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OBJECTIVES Detecting SARS-CoV-2 is key to clinical and epidemiological assessment of CoVID-19. We cross-validated manual and automated high-throughput testing for SARS-CoV-2-RNA, evaluated SARS-CoV-2-loads in nasopharyngeal-oropharyngeal swabs (NOPS), lower respiratory-fluids, and plasma, and analyzed detection rates after lockdown- and relaxation-measures. METHODS Basel-S-gene, Roche-E-gene, and Roche-cobas®6800-Target1 and Target2 were prospectively validated in 1\'344 NOPS submitted during the first pandemic peak (week 13). Follow-up-cohort-(FUP)-1, -2 and -3 comprised 10\'999, 10\'147 and 19\'389 NOPS submitted during 10-week-periods until week 23, 33, and 43, respectively. RESULTS Concordant results were obtained in 1\'308 cases (97%) including 97 (9%) SARS-CoV-2-positives showing high quantitative correlations (Spearman r>0.95; p<0.001) for all assays and high precision by Bland-Altman analysis. Discordant samples (N=36, 3%) had significantly lower SARS-CoV-2-loads (p<0.001). Following lockdown, detection rates declined to <1% in FUP-1 reducing single-test positive predictive values from 99.3% to 85.1%. Following relaxation, rates flared up to 4% and 12% in FUP-2 and -3, but infected patients were younger than during lockdown (34 versus 52 years, p<0.001). In 261 patients providing 936 NOPS, SARS-CoV-2-loads declined by three orders of magnitude within 10 days post-diagnosis (p<0.001). SARS-CoV-2-loads in NOPS correlated with those in time-matched lower respiratory fluids or in plasma, but remained detectable in some cases with negative follow-up NOPS, respectively. CONCLUSION Manual and automated assays significantly correlated qualitatively and quantitatively. Following successful lockdown, declining positive predictive values require independent dual-target-confirmation for reliable assessment. Confirmatory and quantitative follow-up testing should be obtained within <5 days, and consider lower respiratory fluids in symptomatic patients with SARS-CoV-2-negative NOPS. This article is protected by copyright. All rights reserved.
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