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1.
BMC Fam Pract ; 22(1): 256, 2021 12 24.
Article in English | MEDLINE | ID: covidwho-1630383

ABSTRACT

BACKGROUND: There is increased recognition in clinical settings of the importance of documenting, understanding, and addressing patients' social determinants of health (SDOH) to improve health and address health inequities. This study evaluated a pilot of a standardized SDOH screening questionnaire and workflow in an ambulatory clinic within a large integrated health network in Northern California. METHODS: The pilot screened for SDOH needs using an 11-question Epic-compatible paper questionnaire assessing eight SDOH and health behavior domains: financial resource, transportation, stress, depression, intimate partner violence, social connections, physical activity, and alcohol consumption. Eligible patients for the pilot receiving a Medicare wellness, adult annual, or new patient visits during a five-week period (February-March, 2020), and a comparison group from the same time period in 2019 were identified. Sociodemographic data (age, sex, race/ethnicity, and payment type), visit type, length of visit, and responses to SDOH questions were extracted from electronic health records, and a staff experience survey was administered. The evaluation was guided by the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework. RESULTS: Two-hundred eighty-nine patients were eligible for SDOH screening. Responsiveness by domain ranged from 55 to 67%, except for depression. Half of patients had at least one identified social need, the most common being stress (33%), physical activity (22%), alcohol (12%), and social connections (6%). Physical activity needs were identified more in females (81% vs. 19% in males, p < .01) and at new patient/transfer visits (48% vs. 13% at Medicare wellness and 38% at adult wellness visits, p < .05). Average length of visit was 39.8 min, which was 1.7 min longer than that in 2019. Visit lengths were longer among patients 65+ (43.4 min) and patients having public insurance (43.6 min). Most staff agreed that collecting SDOH data was relevant and accepted the SDOH questionnaire and workflow but highlighted opportunities for improvement in training and connecting patients to resources. CONCLUSION: Use of evidence-based SDOH screening questions and associated workflow was effective in gathering patient SDOH information and identifying social needs in an ambulatory setting. Future studies should use qualitative data to understand patient and staff experiences with collecting SDOH information in healthcare settings.


Subject(s)
Social Determinants of Health , Aged , Female , Humans , Male , Medicare , Referral and Consultation , Surveys and Questionnaires , United States , Workflow
2.
Nat Microbiol ; 7(1): 108-119, 2022 01.
Article in English | MEDLINE | ID: covidwho-1574813

ABSTRACT

The global spread and continued evolution of SARS-CoV-2 has driven an unprecedented surge in viral genomic surveillance. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine laboratory processes and results. This challenge will increase with the expanding global production of sequences across a variety of laboratories for epidemiological and clinical interpretation, as well as for genomic surveillance of emerging diseases in future outbreaks. We present SDSI + AmpSeq, an approach that uses 96 synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination throughout the sequencing workflow. We apply SDSIs to the ARTIC Consortium's amplicon design, demonstrate their utility and efficiency in a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases and validate them across 6,676 diagnostic samples at multiple laboratories. We establish that SDSI + AmpSeq provides increased confidence in genomic data by detecting and correcting for relatively common, yet previously unobserved modes of error, including spillover and sample swaps, without impacting genome recovery.


Subject(s)
DNA Primers/standards , SARS-CoV-2/genetics , Sequence Analysis/standards , COVID-19/diagnosis , DNA Primers/chemical synthesis , Genome, Viral/genetics , Humans , Quality Control , RNA, Viral/genetics , Reproducibility of Results , Sequence Analysis/methods , Whole Genome Sequencing , Workflow
3.
BMC Med Genomics ; 14(Suppl 6): 289, 2021 12 14.
Article in English | MEDLINE | ID: covidwho-1571758

