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2.
Elife ; 92020 08 17.
Article in English | MEDLINE | ID: covidwho-2155739

ABSTRACT

Temporal inference from laboratory testing results and triangulation with clinical outcomes extracted from unstructured electronic health record (EHR) provider notes is integral to advancing precision medicine. Here, we studied 246 SARS-CoV-2 PCR-positive (COVIDpos) patients and propensity-matched 2460 SARS-CoV-2 PCR-negative (COVIDneg) patients subjected to around 700,000 lab tests cumulatively across 194 assays. Compared to COVIDneg patients at the time of diagnostic testing, COVIDpos patients tended to have higher plasma fibrinogen levels and lower platelet counts. However, as the infection evolves, COVIDpos patients distinctively show declining fibrinogen, increasing platelet counts, and lower white blood cell counts. Augmented curation of EHRs suggests that only a minority of COVIDpos patients develop thromboembolism, and rarely, disseminated intravascular coagulopathy (DIC), with patients generally not displaying platelet reductions typical of consumptive coagulopathies. These temporal trends provide fine-grained resolution into COVID-19 associated coagulopathy (CAC) and set the stage for personalizing thromboprophylaxis.


Subject(s)
Betacoronavirus/isolation & purification , Blood Coagulation Disorders/diagnosis , Blood Coagulation Tests , Blood Coagulation , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Aged , Betacoronavirus/pathogenicity , Biomarkers/blood , Blood Coagulation Disorders/blood , Blood Coagulation Disorders/virology , COVID-19 , COVID-19 Testing , Coronavirus Infections/blood , Coronavirus Infections/virology , Disease Progression , Female , Fibrinogen/metabolism , Host Microbial Interactions , Humans , Leukocyte Count , Longitudinal Studies , Male , Middle Aged , Pandemics , Platelet Count , Pneumonia, Viral/blood , Pneumonia, Viral/virology , Predictive Value of Tests , Reproducibility of Results , Retrospective Studies , SARS-CoV-2 , Time Factors
3.
JMIR Public Health Surveill ; 7(4): e26460, 2021 04 06.
Article in English | MEDLINE | ID: covidwho-2141312

ABSTRACT

The enormous pressure of the increasing case numbers experienced during the COVID-19 pandemic has given rise to a variety of novel digital systems designed to provide solutions to unprecedented challenges in public health. The field of algorithmic contact tracing, in particular, an area of research that had previously received limited attention, has moved into the spotlight as a crucial factor in containing the pandemic. The use of digital tools to enable more robust and expedited contact tracing and notification, while maintaining privacy and trust in the data generated, is viewed as key to identifying chains of transmission and close contacts, and, consequently, to enabling effective case investigations. Scaling these tools has never been more critical, as global case numbers have exceeded 100 million, as many asymptomatic patients remain undetected, and as COVID-19 variants begin to emerge around the world. In this context, there is increasing attention on blockchain technology as a part of systems for enhanced digital algorithmic contact tracing and reporting. By analyzing the literature that has emerged from this trend, the common characteristics of the designs proposed become apparent. An archetypal system architecture can be derived, taking these characteristics into consideration. However, assessing the utility of this architecture using a recognized evaluation framework shows that the added benefits and features of blockchain technology do not provide significant advantages over conventional centralized systems for algorithmic contact tracing and reporting. From our study, it, therefore, seems that blockchain technology may provide a more significant benefit in other areas of public health beyond contact tracing.


Subject(s)
Algorithms , Blockchain , Contact Tracing , Coronavirus Infections , Privacy , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Female , Humans , Male , Public Health
4.
Ann Intern Med ; 173(10): JC57, 2020 11 17.
Article in English | MEDLINE | ID: covidwho-2110754

ABSTRACT

SOURCE CITATION: Deeks JJ, Dinnes J, Takwoingi Y, et al. Antibody tests for identification of current and past infection with SARS-CoV-2. Cochrane Database Syst Rev. 2020;6:CD013652. 32584464.


Subject(s)
Coronavirus Infections , Pandemics , Pneumonia, Viral , Antibodies, Viral , Betacoronavirus , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Humans , Pneumonia, Viral/epidemiology , SARS-CoV-2 , Sensitivity and Specificity
5.
Front Cell Infect Microbiol ; 12: 976137, 2022.
Article in English | MEDLINE | ID: covidwho-2109734

ABSTRACT

Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus that causes acute watery diarrhea and vomiting in unweaned piglets. Infections result in high mortality and serious economic losses to the swine industry. PEDV attenuated vaccine does not completely protect against all mutant wild-type strains, and PEDV infection can periodically occur. A sensitive, accurate, and simple detection method for PEDV is needed to reduce the occurrence of the disease. In this study, the CRISPR/Cas13a system was combined with recombinase aided amplification to develop a rapid diagnostic method to distinguish PEDV wild-type strains from attenuated vaccine strains. The method is based on isothermal detection at 37°C. The results are used for visual readout. The assay had high sensitivity and specificity, with a detection limit of 101 copies/µL for the gene of interest, and no cross-reactivity with other pathogens. The Cas13a detection worked well with clinical samples. This visual, sensitive, and specific nucleic acid detection method based on CRISPR/Cas13a should be a powerful tool for detecting PEDV.


