Laboratory‐based molecular test alternatives to RT‐PCR for the diagnosis of SARS‐CoV‐2 infection

Background Diagnosing people with a SARS‐CoV‐2 infection played a critical role in managing the COVID‐19 pandemic and remains a priority for the transition to long‐term management of COVID‐19. Initial shortages of extraction and reverse transcription polymerase chain reaction (RT‐PCR) reagents impaired the desired upscaling of testing in many countries, which led to the search for alternatives to RNA extraction/purification and RT‐PCR testing. Reference standard methods for diagnosing the presence of SARS‐CoV‐2 infection rely primarily on real‐time reverse transcription‐polymerase chain reaction (RT‐PCR). Alternatives to RT‐PCR could, if sufficiently accurate, have a positive impact by expanding the range of diagnostic tools available for the timely identification of people infected by SARS‐CoV‐2, access to testing and the use of resources. Objectives To assess the diagnostic accuracy of alternative (to RT‐PCR assays) laboratory‐based molecular tests for diagnosing SARS‐CoV‐2 infection. Search methods We searched the COVID‐19 Open Access Project living evidence database from the University of Bern until 30 September 2020 and the WHO COVID‐19 Research Database until 31 October 2022. We did not apply language restrictions. Selection criteria We included studies of people with suspected or known SARS‐CoV‐2 infection, or where tests were used to screen for infection, and studies evaluating commercially developed laboratory‐based molecular tests for the diagnosis of SARS‐CoV‐2 infection considered as alternatives to RT‐PCR testing. We also included all reference standards to define the presence or absence of SARS‐CoV‐2, including RT‐PCR tests and established clinical diagnostic criteria. Data collection and analysis Two authors independently screened studies and resolved disagreements by discussing them with a third author. Two authors independently extracted data and assessed the risk of bias and applicability of the studies using the QUADAS‐2 tool. We presented sensitivity and specificity, with 95% confidence intervals (CIs), for each test using paired forest plots and summarised results using average sensitivity and specificity using a bivariate random‐effects meta‐analysis. We illustrated the findings per index test category and assay brand compared to the WHO's acceptable sensitivity and specificity threshold for diagnosing SARS‐CoV‐2 infection using nucleic acid tests. Main results We included data from 64 studies reporting 94 cohorts of participants and