S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR

Michael Kidd; Alex Richter; A Best; N Cumley; Jeremy Mirza; Benita Percival; Megan Mayhew; Oliver Megram; Fiona Ashford; Thomas White; Emma Moles-Garcia; Liam Crawford; A Bosworth; Sowsan F Atabani; Tim Plant; Alan McNally

doi:10.1093/infdis/jiab082

S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR

Michael Kidd^*
, Alex Richter
, A Best
, N Cumley
, Jeremy Mirza
, Benita Percival
, Megan Mayhew
, Oliver Megram
, Fiona Ashford
, Thomas White
, Emma Moles-Garcia
, Liam Crawford
, A Bosworth
, Sowsan F Atabani
, Tim Plant
, Alan McNally

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

A SARS-CoV-2 variant B1.1.7 containing mutation Δ69/70 has spread rapidly in the United Kingdom and shows an identifiable profile in ThermoFisher TaqPath RT-qPCR, S gene target failure (SGTF). We analyzed recent test data for trends and significance. Linked cycle threshold (Ct) values for respiratory samples showed that a low Ct for ORF1ab and N were clearly associated with SGTF. Significantly more SGTF samples had higher inferred viral loads between 1×107 and 1×108. Our conclusion is that patients whose samples exhibit the SGTF profile are more likely to have high viral loads, which may explain higher infectivity and rapidity of spread.

Original language	English
Pages (from-to)	1666-1670
Number of pages	5
Journal	The Journal of Infectious Diseases
Volume	223
Issue number	10
Early online date	13 Feb 2021
DOIs	https://doi.org/10.1093/infdis/jiab082
Publication status	Published - 15 May 2021

Keywords

B.1.1.7
COVID-19
Ct values
RT-PCR
S gene dropout
S-variant
SARS-CoV-2
SGTF
TaqPath
VOC-202012/01
viral load
Δ69/70

ASJC Scopus subject areas

Immunology and Allergy
Infectious Diseases

Access to Document

10.1093/infdis/jiab082Licence: None: All rights reserved

Cite this

Kidd, M., Richter, A., Best, A., Cumley, N., Mirza, J., Percival, B., Mayhew, M., Megram, O., Ashford, F., White, T., Moles-Garcia, E., Crawford, L., Bosworth, A., Atabani, S. F., Plant, T., & McNally, A. (2021). S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR. The Journal of Infectious Diseases, 223(10), 1666-1670. https://doi.org/10.1093/infdis/jiab082

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title = "S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR",

abstract = "A SARS-CoV-2 variant B1.1.7 containing mutation Δ69/70 has spread rapidly in the United Kingdom and shows an identifiable profile in ThermoFisher TaqPath RT-qPCR, S gene target failure (SGTF). We analyzed recent test data for trends and significance. Linked cycle threshold (Ct) values for respiratory samples showed that a low Ct for ORF1ab and N were clearly associated with SGTF. Significantly more SGTF samples had higher inferred viral loads between 1×107 and 1×108. Our conclusion is that patients whose samples exhibit the SGTF profile are more likely to have high viral loads, which may explain higher infectivity and rapidity of spread.",

keywords = "B.1.1.7, COVID-19, Ct values, RT-PCR, S gene dropout, S-variant, SARS-CoV-2, SGTF, TaqPath, VOC-202012/01, viral load, Δ69/70",

author = "Michael Kidd and Alex Richter and A Best and N Cumley and Jeremy Mirza and Benita Percival and Megan Mayhew and Oliver Megram and Fiona Ashford and Thomas White and Emma Moles-Garcia and Liam Crawford and A Bosworth and Atabani, \{Sowsan F\} and Tim Plant and Alan McNally",

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Kidd, M, Richter, A, Best, A, Cumley, N, Mirza, J, Percival, B, Mayhew, M, Megram, O, Ashford, F, White, T, Moles-Garcia, E, Crawford, L, Bosworth, A, Atabani, SF, Plant, T & McNally, A 2021, 'S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR', The Journal of Infectious Diseases, vol. 223, no. 10, pp. 1666-1670. https://doi.org/10.1093/infdis/jiab082

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AU - Kidd, Michael

AU - Richter, Alex

AU - Best, A

AU - Cumley, N

AU - Mirza, Jeremy

AU - Percival, Benita

AU - Mayhew, Megan

AU - Megram, Oliver

AU - Ashford, Fiona

AU - White, Thomas

AU - Moles-Garcia, Emma

AU - Crawford, Liam

AU - Bosworth, A

AU - Atabani, Sowsan F

AU - Plant, Tim

AU - McNally, Alan

PY - 2021/5/15

Y1 - 2021/5/15

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AB - A SARS-CoV-2 variant B1.1.7 containing mutation Δ69/70 has spread rapidly in the United Kingdom and shows an identifiable profile in ThermoFisher TaqPath RT-qPCR, S gene target failure (SGTF). We analyzed recent test data for trends and significance. Linked cycle threshold (Ct) values for respiratory samples showed that a low Ct for ORF1ab and N were clearly associated with SGTF. Significantly more SGTF samples had higher inferred viral loads between 1×107 and 1×108. Our conclusion is that patients whose samples exhibit the SGTF profile are more likely to have high viral loads, which may explain higher infectivity and rapidity of spread.

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KW - Ct values

KW - RT-PCR

KW - S gene dropout

KW - S-variant

KW - SARS-CoV-2

KW - SGTF

KW - TaqPath

KW - VOC-202012/01

KW - viral load

KW - Δ69/70

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