02283-21
rioxxterms.versionVoR
dc.contributor.orcidRatcliff, Jeremy [0000-0001-6522-138X]
dc.contributor.orcidBonsall, David [0000-0003-2187-0550]
dc.contributor.orcidJay, Cecilia [0000-0003-2387-9225]
dc.contributor.orcidShankar-Hari, Manu [0000-0002-5338-2538]
dc.contributor.orcidGolubchik, Tanya [0000-0003-2765-9828]
dc.contributor.orcidSimmonds, Peter [0000-0002-7964-4700]
dc.identifier.eissn1098-660X
pubs.funder-project-idWellcome Trust (215522)
cam.issuedOnline2022-03-24


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record