ABSTRACT

BACKGROUND: Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs. Next-generation sequencing (NGS) provides an efficient and unbiased way to identify viral pathogens in host-associated and environmental samples without prior knowledge. Despite the availability of software, data analysis still requires human operations. A mature pipeline is urgently needed when thousands of viral pathogen and viral genome reconstruction samples need to be rapidly identified. RESULTS: In this paper, we present a rapid and accurate workflow to screen metagenomics sequencing data for viral pathogens and other compositions, as well as enable a reference-based assembler to reconstruct viral genomes. Moreover, we tested our workflow on several metagenomics datasets, including a SARS-CoV-2 patient sample with NGS data, pangolins tissues with NGS data, Middle East Respiratory Syndrome (MERS)-infected cells with NGS data, etc. Our workflow demonstrated high accuracy and efficiency when identifying target viruses from large scale NGS metagenomics data. Our workflow was flexible when working with a broad range of NGS datasets from small (kb) to large (100 Gb). This took from a few minutes to a few hours to complete each task. At the same time, our workflow automatically generates reports that incorporate visualized feedback (e.g., metagenomics data quality statistics, host and viral sequence compositions, details about each of the identified viral pathogens and their coverages, and reassembled viral pathogen sequences based on their closest references). CONCLUSIONS: Overall, our system enabled the rapid screening and identification of viral pathogens from metagenomics data, providing an important piece to support viral pathogen research during a pandemic. The visualized report contains information from raw sequence quality to a reconstructed viral sequence, which allows non-professional people to screen their samples for viruses by themselves (Additional file 1).


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Computational Biology/methods , Genome, Viral , Genomics , Metagenomics , SARS-CoV-2/genetics , Algorithms , Animals , Automation , Coronavirus Infections/genetics , High-Throughput Nucleotide Sequencing , Humans , Mass Screening/methods , Pandemics , Pangolins , Reference Values , Software , Transcriptome , Workflow
4.
J Appl Lab Med ; 6(6): 1441-1451, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1493844

ABSTRACT

BACKGROUND: This study outlines the development, implementation, and impact of a laboratory-developed, extraction-free real-time PCR assay as the primary diagnostic test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a pediatric hospital. METHODS: Clinical specimens from both upper and lower respiratory tract sources were validated, including nasopharyngeal aspirates, nasopharyngeal swabs, anterior nares swabs, and tracheal aspirates (n = 333 clinical samples). Testing volumes and laboratory turnaround times were then compared before and after implementation to investigate effects of the workflow changes. RESULTS: Compared to magnetic-bead extraction platforms, extraction-free real-time PCR demonstrated ≥95% positive agreement and ≥97% negative agreement across all tested sources. Implementation of this workflow reduced laboratory turnaround time from an average of 8.8 (+/-5.5) h to 3.6 (+/-1.3) h despite increasing testing volumes (from 1515 to 4884 tests per week over the reported period of testing). CONCLUSIONS: The extraction-free workflow reduced extraction reagent cost for SARS-CoV-2 testing by 97%, shortened sample handling time, and significantly alleviated supply chain scarcities due to the elimination of specialized extraction reagents for routine testing. Overall, this assay is a viable option for laboratories to increase efficiency and navigate reagent shortages for SARS-CoV-2 diagnostic testing.


Subject(s)
COVID-19 Testing , COVID-19 , Child , Hospitals, Pediatric , Humans , Real-Time Polymerase Chain Reaction , SARS-CoV-2 , Sensitivity and Specificity , Workflow
5.
Int J Environ Res Public Health ; 18(20)2021 10 14.
Article in English | MEDLINE | ID: covidwho-1480726

