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Epidemiology and precision of SARS-CoV-2 detection following lockdown and relaxation measures.
- Source :
-
Journal of medical virology [J Med Virol] 2021 Apr; Vol. 93 (4), pp. 2374-2384. Date of Electronic Publication: 2020 Dec 29. - Publication Year :
- 2021
-
Abstract
- 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.<br />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.<br />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.<br />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.<br /> (© 2020 Wiley Periodicals LLC.)
- Subjects :
- Adult
Bronchoalveolar Lavage
COVID-19 prevention & control
COVID-19 transmission
COVID-19 virology
COVID-19 Testing
Disease Transmission, Infectious prevention & control
Female
Genome, Viral
Humans
Male
Middle Aged
Nasopharynx virology
Oropharynx virology
Pandemics
RNA, Viral analysis
RNA, Viral genetics
SARS-CoV-2 genetics
Switzerland epidemiology
Viral Load
COVID-19 epidemiology
Communicable Disease Control methods
SARS-CoV-2 isolation & purification
Subjects
Details
- Language :
- English
- ISSN :
- 1096-9071
- Volume :
- 93
- Issue :
- 4
- Database :
- MEDLINE
- Journal :
- Journal of medical virology
- Publication Type :
- Academic Journal
- Accession number :
- 33314153
- Full Text :
- https://doi.org/10.1002/jmv.26731