Point of care SARS-CoV-2 nucleic acid testing in schools improves school attendance

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Abstract

Background: National lockdowns have led to significant interruption to children’s education globally. In the Autumn term in 2020, school absence in England and Wales was almost five times higher than the same period in 2019. Transmission of SARS-CoV-2 in schools and ongoing interruption to education remains a concern. However, evaluation of rapid point of care (POC) polymerase chain reaction (PCR) testing in British schools has not been undertaken.

Methods: This is a survey of secondary schools in England that implemented PCR-based rapid POC testing. The study aims to measure the prevalence of SARS-CoV-2 infection in schools, to assess the impact of this testing on school attendance and closures, and to describe schools experiences with testing. All schools utilised the SAMBA II SARS-CoV-2 testing platform.

Results: 12 fee-paying secondary schools in England were included. Between September 1 ^st 2020 and December 16 ^th 2020, 697 on site rapid POC PCR tests were performed and 6.7% of these were positive for SARS-CoV-2 infection. There were five outbreaks in three schools during this time which were contained. Seven groups of close contacts within the school known as bubbles had to quarantine but there were no school closures. 84% of those tested were absent from school for less than one day whilst awaiting their test result. This potentially saved between 1047 and 1570 days off school in those testing negative compared to the NHS PCR laboratory test. Schools reported a positive impact of having a rapid testing platform as it allowed them to function as fully as possible during this pandemic.

Conclusions: Rapid POC PCR testing platforms should be widely available and utilised in school settings. Reliable positive tests will prevent outbreaks and uncontrolled spread of infection within school settings. Reliable negative test results will reassure students, parents and staff and prevent disruption to education.

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Most cited references 11

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Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study

Nathan J. Brendish, Stephen Poole, Vasanth Naidu … (2020)

Background The management of the COVID-19 pandemic is hampered by long delays associated with centralised laboratory PCR testing. In hospitals, these delays lead to poor patient flow and nosocomial transmission. Rapid, accurate tests are therefore urgently needed in preparation for the next wave of the pandemic. Methods We did a prospective, interventional, non-randomised, controlled study of molecular point-of-care testing in patients aged 18 years or older presenting with suspected COVID-19 to the emergency department or other acute areas of Southampton General Hospital during the first wave of the pandemic in the UK. Nose and throat swab samples taken at admission from patients in the point-of-care testing group were tested with the QIAstat-Dx Respiratory SARS-CoV-2 Panel. Samples taken from patients in a contemporaneous control group were tested by laboratory PCR. The primary outcome was time to results in the full cohort. This study is registered with ISRCTN (ISRCTN14966673) and is completed. Findings Between March 20 and April 29, 2020, 517 patients were assessed for eligibility, of whom 499 were recruited to the point-of-care testing group and tested by the QIAstat-Dx Respiratory SARS-CoV-2 Panel. 555 contemporaneously identified patients were included in the control group and tested by laboratory PCR. The two groups were similar with regard to the distribution of sex, age, and ethnicity. 197 (39%) patients in the point-of-care testing group and 155 (28%) in the control group tested positive for COVID-19 (difference 11·5% [95% CI 5·8–17·2], p=0·0001). Median time to results was 1·7 h (IQR 1·6–1·9) in the point-of-care testing group and 21·3 h (16·0–27·9) in the control group (difference 19·6 h [19·0–20·3], p<0·0001). A Cox proportional hazards regression model controlling for age, sex, time of presentation, and severity of illness also showed that time to results was significantly shorter in the point-of-care testing group than in the control group (hazard ratio 4023 [95% CI 545–29 696], p<0·0001). Interpretation Point-of-care testing is associated with large reductions in time to results and could lead to improvements in infection control measures and patient flow compared with centralised laboratory PCR testing. Funding University Hospitals Southampton NHS Foundation Trust.