ABSTRACT

With the development of information and technology, especially with the boom in big data, healthcare support systems are becoming much better. Patient data can be collected, retrieved, and stored in real time. These data are valuable and meaningful for monitoring, diagnosing, and further applications in data analysis and decision-making. Essentially, the data can be divided into three types, namely, statistical, image-based, and sequential data. Each type has a different method of retrieval, processing, and deployment. Additionally, the application of machine learning (ML) and deep learning (DL) in healthcare support systems is growing more rapidly than ever. Numerous high-performance architectures are proposed to optimize decision-making. As reliability and stability are the most important factors in the healthcare support system, enhancing the predicted performance and maintaining the stability of the model are always the top priority. The main idea of our study comes from ensemble techniques. Numerous studies and data science competitions show that by combining several weak models into one, ensemble models can attain outstanding performance and reliability. We propose three deep ensemble learning (DEL) approaches, each with stable and reliable performance, that are workable on the above-mentioned data types. These are deep-stacked generalization ensemble learning, gradient deep learning boosting, and deep aggregation learning. The experiment results show that our proposed approaches achieve more vigorous and reliable performance than traditional ML and DL techniques on statistical, image-based, and sequential benchmark datasets. In particular, on the Heart Disease UCI dataset, representing the statistical type, the gradient deep learning boosting approach dominates the others with accuracy, recall, F1-score, Matthews correlation coefficient, and area under the curve values of 0.87, 0.81, 0.83, 0.73, and 0.91, respectively. On the X-ray dataset, representing the image-based type, the deep aggregation learning approach shows the highest performance with values of 0.91, 0.97, 0.93, 0.80, and 0.94, respectively. On the Depresjon dataset, representing the sequence type, the deep-stacked generalization ensemble learning approach outperforms the others with values of 0.91, 0.84, 0.86, 0.8, and 0.94, respectively. Overall, we conclude that applying DL models using our proposed approaches is a promising method for the healthcare support system to enhance prediction and diagnosis performance. Furthermore, our study reveals that these approaches are flexible and easy to apply to achieve optimal performance.


Subject(s)
Benchmarking , Machine Learning , Delivery of Health Care , Humans , Reproducibility of Results , Workflow
7.
Anal Bioanal Chem ; 413(29): 7251-7263, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1460298

ABSTRACT

Supply shortage for the development and production of preventive, therapeutic, and diagnosis tools during the COVID-19 pandemic is an important issue affecting the wealthy and poor nations alike. Antibodies and antigens are especially needed for the production of immunological-based testing tools such as point-of-care tests. Here, we propose a simple and quick magnetic nanoparticle (MNP)-based separation/isolation approach for the repurposing of infected human samples to produce specific antibodies and antigen cocktails. Initially, an antibody cocktail was purified from serums via precipitation and immunoaffinity chromatography. Purified antibodies were conjugated onto MNPs and used as an affinity matrix to separate antigens. The characterization process was performed by ELISA, SDS-PAGE, electrochemistry, isothermal titration calorimetry, and LC-Q-TOF-MS/MS analyses. The MNP-separated peptides can be used for mass spectrometry-based as well as paper-based lateral flow assay diagnostic. The exploitation of the current workflow for the development of efficient diagnostic tools, specific treatments, and fundamental research can significantly impact the present or eventual pandemic. This workflow can be considered as a two birds, one stone-like strategy.


Subject(s)
Antibodies, Viral/isolation & purification , Antigens, Viral/isolation & purification , COVID-19/diagnosis , Cost-Benefit Analysis , Immunoassay/economics , SARS-CoV-2/isolation & purification , Viremia/virology , Antibodies, Viral/blood , Antigens, Viral/blood , COVID-19/virology , Calorimetry , Electrophoresis, Polyacrylamide Gel , Enzyme-Linked Immunosorbent Assay , Humans , SARS-CoV-2/immunology , Specimen Handling , Tandem Mass Spectrometry , Viremia/blood , Workflow
8.
J Ambul Care Manage ; 44(4): 293-303, 2021.
Article in English | MEDLINE | ID: covidwho-1447660

ABSTRACT

COVID-19 necessitated significant care redesign, including new ambulatory workflows to handle surge volumes, protect patients and staff, and ensure timely reliable care. Opportunities also exist to harvest lessons from workflow innovations to benefit routine care. We describe a dedicated COVID-19 ambulatory unit for closing testing and follow-up loops characterized by standardized workflows and electronic communication, documentation, and order placement. More than 85% of follow-ups were completed within 24 hours, with no observed staff, nor patient infections associated with unit operations. Identified issues include role confusion, staffing and gatekeeping bottlenecks, and patient reluctance to visit in person or discuss concerns with phone screeners.


