Meta-analysis of rapid direct-to-PCR assays for the qualitative detection of SARS-CoV-2

Abstract

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing COVID-19 pandemic present significant challenges to current diagnostic and therapeutic patient care pathways including whether new in vitro diagnostic tests can accurately identify and rule out current SARS-CoV-2 infection. The gold standard diagnostic test to identify a current SARS-CoV-2 infection is a central laboratory-based molecular assay using reverse transcription polymerase chain reaction (RT-PCR) with very high accuracy of detection but which typically requires 1-2 days turn-around for results. Therefore, rapid RTPCR assays and systems have been developed which can be deployed locally (near-patient or point of care (POC), provide faster results and not impact on already stressed central laboratory capacity. Rapid test results can be returned within the same clinical encounter, facilitating timely decisions that optimise the patient care pathway and support more rapid COVID-19 diagnosis, isolation and contract tracing activities. Direct-to-PCR is an evolution of RT-PCR in which the patient sample is added directly to an amplification reaction without being subjected to prior nucleic acid extraction, purification, or quantification to reduce the time and monetary resources required to process samples. Rapid, direct-to-PCR systems further increase the speed of testing by combining rapid PCR instruments with direct-to-PCR assays, to generate results in less than two hours. This appears to be the first meta-analysis assessing the accuracy of rapid direct-to-PCR in the detection of SARS-CoV-2. In total, 10,957 unique records were identified and screened using a search string evaluation, 420 full-text reports and/or supplemental materials were assessed for inclusion. This resulted in 14 studies reporting 20 datasets with 4593 patient samples (1391 positive) included in the analysis. The overall agreement between the rapid direct RT-PCR and gold standard centralised laboratory RT-PCR was 97.1% with 93.60% positive percent agreement and 98.63% negative percent agreement. The Cohens kappa statistical coefficient k = 0.93, indicating an almost perfect agreement and Youden Index = 0.92. These results indicate that direct-to-PCR assays can perform equivalently to the standard centralised laboratory PCR systems for the detection of SARS-CoV-2. Objectives: To assess the efficacy of rapid direct-to-PCR assays and systems for the detection of SARS-CoV-2 in the hospital, care home and medical research population in England from November 2020 to April 2021. Search methods: Electronic searches of the Cochrane COVID-19 Study Register (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on the 30th of April 2020. Please see the PRISMA flow diagram below (figure 2). Selection criteria: Studies of subjects with either suspected SARS-CoV-2 infection, known SARS-CoV-2 infection or known absence of infection, or those who were being screened for infection were included. Commercially available and research use rapid direct-to-PCR assays (without RNA extraction and purification reporting results within two hours) were included in the study. Data collection, extraction and analysis: Studies were screened independently, in duplicate with any disagreements resolved by discussion with a third author. Study characteristics were extracted by one author and checked by a second; extraction of study results and assessments of risk of bias and applicability were undertaken independently in duplicate. Where studies were not publicly available, sites that undertook in-service evaluations of rapid direct-to-PCR system were contacted and asked to supply anonymised datasets. Both reviewers independently performed data extraction and verification and calculated 2x2 contingency tables of the number of true positives, false positives, false negatives and true negatives. They resolved any disagreements by discussion and by review with the third reviewer. Main results: Twenty study cohorts were included (described in 14 study reports, including 4 unpublished reports), reporting results for 4593 samples (1391 with confirmed SARS-CoV-2). Studies were mainly from Europe and North America, and evaluated nine direct-to-PCR assays. Conclusions: This appears to be the first meta-analysis assessing the accuracy of rapid direct-to-PCR in the detection of SARS-CoV-2. In total, 10,957 unique records were identified and screened using a search string evaluation, 420 full-text reports and/or supplemental materials were assessed for inclusion. This resulted in 14 studies reporting 20 datasets with 4593 patient samples (1391 positive) included in the analysis. The overall agreement between the rapid direct RT-PCR and gold standard centralised laboratory RT-PCR was 97.10% with 93.60% positive percent agreement and 98.63% negative percent agreement. The Cohens kappa statistical coefficient k = 0.93, indicating an almost perfect agreement and Youden Index = 0.92. These results show that direct-to-PCR assay perform equivalently to the gold standard centralised laboratory RT-PCR systems for the detection of SARS-CoV-2.