Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing

Tom Fowler; Edward Blandford; David Chapman; Matthias E Futschik; Raghavendran Kulasegaran-Shylini; Sarah Tunkel; Carolyn Lewis; Alasdair Fellows; Ellie Sheppard; Leanne McCabe; Peter Marks; Paul E Klapper; Andrew Dodgson; Malur Sudhanva; Mike Kidd; Andy Vail; Susan Hopkins; Tim Peto

doi:10.1016/j.diagmicrobio.2024.116577

Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing

Tom Fowler, Edward Blandford, David Chapman, Matthias E Futschik, Raghavendran Kulasegaran-Shylini, Sarah Tunkel, Carolyn Lewis, Alasdair Fellows, Ellie Sheppard, Leanne McCabe, Peter Marks, Paul E Klapper, Andrew Dodgson, Malur Sudhanva, Mike Kidd, Andy Vail, Susan Hopkins, Tim Peto

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Abstract

PURPOSE: The Omicron variant of SARS-CoV-2 raised concerns about the best sampling sites for PCR testing, with early indications suggesting throat swab samples were better than nasal swab samples. Our study evaluated the sensitivity of detecting SARS-CoV-2 across different swabbing sites.

METHODS: Participants undergoing testing at NHS Test and Trace sites in England provided self-collected samples using nose only, throat only, and combined nose and throat swabs, which were analysed by realtime PCR.

RESULTS: Among 815 participants, combined swabs had higher viral concentrations than nose only or throat only swabs. Sensitivity for detecting SARS-CoV-2 by PCR was 91 % for nose only and 97 % for throat only, relative to the combined approach. VC remained stable in nose swabs but declined in throat swabs with time.

CONCLUSIONS: Combined nose and throat swabbing remains the most effective method for SARS-CoV-2 detection. If a single swab is used, a throat swab has a higher sensitivity than nose swabs, although VC in the throat decreases faster in later infection stages. The variations in VC over time and intra-person variation between sampling sites underscore the complexity of viral dynamics, highlighting the importance of considering both nose and throat samples for comprehensive testing.

Original language	English
Article number	116577
Journal	Diagnostic Microbiology and Infectious Disease
Volume	111
Issue number	1
Early online date	28 Oct 2024
DOIs	https://doi.org/10.1016/j.diagmicrobio.2024.116577
Publication status	E-pub ahead of print - 28 Oct 2024

ASJC Scopus subject areas

Microbiology (medical)
Infectious Diseases

Keywords

COVID-19 PCR testing
Combined nose & throat swabbing
Omicron variant
Self-test
Viral concentration

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.diagmicrobio.2024.116577

1-s2.0-S0732889324004024-mainFinal published version, 1.31 MBLicence: CC BY

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Fowler, T., Blandford, E., Chapman, D., Futschik, M. E., Kulasegaran-Shylini, R., Tunkel, S., Lewis, C., Fellows, A., Sheppard, E., McCabe, L., Marks, P., Klapper, P. E., Dodgson, A., Sudhanva, M., Kidd, M., Vail, A., Hopkins, S., & Peto, T. (2025). Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing. Diagnostic Microbiology and Infectious Disease, 111(1), Article 116577. Advance online publication. https://doi.org/10.1016/j.diagmicrobio.2024.116577

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title = "Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing",

abstract = "PURPOSE: The Omicron variant of SARS-CoV-2 raised concerns about the best sampling sites for PCR testing, with early indications suggesting throat swab samples were better than nasal swab samples. Our study evaluated the sensitivity of detecting SARS-CoV-2 across different swabbing sites.METHODS: Participants undergoing testing at NHS Test and Trace sites in England provided self-collected samples using nose only, throat only, and combined nose and throat swabs, which were analysed by realtime PCR.RESULTS: Among 815 participants, combined swabs had higher viral concentrations than nose only or throat only swabs. Sensitivity for detecting SARS-CoV-2 by PCR was 91 % for nose only and 97 % for throat only, relative to the combined approach. VC remained stable in nose swabs but declined in throat swabs with time.CONCLUSIONS: Combined nose and throat swabbing remains the most effective method for SARS-CoV-2 detection. If a single swab is used, a throat swab has a higher sensitivity than nose swabs, although VC in the throat decreases faster in later infection stages. The variations in VC over time and intra-person variation between sampling sites underscore the complexity of viral dynamics, highlighting the importance of considering both nose and throat samples for comprehensive testing.",

keywords = "COVID-19 PCR testing, Combined nose & throat swabbing, Omicron variant, Self-test, Viral concentration",

author = "Tom Fowler and Edward Blandford and David Chapman and Futschik, {Matthias E} and Raghavendran Kulasegaran-Shylini and Sarah Tunkel and Carolyn Lewis and Alasdair Fellows and Ellie Sheppard and Leanne McCabe and Peter Marks and Klapper, {Paul E} and Andrew Dodgson and Malur Sudhanva and Mike Kidd and Andy Vail and Susan Hopkins and Tim Peto",

