Diagnostic accuracy of non-invasive SARS-CoV-2 screening tests: a national prospective analysis

Abstract

Background: Providing non-invasive, accurate and affordable SARS-CoV-2 tests represents a public health priority, to better control the spread of the virus while protecting healthcare workers. Saliva is a robust alternative to nasopharyngeal (NP) swabs, but there is heterogeneity in collection and pre-analytical methods. Methods: Relying on a national COVID-19 Public Health Programme, we prospectively recruited 3,488 symptomatic and asymptomatic adults attending the Monaco community centre for NP RT-PCR testing from February 2021–2023. Saliva was concomitantly obtained with either a buccal swab or an oral sponge (OS) and analysed by an RT-PCR assay and a fully automated electrochemiluminescence enzyme immunoassay (ECLIA) rapid antigen test (RAT). Results: The sensitivity of the buccal RT-PCR varied according to previous SARS-CoV-2 infection, vaccination, and the presence of symptoms, while it remained around 95% for the OS RT-PCR. The specificity of the buccal RT-PCR approached 100% and was around 95% for the OS-RT PCR. The RAT sensitivity was 66.9% and 69.1% compared to NP and OS RT-PCR assays and increased to 71% and 97% in case of a high viral load (Ct < 25), respectively. Conclusions: RT-PCR assay using OS saliva showed high accuracy in symptomatic and non-symptomatic adults, including the identification of negative nasopharyngeal swabs. This method allows self-collection without any prior conditions for the patient nor laboratory pre-analytical steps. The ECLIA RAT offers high throughput but is only useful in individuals with high viral loads. Our findings encompassed the latest SARS-CoV-2 omicron subvariants, such as BA.4&5 and the XBB series. Trial registration: Registry: ClinicalTrials.gov. Registration number: NCT05074745. Registration date: 12-10-2021.