Large-scale silane bead-based SARS-CoV-2 testing of a nursing home in Spain identifies a viral reservoir during lockdown period
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Abstract
Background
Spain is one of the countries most heavily affected by the COVID-19 pandemic. As in other countries such as UK and USA, nursing homes have been an important human reservoir for the virus and the population with the highest mortality worldwide. The presence of asymptomatic carriers within nursing homes is one of the factors that could provoke new outbreaks during the relaxing of lockdown measures.
Methods
We developed a high-throughput protocol for RNA extraction of patient samples based on silane magnetic beads in multi-well plates. The sensitivity, specificity and reproducibility rates were assessed using positive and negative clinical samples from the Clinica Universidad de Navarra, Spain. We utilized the protocol to test a pilot cohort of 138 residents and 87 staff from a nursing home in Northern Navarre, Spain.
Findings
Our protocol showed high sensitivity (100%), specificity (96·0%) and linear correlation with PCR cycle threshold values obtained with a standard testing kit (R 2 = 0·807, p=3E-05). Testing of 225 individuals from the nursing home revealed 63 residents (46%) and 14 staff (16%) positive for SARS-CoV-2. Only 18 of the positive residents (28·6%) were symptomatic at time of testing. During follow-up, 6 PCR-negative symptomatic residents were retested and resulted positive. One-month mortality among positive residents was higher than in negative residents (15·9% vs 1·3%), regardless of age or comorbidities.
Interpretation
Rapid silane bead-based RNA extraction expanded the testing capabilities and COVID-19 patients were promptly identified. Personal and public health measures were enacted to avoid spreading and tighten clinical surveillance. The ability to easily adapt the technical capabilities of academic research centers to large-scale testing for SARS-CoV-2 could provide an invaluable tool for ensuring a safe lifting of lockdown in countries with high numbers of cases.
Funding
European Molecular Biology Organization and Genomics Unit, Cima Universidad de Navarra.
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SciScore for 10.1101/2021.02.08.21251358: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethical Statement: The study was approved by the Medical Research Ethical Committee of the University of Navarra (protocol number 2020·077).
Consent: Informed consent was obtained by all participants of the study.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable The median age was 61, and 57·1% were women. Table 2: Resources
Software and Algorithms Sentences Resources Role of the funding source: DLA’s work in Genomics is funded by a long-term European Molecular Biology Organization (EMBO) fellowship. Genomicssuggested: (UTHSCSA Genomics Core, RRID:SCR_012239)Results from OddPub: We did not detect open data. We …
SciScore for 10.1101/2021.02.08.21251358: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethical Statement: The study was approved by the Medical Research Ethical Committee of the University of Navarra (protocol number 2020·077).
Consent: Informed consent was obtained by all participants of the study.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable The median age was 61, and 57·1% were women. Table 2: Resources
Software and Algorithms Sentences Resources Role of the funding source: DLA’s work in Genomics is funded by a long-term European Molecular Biology Organization (EMBO) fellowship. Genomicssuggested: (UTHSCSA Genomics Core, RRID:SCR_012239)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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