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Fowler, T, Blandford, E, Chapman, D , Futschik, ME, Kulasegaran-Shylini, R, Tunkel, S, Lewis, C, Fellows, A, Sheppard, E, McCabe, L, Marks, P, Klapper, PE, Dodgson, A, Sudhanva, M, Kidd, M, Vail, A, Hopkins, S & Peto, T 2025, 'Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing', Diagnostic Microbiology and Infectious Disease, vol. 111, no. 1, 116577. https://doi.org/10.1016/j.diagmicrobio.2024.116577

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T1 - Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing

AU - Fowler, Tom

AU - Blandford, Edward

AU - Chapman, David

AU - Futschik, Matthias E

AU - Kulasegaran-Shylini, Raghavendran

AU - Tunkel, Sarah

AU - Lewis, Carolyn

AU - Fellows, Alasdair

AU - Sheppard, Ellie

AU - McCabe, Leanne

AU - Marks, Peter

AU - Klapper, Paul E

AU - Dodgson, Andrew

AU - Sudhanva, Malur

AU - Kidd, Mike

AU - Vail, Andy

AU - Hopkins, Susan

AU - Peto, Tim

PY - 2024/10/28

Y1 - 2024/10/28

N2 - PURPOSE: The Omicron variant of SARS-CoV-2 raised concerns about the best sampling sites for PCR testing, with early indications suggesting throat swab samples were better than nasal swab samples. Our study evaluated the sensitivity of detecting SARS-CoV-2 across different swabbing sites.METHODS: Participants undergoing testing at NHS Test and Trace sites in England provided self-collected samples using nose only, throat only, and combined nose and throat swabs, which were analysed by realtime PCR.RESULTS: Among 815 participants, combined swabs had higher viral concentrations than nose only or throat only swabs. Sensitivity for detecting SARS-CoV-2 by PCR was 91 % for nose only and 97 % for throat only, relative to the combined approach. VC remained stable in nose swabs but declined in throat swabs with time.CONCLUSIONS: Combined nose and throat swabbing remains the most effective method for SARS-CoV-2 detection. If a single swab is used, a throat swab has a higher sensitivity than nose swabs, although VC in the throat decreases faster in later infection stages. The variations in VC over time and intra-person variation between sampling sites underscore the complexity of viral dynamics, highlighting the importance of considering both nose and throat samples for comprehensive testing.

AB - PURPOSE: The Omicron variant of SARS-CoV-2 raised concerns about the best sampling sites for PCR testing, with early indications suggesting throat swab samples were better than nasal swab samples. Our study evaluated the sensitivity of detecting SARS-CoV-2 across different swabbing sites.METHODS: Participants undergoing testing at NHS Test and Trace sites in England provided self-collected samples using nose only, throat only, and combined nose and throat swabs, which were analysed by realtime PCR.RESULTS: Among 815 participants, combined swabs had higher viral concentrations than nose only or throat only swabs. Sensitivity for detecting SARS-CoV-2 by PCR was 91 % for nose only and 97 % for throat only, relative to the combined approach. VC remained stable in nose swabs but declined in throat swabs with time.CONCLUSIONS: Combined nose and throat swabbing remains the most effective method for SARS-CoV-2 detection. If a single swab is used, a throat swab has a higher sensitivity than nose swabs, although VC in the throat decreases faster in later infection stages. The variations in VC over time and intra-person variation between sampling sites underscore the complexity of viral dynamics, highlighting the importance of considering both nose and throat samples for comprehensive testing.

KW - COVID-19 PCR testing

KW - Combined nose & throat swabbing

KW - Omicron variant

KW - Self-test

KW - Viral concentration

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DO - 10.1016/j.diagmicrobio.2024.116577

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SN - 0732-8893

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JO - Diagnostic Microbiology and Infectious Disease

JF - Diagnostic Microbiology and Infectious Disease

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ER -

Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing

Abstract

ASJC Scopus subject areas

Keywords

UN SDGs

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