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

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.

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 94% [95% CI 85-98]; 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.

Figure 1

CovidNudge 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 2

Profile 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.