TY - JOUR
T1 - SARS-CoV-2 Testing in the Community
T2 - Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time
AU - The COVID-19 Genomics UK (COG-UK) Consortium
AU - Ashford, Fiona
AU - Best, Angus
AU - Dunn, Steven J.
AU - Ahmed, Zahra
AU - Siddiqui, Henna
AU - Melville, Jordan
AU - Wilkinson, Samuel
AU - Mirza, Jeremy
AU - Cumley, Nicola
AU - Stockton, Joanne
AU - Ferguson, Jack
AU - Wheatley, Lucy
AU - Ratcliffe, Elizabeth
AU - Casey, Anna
AU - Plant, Tim
AU - Quick, Joshua
AU - Richter, Alex
AU - Loman, Nicholas
AU - McNally, Alan
AU - Aggarwal, Dinesh
AU - Blane, Beth
AU - Brooks, Ellena
AU - Carabelli, Alessandro M.
AU - Churcher, Carol M.
AU - Galai, Katerina
AU - Girgis, Sophia T.
AU - Gupta, Ravi K.
AU - Hadjirin, Nazreen F.
AU - Leek, Danielle
AU - Ludden, Catherine
AU - McManus, Georgina M.
AU - Palmer, Sophie
AU - Peacock, Sharon J.
AU - Smith, Kim S.
AU - Allara, Elias
AU - Bibby, David
AU - Bishop, Chloe
AU - Bosworth, Andrew
AU - Bradshaw, Daniel
AU - Chalker, Vicki
AU - Chand, Meera
AU - Dabrera, Gavin
AU - Ellaby, Nicholas
AU - Gallagher, Eileen
AU - Groves, Natalie
AU - Harrison, Ian
AU - Hartman, Hassan
AU - Hopes, Richard
AU - Hubb, Jonathan
AU - Hutchings, Stephanie
AU - Lackenby, Angie
AU - Ledesma, Juan
AU - Lee, David
AU - Manesis, Nikos
AU - Manso, Carmen
AU - Mbisa, Tamyo
AU - Miah, Shahjahan
AU - Muir, Peter
AU - Myers, Richard
AU - Osman, Husam
AU - Patel, Vineet
AU - Pearson, Clare
AU - Platt, Steven
AU - Pymont, Hannah M.
AU - Ramsay, Mary
AU - Robinson, Esther
AU - Schaefer, Ulf
AU - Thornton, Alicia
AU - Twohig, Katherine A.
AU - Vipond, Ian B.
AU - Williams, David
AU - Hamilton, William L.
AU - Warne, Ben
AU - Aigrain, Louise
AU - Alderton, Alex
AU - Amato, Roberto
AU - Ariani, Cristina V.
AU - Barrett, Jeff
AU - Bassett, Andrew R.
AU - Beale, Mathew A.
AU - Beaver, Charlotte
AU - Bellis, Katherine L.
AU - Betteridge, Emma
AU - Bonfield, James
AU - Bronner, Iraad F.
AU - Chapman, Michael H.S.
AU - Danesh, John
AU - Davies, Robert
AU - Dorman, Matthew J.
AU - Drury, Eleanor
AU - Durham, Jillian
AU - Farr, Ben W.
AU - Foulser, Luke
AU - Goncalves, Sonia
AU - Goodwin, Scott
AU - Gourtovaia, Marina
AU - Harrison, Ewan M.
AU - Jackson, David K.
AU - James, Keith
AU - Jamrozy, Dorota
N1 - Publisher Copyright:
© 2022 American Society for Microbiology.
PY - 2022/4
Y1 - 2022/4
N2 - Genome sequencing is a powerful tool for identifying SARS-CoV-2 variant lineages; however, there can be limitations due to sequence dropout when used to identify specific key mutations. Recently, ThermoFisher Scientific has developed genotyping assays to help bridge the gap between testing capacity and sequencing capability to generate real-time genotyping results based on specific variants. Over a 6-week period during the months of April and May 2021, we set out to assess the ThermoFisher TaqMan mutation panel genotyping assay, initially for three mutations of concern and then for an additional two mutations of concern, against SARS-CoV-2- positive clinical samples and the corresponding COVID-19 Genomics UK Consortium (COG-UK) sequencing data. We demonstrate that genotyping is a powerful in-depth technique for identifying specific mutations, is an excellent complement to genome sequencing, and has real clinical health value potential, allowing laboratories to report and take action on variants of concern much more quickly.
AB - Genome sequencing is a powerful tool for identifying SARS-CoV-2 variant lineages; however, there can be limitations due to sequence dropout when used to identify specific key mutations. Recently, ThermoFisher Scientific has developed genotyping assays to help bridge the gap between testing capacity and sequencing capability to generate real-time genotyping results based on specific variants. Over a 6-week period during the months of April and May 2021, we set out to assess the ThermoFisher TaqMan mutation panel genotyping assay, initially for three mutations of concern and then for an additional two mutations of concern, against SARS-CoV-2- positive clinical samples and the corresponding COVID-19 Genomics UK Consortium (COG-UK) sequencing data. We demonstrate that genotyping is a powerful in-depth technique for identifying specific mutations, is an excellent complement to genome sequencing, and has real clinical health value potential, allowing laboratories to report and take action on variants of concern much more quickly.
KW - genome sequencing
KW - genotyping
KW - PCR
KW - real time
KW - SARS-CoV-2
KW - SNPs
KW - variants of concern
UR - https://www.scopus.com/pages/publications/85128797135
U2 - 10.1128/jcm.02408-21
DO - 10.1128/jcm.02408-21
M3 - Article
C2 - 35369709
AN - SCOPUS:85128797135
SN - 0095-1137
VL - 60
JO - Journal of Clinical Microbiology
JF - Journal of Clinical Microbiology
IS - 4
ER -
SDG 3 Good Health and Well-being