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Assessing a novel, lab-free, point-of-care test for SARS-CoV-2 (CovidNudge): a diagnostic accuracy study

Malick Gibani, Christofer Toumazou, Mohammadreza Sohbati … (2020)

Background Access to rapid diagnosis is key to the control and management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Laboratory RT-PCR testing is the current standard of care but usually requires a centralised laboratory and significant infrastructure. We describe our diagnostic accuracy assessment of a novel, rapid point-of-care real time RT-PCR CovidNudge test, which requires no laboratory handling or sample pre-processing. Methods Between April and May, 2020, we obtained two nasopharyngeal swab samples from individuals in three hospitals in London and Oxford (UK). Samples were collected from three groups: self-referred health-care workers with suspected COVID-19; patients attending emergency departments with suspected COVID-19; and hospital inpatient admissions with or without suspected COVID-19. For the CovidNudge test, nasopharyngeal swabs were inserted directly into a cartridge which contains all reagents and components required for RT-PCR reactions, including multiple technical replicates of seven SARS-CoV-2 gene targets (rdrp1, rdrp2, e-gene, n-gene, n1, n2 and n3) and human ribonuclease P (RNaseP) as sample adequacy control. Swab samples were tested in parallel using the CovidNudge platform, and with standard laboratory RT-PCR using swabs in viral transport medium for processing in a central laboratory. The primary analysis was to compare the sensitivity and specificity of the point-of-care CovidNudge test with laboratory-based testing. Findings We obtained 386 paired samples: 280 (73%) from self-referred health-care workers, 15 (4%) from patients in the emergency department, and 91 (23%) hospital inpatient admissions. Of the 386 paired samples, 67 tested positive on the CovidNudge point-of-care platform and 71 with standard laboratory RT-PCR. The overall sensitivity of the point-of-care test compared with laboratory-based testing was 94% (95% CI 86–98) with an overall specificity of 100% (99–100). The sensitivity of the test varied by group (self-referred healthcare workers 93% [95% CI 84–98]; patients in the emergency department 100% [48–100]; and hospital inpatient admissions 100% [29–100]). Specificity was consistent between groups (self-referred health-care workers 100% [95% CI 98–100%]; patients in the emergency department 100% [69–100]; and hospital inpatient admissions 100% [96–100]). Point of care testing performance was similar during a period of high background prevalence of laboratory positive tests (25% [95% 20–31] in April, 2020) and low prevalence (3% [95% 1–9] in inpatient screening). Amplification of viral nucleocapsid (n1, n2, and n3) and envelope protein gene (e-gene) were most sensitive for detection of spiked SARS-CoV-2 RNA. Interpretation The CovidNudge platform was a sensitive, specific, and rapid point of care test for the presence of SARS-CoV-2 without laboratory handling or sample pre-processing. The device, which has been implemented in UK hospitals since May, 2020, could enable rapid decisions for clinical care and testing programmes. Funding National Institute of Health Research (NIHR) Imperial Biomedical Research Centre, NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Oxford University in partnership with Public Health England, NIHR Biomedical Research Centre Oxford, and DnaNudge.

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Point of care nucleic acid testing for SARS-CoV-2 in hospitalised patients: a clinical validation trial and implementation study.

Dami A. Collier, Sonny M Assennato, Ben Warne … (2020)

Summary There is urgent need for rapid SARS-CoV-2 testing in hospital to limit nosocomial spread. We report an evaluation of point of care (POC) nucleic acid amplification testing (NAAT) in 149 participants with parallel combined nasal/throat swabbing for POC versus standard lab RT-PCR testing. Median time to result is 2.6 (IQR 2.3 to 4.8) versus 26.4 hours (IQR 21.4 to 31.4, p<0.001) with 32 (21.5%) positive and 117 (78.5%) negative. Cohen's kappa correlation between tests is 0.96 (95%CI 0.91, 1.00). When comparing nearly 1000 tests pre- and post- implementation, median time to definitive bed placement from admission is 23.4 (8.6-41.9) versus 17.1 hours (9.0-28.8), p=0.02. Mean length of stay on COVID-19 ‘holding’ wards is 58.5 versus 29.9 hours (p<0.001). POC testing increases isolation room availability, avoids bed closures, allows discharge to care homes and expedites access to hospital procedures. POC testing could mitigate the impact of COVID-19 on hospital systems.

