| Literature DB >> 32964211 |
Malick M Gibani1,2, Christofer Toumazou3,4, Mohammadreza Sohbati3, Rashmita Sahoo3, Maria Karvela3, Tsz-Kin Hon3, Sara De Mateo3, Alison Burdett4, K Y Felice Leung3, Jake Barnett3, Arman Orbeladze3, Song Luan3, Stavros Pournias3, Jiayang Sun3, Barney Flower1,2, Judith Bedzo-Nutakor3, Maisarah Amran2, Rachael Quinlan1, Keira Skolimowska1,2, Carolina Herrera1, Aileen Rowan1, Anjna Badhan1, Robert Klaber2, Gary Davies5, David Muir2, Paul Randell2, Derrick Crook6, Graham P Taylor1, Wendy Barclay1, Nabeela Mughal1,2,5, Luke S P Moore1,2,5, Katie Jeffery6,7, Graham S Cooke1,2.
Abstract
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.Entities:
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Year: 2020 PMID: 32964211 PMCID: PMC7498257 DOI: 10.1016/S2666-5247(20)30121-X
Source DB: PubMed Journal: Lancet Microbe ISSN: 2666-5247
Figure 1CovidNudge point of care diagnostic for SARS-CoV-2
(A) Schematic of the workflow. A swab is collected and loaded directly into the sealed DnaCartridge, comprising a sample preparation unit (SPU) and amplification unit (AU). The DnaCartridge is placed into a slot on the lower half of the processing unit called the NudgeBox, where the SPU mixing chamber fits on top of a motor-driven spigot and the amplification unit sits on top of an active heating and cooling plate. The spigot also connects the DnaCartridge mixing chamber to the pneumatic subsystem. By sliding the upper half to close the NudgeBox, the imaging system aligns on top of the DnaCartridge amplification unit. The upper half also consists of a thermal subsystem which is thermally connected to a mesh plate sitting on top of the amplification unit, which drives the PCR reaction. Data are delivered by WiFi to a cloud-based analysis platform and results are delivered directly to the patient's electronic health record or smartphone app. (B) Schematic of SPU. The test starts with moving the lysis buffer to the swab chamber. The lysis kills and deactivates the (viral) sample and releases the sample RNA. Silica frit filters are mounted on to the port in the mixing chamber which can capture RNA molecules. The lysis buffer moves from the swab chamber to the mixing chamber and the extracted RNA strands bind to the silica frit filter. In the next step, wash buffer is passed through the mixing chamber and any debris is removed. In the third step, the elution buffer releases the RNA strands from the frit. The elution buffer containing the sample RNA is used to reconstitute the lyophilised RT master mix. In the last step of sample preparation, the mixing chamber turns toward the amplification unit filling port of the SPU to fill the amplification unit. (C) Schematic of the amplification unit. The wells are formed by sealing a mesh membrane to the bottom of the chassis, each less than 1·8 μL in volume. Primers and probes for each assay are spotted in nL into the wells, and air dried. To provide redundancy and increase reliability, they are distributed into several wells. The spotting pattern is used by the algorithm to analyse the PCR amplification signals. Each well is represented by a circle coloured according to its assay deposition. Crossed wells indicate the targets replicated that have amplified in a specific reaction.
Figure 2Profile of clinical study
Tests were considered valid if at least three of six replicates of RNaseP amplified. Suspected COVID-19 in the emergency department was defined as a patient presenting with any of the following: temperature of 37·8°C or more; clinical evidence of pneumonia (eg, cough or dyspnoea); or hypoxia or an abnormal chest radiograph. Health-care workers were eligible for testing if they self-reported any of the following symptoms: fever of 37·8°C or more or subjective fever, fatigue or malaise, cough or sputum production, muscle aches, headache, sore throat, or profound loss of smell and taste. NHS=UK National Health Service.
Clinical assessment of point of care testing for SARS-CoV-2 compared with laboratory RT-PCR
| Positive | Negative | Positive | Negative | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total | 386 | 71 | 315 | 67 | 319 | 0·18 (0·15–0·23) | 94% (86–98) | 100% (99–100) | 1·00 (0·94–1·00) | 0·99 (0·97–1·00) | 0·06 (0·02–0·15) | |
| Sample context | ||||||||||||
| Symptomatic staff testing | 280 | 63 | 217 | 59 | 221 | 0·23 (0·18–0·28) | 94% (85–98) | 100% (98–100) | 1·00 (0·94–1·00) | 0·98 (0·95–1·00) | 0·06 (0·02–0·16) | |
| Emergency department | 15 | 5 | 10 | 5 | 10 | 0·33 (0·12–0·62) | 100% (48–100) | 100% (69–100) | 1·00 (0·48–1·00) | 1·00 (0·69–1·00) | 0·00 (NC) | |
| All hospital admissions | 91 | 3 | 88 | 3 | 88 | 0·03 (0·01–0·09) | 100% (29–100) | 100% (96–100) | 1·00 (0·29–1·00) | 1·00 (0·96–1·00) | 0·00 (NC) | |
| Sample period | ||||||||||||
| April, 2020 | 272 | 68 | 204 | 64 | 208 | 0·25 (0·20–0·31) | 94% (86–98) | 100% (98–100) | 1·00 (0·94–1·00) | 0·98 (0·95–0·99) | 0·06 (0·02–0·16) | |
| May, 2020 | 114 | 3 | 111 | 3 | 111 | 0·03 (0·01–0·07) | 100% (29–100) | 100% (97–100) | 1·00 (0·29–1·00) | 1·00 (0·97–1·00) | 0·00 (NC) | |
Data are for paired samples collected contemporaneously. 24 samples that were invalid on the point of care test and eight that were invalid on the NHS laboratory test were not included. Results are presented according to location of testing, context of testing, laboratory platform, and period of testing. All samples were collected via nasopharyngeal swabs. SARS-CoV-2=severe acute respiratory syndrome coronavirus 2. NC=not calculable.