Subject(s)
Ambulatory Care Facilities/organization & administration , COVID-19/therapy , Continuity of Patient Care/organization & administration , Pneumonia, Viral/therapy , Respiratory Care Units/organization & administration , Adult , Aged , Boston/epidemiology , COVID-19/epidemiology , Female , Humans , Male , Middle Aged , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Referral and Consultation/statistics & numerical data , SARS-CoV-2 , Systems Analysis , Workflow
9.
Scand J Trauma Resusc Emerg Med ; 29(1): 135, 2021 Sep 14.
Article in English | MEDLINE | ID: covidwho-1430466

ABSTRACT

BACKGROUND: During the SARS-CoV-2 pandemic, the French Government imposed various containment strategies, such as severe lockdown (SL) or moderate lockdown (ML). The aim of this study was to evaluate the effect of both strategies on severe trauma admissions and ICU capacity in Ile-de-France region (Paris Area). MAIN TEXT: We conducted a multicenter cohort-based observational study from 1stJanuary 2017 to 31th December 2020, including all consecutive trauma patients admitted to the trauma centers of Ile-de-France region participating in the national registry (Traumabase®). Two periods were defined, the "non-pandemic period" (NPP) from 2017 to 2019, and the "pandemic period" (PP) concerning those admitted in 2020. The number of ICU beds released during 2020 pandemic period (overall period, SL and ML) was estimated by multiplying difference in trauma admissions by the median length of stay during the same week of pandemic period (ICU day-beds in 2020). A 15% yearly reduction of trauma patients was observed during the PP, associated with the release of 6422 ICU day-beds in 2020. During SL and ML, the observed decrease in trauma admission was respectively 49 and 39% compared with similar dates of the NPP. The number of beds released was 1531 days-beds in SL and 679 day-beds in ML. Those reductions respectively accounted for 4.5 and 6.0% of the overall ICU admission for COVID-19 in Ile-de-France. CONCLUSION: The lockdown strategies during pandemic resulted in a reduction of severe trauma admissions. In addition to the social distancing effect, lockdown strategies freed up an important number of ICU beds in trauma centers, available for severe COVID-19 patients.


Subject(s)
COVID-19 , Communicable Disease Control , Humans , Pandemics/prevention & control , SARS-CoV-2 , Workflow
10.
PLoS One ; 16(9): e0256813, 2021.
Article in English | MEDLINE | ID: covidwho-1410652

