Epidemiology and precision of SARS-CoV-2 detection following lockdown and relaxation measures.
Adult
Bronchoalveolar Lavage
COVID-19
/ epidemiology
COVID-19 Testing
Communicable Disease Control
/ methods
Disease Transmission, Infectious
/ prevention & control
Female
Genome, Viral
Humans
Male
Middle Aged
Nasopharynx
/ virology
Oropharynx
/ virology
Pandemics
RNA, Viral
/ analysis
SARS-CoV-2
/ genetics
Switzerland
/ epidemiology
Viral Load
Basel-SCoV2-ORF8-97bp
Basel-SCoV2-S-112bp
CoVID-19
NAAT
PCR
QNAT
bronchoalveolar lavage
severe acute respiratory syndrome coronavirus 2
tracheal secretion
Journal
Journal of medical virology
ISSN: 1096-9071
Titre abrégé: J Med Virol
Pays: United States
ID NLM: 7705876
Informations de publication
Date de publication:
04 2021
04 2021
Historique:
received:
22
11
2020
accepted:
11
12
2020
pubmed:
15
12
2020
medline:
20
3
2021
entrez:
14
12
2020
Statut:
ppublish
Résumé
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. 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. 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. 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.
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2374-2384Subventions
Organisme : Universität Basel
ID : Personal Appointment Grant to HHH
Informations de copyright
© 2020 Wiley Periodicals LLC.
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