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Epidemiology and precision of SARS‐CoV‐2 detection following lockdown and relaxation measures
Author(s) -
Leuzinger Karoline,
Gosert Rainer,
Søgaard Kirstine K.,
Naegele Klaudia,
Bielicki Julia,
Roloff Tim,
Bingisser Roland,
Nickel Christian H.,
Khanina,
Sutter Sarah Tschudin,
Widmer Andreas F.,
Rentsch Katharina,
Pargger Hans,
Siegemund Martin,
Stolz Daiana,
Tamm Michael,
Bassetti Stefano,
Osthoff Michael,
Battegay Manuel,
Egli Adrian,
Hirsch Hans H.
Publication year - 2021
Publication title -
journal of medical virology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.782
H-Index - 121
eISSN - 1096-9071
pISSN - 0146-6615
DOI - 10.1002/jmv.26731
Subject(s) - covid-19 , medicine , epidemiology , coronavirus , virology , outbreak , disease , infectious disease (medical specialty)
Objectives Detecting severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is key to the 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 1344 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 a 10‐week period until Weeks 23, 33, and 43, respectively. Results Concordant results were obtained in 1308 cases (97%), including 97 (9%) SARS‐CoV‐2‐positives showing high quantitative correlations (Spearman's r > .95; p < .001) for all assays and high precision by Bland–Altman analysis. Discordant samples ( N = 36, 3%) had significantly lower SARS‐CoV‐2 loads ( p < .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 vs. 52 years, p < .001). In 261 patients providing 936 NOPS, SARS‐CoV‐2 loads declined by three orders of magnitude within 10 days postdiagnosis ( p < .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 a 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.