ABSTRACT

There is a worldwide need for reagents to perform SARS-CoV-2 detection. Some laboratories have implemented kit-free protocols, but many others do not have the capacity to develop these and/or perform manual processing. We provide multiple workflows for SARS-CoV-2 nucleic acid detection in clinical samples by comparing several commercially available RNA extraction methods: QIAamp Viral RNA Mini Kit (QIAgen), RNAdvance Blood/Viral (Beckman) and Mag-Bind Viral DNA/RNA 96 Kit (Omega Bio-tek). We also compared One-step RT-qPCR reagents: TaqMan Fast Virus 1-Step Master Mix (FastVirus, ThermoFisher Scientific), qPCRBIO Probe 1-Step Go Lo-ROX (PCR Biosystems) and Luna® Universal Probe One-Step RT-qPCR Kit (Luna, NEB). We used primer-probes that detect viral N (EUA CDC) and RdRP. RNA extraction methods provided similar results, with Beckman performing better with our primer-probe combinations. Luna proved most sensitive although overall the three reagents did not show significant differences. N detection was more reliable than that of RdRP, particularly in samples with low viral titres. Importantly, we demonstrated that heat treatment of nasopharyngeal swabs at 70°C for 10 or 30 min, or 90°C for 10 or 30 min (both original variant and B 1.1.7) inactivated SARS-CoV-2 employing plaque assays, and had minimal impact on the sensitivity of the qPCR in clinical samples. These findings make SARS-CoV-2 testing portable in settings that do not have CL-3 facilities. In summary, we provide several testing pipelines that can be easily implemented in other laboratories and have made all our protocols and SOPs freely available at https://osf.io/uebvj/.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Hot Temperature , RNA, Viral/genetics , SARS-CoV-2/genetics , Virus Inactivation , COVID-19/epidemiology , COVID-19/virology , Epidemics/prevention & control , Humans , Nasopharynx/virology , Reagent Kits, Diagnostic , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/physiology , Sensitivity and Specificity , Specimen Handling/methods , Workflow
11.
Scand J Trauma Resusc Emerg Med ; 29(1): 135, 2021 Sep 14.
Article in English | MEDLINE | ID: covidwho-1405990

ABSTRACT

BACKGROUND: During the SARS-CoV-2 pandemic, the French Government imposed various containment strategies, such as severe lockdown (SL) or moderate lockdown (ML). The aim of this study was to evaluate the effect of both strategies on severe trauma admissions and ICU capacity in Ile-de-France region (Paris Area). MAIN TEXT: We conducted a multicenter cohort-based observational study from 1stJanuary 2017 to 31th December 2020, including all consecutive trauma patients admitted to the trauma centers of Ile-de-France region participating in the national registry (Traumabase®). Two periods were defined, the "non-pandemic period" (NPP) from 2017 to 2019, and the "pandemic period" (PP) concerning those admitted in 2020. The number of ICU beds released during 2020 pandemic period (overall period, SL and ML) was estimated by multiplying difference in trauma admissions by the median length of stay during the same week of pandemic period (ICU day-beds in 2020). A 15% yearly reduction of trauma patients was observed during the PP, associated with the release of 6422 ICU day-beds in 2020. During SL and ML, the observed decrease in trauma admission was respectively 49 and 39% compared with similar dates of the NPP. The number of beds released was 1531 days-beds in SL and 679 day-beds in ML. Those reductions respectively accounted for 4.5 and 6.0% of the overall ICU admission for COVID-19 in Ile-de-France. CONCLUSION: The lockdown strategies during pandemic resulted in a reduction of severe trauma admissions. In addition to the social distancing effect, lockdown strategies freed up an important number of ICU beds in trauma centers, available for severe COVID-19 patients.


Subject(s)
COVID-19 , Communicable Disease Control , Humans , Pandemics/prevention & control , SARS-CoV-2 , Workflow
12.
J Infect ; 83(5): 589-593, 2021 11.
Article in English | MEDLINE | ID: covidwho-1401632

ABSTRACT

INTRODUCTION: The large number of asymptomatic SARS-CoV-2 infections necessitates general screening of employees. We evaluate the performance of a SARS-CoV-2 screening program in asymptomatic healthcare-workers (HCW), utilizing self-sampled gargling-solution and sample pooling for RT-qPCR. METHODS: We conducted a cross-sectional retrospective study to collect real-life data on the performance of a screening-workflow based on automated-pooling and high-throughput qPCR testing over a 3-month-period at the University Hospital Hamburg. RESULTS: Matrix validation reveals that lower limit of detection for SARS-CoV-2 RNA in gargling-solution was 180 copies/mL (5-sample-pool). A total of 55,122 self-collected gargle samples (= 7513 HCWs) was analyzed. The median time to result was 8.5 hours (IQR 7.2-10.8). Of 11,192 pools analyzed, 11,041 (98.7%) were negative, 69 (0.6%) were positive and 82 (0.7%) were invalid. Individual testing of pool participants revealed 57 SARS-CoV-2 previously unrecognized infections. All 57 HCWs were either pre-symptomatic or asymptomatic (prevalence 0.76%,CI95%0.58-0.98%). Accuracy based on HCWs with gargle-solution and NP-swab available within 3-day-interval (N = 521) was 99.5% (CI95%98.3-99.9%), sensitivity 88.9% (CI95%65.3-98.6%) while specificity 99.8% (CI95%98.9-99.9). CONCLUSION: This workflow was highly effective in identifying SARS-CoV-2 positive HCWs, thereby lowering the potential of inter-HCW and HCW-patient transmissions. Automated-sample-pooling helped to conserve qPCR reagents and represents a promising alternative strategy to antigen testing in mass-screening programs.