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Author and article information

Contributors

Dami A. Collier: Role: ConceptualizationRole: Data CurationRole: Formal AnalysisRole: Funding AcquisitionRole: MethodologyRole: Project AdministrationRole: Writing – Original Draft PreparationRole: Writing – Review & Editing

Rachel Bousfield: Role: ConceptualizationRole: Writing – Original Draft PreparationRole: Writing – Review & Editing

Effrossyni Gkrania-Klotsas: Role: ConceptualizationRole: MethodologyRole: Writing – Original Draft PreparationRole: Writing – Review & Editing

ORCID: https://orcid.org/0000-0002-0930-8330

Ravindra K. Gupta: Role: ConceptualizationRole: Funding AcquisitionRole: MethodologyRole: SupervisionRole: Writing – Original Draft PreparationRole: Writing – Review & Editing

ORCID: https://orcid.org/0000-0001-9751-1808

Journal

Journal ID (nlm-ta): Wellcome Open Res

Journal ID (iso-abbrev): Wellcome Open Res

Title: Wellcome Open Research

Publisher: F1000 Research Limited (London, UK )

ISSN (Electronic): 2398-502X

Publication date (Electronic): 6 September 2022

Publication date Collection: 2022

Volume: 7

Electronic Location Identifier: 8

Affiliations

[1 ]Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, CB2 0SP, UK

[2 ]Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK

[3 ]Division of Infection and Immunity, University College London, London, WC1E 6BT, UK

[4 ]Department of Infectious Diseases, Cambridge University Hospitals, NHS Trust, Cambridge, CB2 0QQ, UK

[5 ]MRC Epidemiology Unit, University of Cambridge, Cambridge, CB22 0SL, UK

[6 ]Africa Health Research Institute, Durban, South Africa

[1 ]Hospital for Tropical Diseases, Division of Infection, University College London Hospitals NHS Foundation Trust, London, UK

[1 ]Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, MA, USA

[2 ]Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA

[1 ]Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, MA, USA

[2 ]Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA

university college london, UK

[1 ]Hospital for Tropical Diseases, Division of Infection, University College London Hospitals NHS Foundation Trust, London, UK

university college london, UK

Author notes

[a ] adc82@ 123456cam.ac.uk

[b ] rkg20@ 123456cam.ac.uk

No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: I am an editor for the Diagnostics section of the Infectious Diseases Society of America's COVID-19 Real-time Learning Network

Competing interests: No competing interests were disclosed.

Author information

Effrossyni Gkrania-Klotsas https://orcid.org/0000-0002-0930-8330

Ravindra K. Gupta https://orcid.org/0000-0001-9751-1808

Article

DOI: 10.12688/wellcomeopenres.17213.2

PMC ID: 9530621

SO-VID: 44c26063-33f0-4dd1-b927-316cbd022339

License:

This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date accepted : 8 August 2022

Funding

Funded by: Wellcome Trust

Award ID: 206440

Funded by: Wellcome Trust

Award ID: 108082

This work is supported by the Wellcome Trust through a Wellcome Trust Senior Fellowship in Clinical Science to RKG [108082, <a href=https://doi.org/10.35802/108082>https://doi.org/10.35802/108082</a>] and a Wellcome Trust Clinical PhD Research Fellowship to DAC [206440, <a href=https://doi.org/10.35802/206440>https://doi.org/10.35802/206440</a>].

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Point of care SARS-CoV-2 nucleic acid testing in schools improves school attendance

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Most cited references 11

Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study

Assessing a novel, lab-free, point-of-care test for SARS-CoV-2 (CovidNudge): a diagnostic accuracy study

Point of care nucleic acid testing for SARS-CoV-2 in hospitalised patients: a clinical validation trial and implementation study.

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