ABSTRACT
Clinical trials of SARS-CoV-2 therapeutics often include virological secondary endpoints to compare viral clearance and viral load reduction between treatment and placebo arms. This is typically achieved using RT-qPCR, which cannot differentiate replicant competent virus from non-viable virus or free RNA, limiting its utility as an endpoint. Culture based methods for SARS-CoV-2 exist; however, these are often insensitive and poorly standardised for use as clinical trial endpoints. We report optimisation of a culture-based approach evaluating three cell lines, three detection methods, and key culture parameters. We show that Vero-ACE2-TMPRSS2 (VAT) cells in combination with RT-qPCR of culture supernatants from the first passage provides the greatest overall detection of Delta viral replication (22/32, 68.8%), being able to identify viable virus in 83.3% (20/24) of clinical samples with initial Ct values <30. Likewise, we demonstrate that RT-qPCR using culture supernatants from the first passage of Vero hSLAM cells provides the highest overall detection of Omicron viral replication (9/31, 29%), detecting live virus in 39.1% (9/23) of clinical samples with initial Ct values < 25. This assessment demonstrates that combining RT-qPCR with virological end point analysis has utility in clinical trials of therapeutics for SARS-CoV-2; however, techniques may require optimising based on dominant circulating strain.
ABSTRACT
ObjectivesTo compare self-taken and healthcare worker (HCW)-taken throat/nasal swabs to perform rapid diagnostic tests (RDT) for SARS-CoV-2, and how these compare to RT-PCR. We hypothesised that self-taken samples are non-inferior for use with RDTs and in clinical and research settings could have substantial individual and public health benefit. DesignA prospective diagnostic accuracy evaluation as part of the Facilitating Accelerated Clinical Evaluation of Novel Diagnostic Tests for COVID -19 (FALCON C-19), workstream C (undifferentiated community testing). SettingNHS Test and Trace drive-through community PCR testing site (Liverpool, UK). Participants Eligible participants 18 years or older with symptoms of COVID-19. 250 participants recruited; one withdrew before analysis. SamplingSelf-administered throat/nasal swab for the Covios(R) RDT, a trained HCW taken throat/nasal sample for PCR and HCW comparison throat/nasal swab for RDT. Main outcome measuresSensitivity, specificity, and positive and negative predictive values (PPV, NPV) were calculated; comparisons between self-taken and HCW-taken samples used McNemars test. ResultsSeventy-five participants (75/249, 30.1%) were positive by RT-PCR. RDTs with self-taken swabs had a sensitivity of 90.5% (67/74, 95% CI: 83.9-97.2), compared to 78.4% (58/74, 95% CI: 69.0-87.8) for HCW-taken swabs (absolute difference 12.2%, 95% CI: 4.7-19.6, p=0.003). Specificity for self-taken swabs was 99.4% (173/174, 95% CI: 98.3-100.0), versus 98.9% (172/174, 95% CI: 97.3-100.0) for HCW-taken swabs (absolute difference 0.6%, 95% CI: 0.5-1.7, p=0.317). The PPV of self-taken RDTs (98.5%, 67/68, 95% CI: 95.7-100.0) and HCW-taken RDTs (96.7%, 58/60, 95% CI 92.1-100.0) were not significantly different (p=0.262). However, the NPV of self-taken swab RDTs was significantly higher (96.1%, 173/180, 95% CI: 93.2-98.9) than HCW-taken RDTs (91.5%, 172/188, 95% CI 87.5-95.5, p=0.003). ConclusionSelf-taken swabs for COVID-19 testing offer substantial individual benefits in terms of convenience, accuracy, and reduced risk of transmitting infection. Our results demonstrate that self-taken throat/nasal samples can be used by lay individuals as part of rapid testing programmes for symptomatic adults. Trial RegistrationIRAS ID:28422, clinical trial ID: NCT04408170 SummaryO_ST_ABSWhat is already known on this topic?C_ST_ABSO_LIRapid diagnostic tests (RDTs)for SARS-CoV-2 Ag are a cheaper point-of-care alternative to RT-PCR for diagnosing COVID-19 disease. C_LIO_LIThe accuracy of tests can vary dependent on sampling technique, test processing and reading of results. C_LI What this study adds?O_LISelf-taken throat-nasal swabs for RDTs can be used by symptomatic adults to give reliable results to diagnose SARS-CoV-2. C_LIO_LISelf-sampling can be implemented with little training and no assistance. C_LI