Subject(s)
COVID-19 , SARS-CoV-2 , Cross-Sectional Studies , Delivery of Health Care , Humans , RNA, Viral , Retrospective Studies , Workflow
13.
Stat Med ; 40(27): 6209-6234, 2021 11 30.
Article in English | MEDLINE | ID: covidwho-1396957

ABSTRACT

This tutorial shows how to build, fit, and criticize disease transmission models in Stan, and should be useful to researchers interested in modeling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and other infectious diseases in a Bayesian framework. Bayesian modeling provides a principled way to quantify uncertainty and incorporate both data and prior knowledge into the model estimates. Stan is an expressive probabilistic programming language that abstracts the inference and allows users to focus on the modeling. As a result, Stan code is readable and easily extensible, which makes the modeler's work more transparent. Furthermore, Stan's main inference engine, Hamiltonian Monte Carlo sampling, is amiable to diagnostics, which means the user can verify whether the obtained inference is reliable. In this tutorial, we demonstrate how to formulate, fit, and diagnose a compartmental transmission model in Stan, first with a simple susceptible-infected-recovered model, then with a more elaborate transmission model used during the SARS-CoV-2 pandemic. We also cover advanced topics which can further help practitioners fit sophisticated models; notably, how to use simulations to probe the model and priors, and computational techniques to scale-up models based on ordinary differential equations.


Subject(s)
COVID-19 , SARS-CoV-2 , Bayes Theorem , Humans , Monte Carlo Method , Workflow
14.
Mol Syst Biol ; 17(3): e9923, 2021 03.
Article in English | MEDLINE | ID: covidwho-1389839

ABSTRACT

Molecular knowledge of biological processes is a cornerstone in omics data analysis. Applied to single-cell data, such analyses provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across resources, and not linked to intracellular processes. To address this gap, we combined over 100 resources covering interactions and roles of proteins in inter- and intracellular signaling, as well as transcriptional and post-transcriptional regulation. We added protein complex information and annotations on function, localization, and role in diseases for each protein. The resource is available for human, and via homology translation for mouse and rat. The data are accessible via OmniPath's web service (https://omnipathdb.org/), a Cytoscape plug-in, and packages in R/Bioconductor and Python, providing access options for computational and experimental scientists. We created workflows with tutorials to facilitate the analysis of cell-cell interactions and affected downstream intracellular signaling processes. OmniPath provides a single access point to knowledge spanning intra- and intercellular processes for data analysis, as we demonstrate in applications studying SARS-CoV-2 infection and ulcerative colitis.


Subject(s)
COVID-19/metabolism , Colitis, Ulcerative/metabolism , Computational Biology/methods , Proteins/metabolism , Signal Transduction , Animals , Cell Communication , Colitis, Ulcerative/pathology , Databases, Factual , Enzymes/metabolism , Humans , Mice , Protein Processing, Post-Translational , Proteins/genetics , Rats , Single-Cell Analysis , Software , Workflow
15.
PLoS One ; 16(7): e0252509, 2021.
Article in English | MEDLINE | ID: covidwho-1388919

ABSTRACT

The current global pandemic due to the SARS-CoV-2 has pushed the limits of global health systems across all aspects of clinical care, including laboratory diagnostics. Supply chain disruptions and rapidly-shifting markets have resulted in flash-scarcity of commercial laboratory reagents; this has motivated health care providers to search for alternative workflows to cope with the international increase in demand for SARS-CoV-2 testing. The aim of this study is to present a reproducible workflow for real time RT-PCR SARS-CoV-2 testing using OT-2 open-source liquid-handling robots (Opentrons, NY). We have developed a framework that includes a code template which is helpful for building different stand-alone robotic stations, capable of performing specific protocols. Such stations can be combined together to create a complex multi-stage workflow, from sample setup to real time RT-PCR. Using our open-source code, it is easy to create new stations or workflows from scratch, adapt existing templates to update the experimental protocols, or to fine-tune the code to fit specific needs. Using this framework, we developed the code for two different workflows and evaluated them using external quality assessment (EQA) samples from the European Molecular Genetics Quality Network (EMQN). The affordability of this platform makes automated SARS-CoV-2 PCR testing accessible for most laboratories and hospitals with qualified bioinformatics personnel. This platform also allows for flexibility, as it is not dependent on any specific commercial kit, and thus it can be quickly adapted to protocol changes, reagent, consumable shortages, or any other temporary material constraints.


Subject(s)
COVID-19 Nucleic Acid Testing/instrumentation , SARS-CoV-2/isolation & purification , Clinical Coding , Early Diagnosis , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/instrumentation , Reverse Transcriptase Polymerase Chain Reaction/instrumentation , Robotics , SARS-CoV-2/genetics , Workflow
16.
Cytometry A ; 97(9): 882-886, 2020 09.
Article in English | MEDLINE | ID: covidwho-1384154

ABSTRACT

Operating shared resource laboratories (SRLs) in times of pandemic is a challenge for research institutions. In a multiuser, high-turnover working space, the transmission of infectious agents is difficult to control. To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS-CoV-2 between users and staff. Here, we describe the resulting guidelines and explain their rationale, with a focus on separating users in space and time, protective face masks, and keeping surfaces virus-free. These recommendations may prove useful for other types of SRLs. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.


Subject(s)
Betacoronavirus/pathogenicity , Biomedical Research/organization & administration , Coronavirus Infections/prevention & control , Infection Control , Laboratories/organization & administration , Microscopy , Occupational Health , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , COVID-19 , Cooperative Behavior , Coronavirus Infections/transmission , Coronavirus Infections/virology , Decontamination , Equipment Contamination/prevention & control , Germany , Humans , Occupational Exposure/prevention & control , Personal Protective Equipment , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Protective Factors , Research Personnel/organization & administration , Risk Assessment , Risk Factors , SARS-CoV-2 , Workflow
18.
J Mol Diagn ; 23(9): 1085-1096, 2021 09.
Article in English | MEDLINE | ID: covidwho-1370607

ABSTRACT

Widespread high-throughput testing for identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by RT-PCR has been a foundation in the response to the coronavirus disease 2019 (COVID-19) pandemic. Quality assurance metrics for these RT-PCR tests are still evolving as testing is widely implemented. As testing increases, it is important to understand performance characteristics and the errors associated with these tests. Herein, we investigate a high-throughput, laboratory-developed SARS-CoV-2 RT-PCR assay to determine whether modeling can generate quality control metrics that identify false-positive (FP) results due to contamination. This study reviewed repeated clinical samples focusing on positive samples that test negative on re-extraction and PCR, likely representing false positives. To identify and predict false-positive samples, we constructed machine learning-derived models based on the extraction method used. These models identified variables associated with false-positive results across all methods, with sensitivities for predicting FP results ranging between 67% and 100%. Application of the models to all results predicted a total FP rate of 0.08% across all samples, or 2.3% of positive results, similar to reports for other RT-PCR tests for RNA viruses. These models can predict quality control parameters, enabling laboratories to generate decision trees that reduce interpretation errors, allow for automated reflex testing of samples with a high FP probability, improve workflow efficiency, and increase diagnostic accuracy for patient care.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , RNA, Viral/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/methods , Automation, Laboratory , Carrier State/virology , Decision Support Systems, Clinical , False Positive Reactions , High-Throughput Nucleotide Sequencing/methods , Humans , Machine Learning , SARS-CoV-2/genetics , Viral Load , Workflow
19.
J Health Organ Manag ; ahead-of-print(ahead-of-print)2021 Aug 23.
Article in English | MEDLINE | ID: covidwho-1367129

ABSTRACT

PURPOSE: The COVID-19 pandemic has changed the way hospitals work. Strategies that were detached from the boundaries of departments and responsibilities in the COVID-19 pandemic have proven themselves under extreme conditions and show a beneficial influence on patient flow and resource management as well as on the communication culture. The continuation of closer interdisciplinary and cross-sectoral co-operation in a "new clinical routine" could have a positive impact on personnel concepts, communication strategies, and the management of acute care capacities and patient pathways. DESIGN/METHODOLOGY/APPROACH: The aim of the paper is to critically discuss the knowledge gained in the context of the COVID-19 pandemic from the various approaches in patient flow and capacity management as well as interdisciplinary co-operation. More recent research has evaluated patient pathway management, personnel planning and communication measures with regard to their effect and practicability for continuation in everyday clinical practice. FINDINGS: Patient flows and acute care capacities can be more efficiently managed by continuing a culture change towards closer interdisciplinary and intersectoral co-operation and technologies that support this with telemedicine functionalities and regional healthcare data interoperability. Together with a bi-directional, more frequent and open communication and feedback culture, it could form a "new clinical routine". ORIGINALITY/VALUE: This paper discusses a holistic approach on the way away from silo thinking towards cross-departmental collaboration.


Subject(s)
COVID-19/epidemiology , Cooperative Behavior , Hospital Administration , Pneumonia, Viral/epidemiology , Workflow , Female , Humans , Male , Pandemics , Pneumonia, Viral/virology , SARS-CoV-2
20.
Medicine (Baltimore) ; 100(33): e26760, 2021 Aug 20.
Article in English | MEDLINE | ID: covidwho-1367077

ABSTRACT

ABSTRACT: The present study reported early clinical outcomes and perioperative precautions for medical staffs during joint arthroplasty procedures in SARS-CoV-2-infected patients.The medical records of 8 patients with SARS-CoV-2 infection who underwent joint arthroplasty from January 19 to September 24, 2020 were retrospectively reviewed and analyzed. Perioperative precautions and follow-up (time length varies from 6 month to 13 months, 11 months in average) for SARS-CoV-2 infection of medical staffs were reported.All patients recovered well from both the primary disease and SARS-CoV-2 infection. Significant improved Visual analogue scale was observed with no major complications or recurrence of the COVID-19 at discharge. There was no evidence indicating SARS-CoV-2 infection in any health providers.Elective joint arthroplasties for patients in recovery period of SARS-CoV-2 infection could be continued under comprehensive preoperative evaluation and appropriate medical protection. For patients with currently confirmed or highly suspected COVID-19, the operation should be carried out only if it was essential.


Subject(s)
Arthroplasty, Replacement, Hip , COVID-19/transmission , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Medical Staff, Hospital , Perioperative Care/methods , Aged , Aged, 80 and over , Arthroplasty, Replacement, Hip/adverse effects , Clinical Protocols , Female , Hip/diagnostic imaging , Humans , Male , Middle Aged , Pandemics , Personal Protective Equipment , Postoperative Care , Postoperative Complications , Retrospective Studies , SARS-CoV-2 , Treatment Outcome , Workflow
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