Subject(s)
Coronavirus Infections , Nucleic Acids , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Clustered Regularly Interspaced Short Palindromic Repeats , Coronavirus Infections/diagnosis , Coronavirus Infections/genetics , Coronavirus Infections/veterinary , Diarrhea , Porcine epidemic diarrhea virus/genetics , Recombinases , Sensitivity and Specificity , Swine , Swine Diseases/genetics , Vaccines, Attenuated/genetics
6.
Scand J Trauma Resusc Emerg Med ; 28(1): 106, 2020 Oct 27.
Article in English | MEDLINE | ID: covidwho-2098375

ABSTRACT

BACKGROUND: Novel coronavirus disease 2019 (COVID-19) is a global public health emergency. Here, we developed and validated a practical model based on the data from a multi-center cohort in China for early identification and prediction of which patients will be admitted to the intensive care unit (ICU). METHODS: Data of 1087 patients with laboratory-confirmed COVID-19 were collected from 49 sites between January 2 and February 28, 2020, in Sichuan and Wuhan. Patients were randomly categorized into the training and validation cohorts (7:3). The least absolute shrinkage and selection operator and logistic regression analyzes were used to develop the nomogram. The performance of the nomogram was evaluated for the C-index, calibration, discrimination, and clinical usefulness. Further, the nomogram was externally validated in a different cohort. RESULTS: The individualized prediction nomogram included 6 predictors: age, respiratory rate, systolic blood pressure, smoking status, fever, and chronic kidney disease. The model demonstrated a high discriminative ability in the training cohort (C-index = 0.829), which was confirmed in the external validation cohort (C-index = 0.776). In addition, the calibration plots confirmed good concordance for predicting the risk of ICU admission. Decision curve analysis revealed that the prediction nomogram was clinically useful. CONCLUSION: We established an early prediction model incorporating clinical characteristics that could be quickly obtained on hospital admission, even in community health centers. This model can be conveniently used to predict the individual risk for ICU admission of patients with COVID-19 and optimize the use of limited resources.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Coronavirus Infections/therapy , Hospitalization , Intensive Care Units , Pneumonia, Viral/epidemiology , Pneumonia, Viral/therapy , Adult , Aged , COVID-19 , China , Coronavirus Infections/diagnosis , Female , Humans , Logistic Models , Male , Middle Aged , Nomograms , Pandemics , Pneumonia, Viral/diagnosis , Retrospective Studies , Risk Assessment , SARS-CoV-2
11.
Infect Control Hosp Epidemiol ; 41(11): 1328-1330, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-2096354

ABSTRACT

Environmental surface testing was performed to search for evidence of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) environmental contamination by an asymptomatic SARS-CoV-2 carrier with persistently high viral loads under isolation. No evidence of environmental contamination was found. Further studies are needed to measure environmental contamination by SARS-CoV-2 carriers and to determine reasonable isolation periods.


Subject(s)
Asymptomatic Infections , Betacoronavirus/isolation & purification , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Fomites/virology , Pneumonia, Viral/diagnosis , Quarantine/methods , Viral Load , Adult , COVID-19 , COVID-19 Testing , Child , Coronavirus Infections/prevention & control , Coronavirus Infections/transmission , Coronavirus Infections/virology , Female , Humans , Pandemics/prevention & control , Patients' Rooms , Pneumonia, Viral/prevention & control , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Quarantine/standards , SARS-CoV-2
12.
Infect Control Hosp Epidemiol ; 41(11): 1258-1265, 2020 11.
Article in English | MEDLINE | ID: covidwho-2096345

ABSTRACT

BACKGROUND: The role of severe respiratory coronavirus virus 2 (SARS-CoV-2)-laden aerosols in the transmission of coronavirus disease 2019 (COVID-19) remains uncertain. Discordant findings of SARS-CoV-2 RNA in air samples were noted in early reports. METHODS: Sampling of air close to 6 asymptomatic and symptomatic COVID-19 patients with and without surgical masks was performed with sampling devices using sterile gelatin filters. Frequently touched environmental surfaces near 21 patients were swabbed before daily environmental disinfection. The correlation between the viral loads of patients' clinical samples and environmental samples was analyzed. RESULTS: All air samples were negative for SARS-CoV-2 RNA in the 6 patients singly isolated inside airborne infection isolation rooms (AIIRs) with 12 air changes per hour. Of 377 environmental samples near 21 patients, 19 (5.0%) were positive by reverse-transcription polymerase chain reaction (RT-PCR) assay, with a median viral load of 9.2 × 102 copies/mL (range, 1.1 × 102 to 9.4 × 104 copies/mL). The contamination rate was highest on patients' mobile phones (6 of 77, 7.8%), followed by bed rails (4 of 74, 5.4%) and toilet door handles (4 of 76, 5.3%). We detected a significant correlation between viral load ranges in clinical samples and positivity rate of environmental samples (P < .001). CONCLUSION: SARS-CoV-2 RNA was not detectable by air samplers, which suggests that the airborne route is not the predominant mode of transmission of SARS-CoV-2. Wearing a surgical mask, appropriate hand hygiene, and thorough environmental disinfection are sufficient infection control measures for COVID-19 patients isolated singly in AIIRs. However, this conclusion may not apply during aerosol-generating procedures or in cohort wards with large numbers of COVID-19 patients.


Subject(s)
Air Microbiology , Betacoronavirus/isolation & purification , Coronavirus Infections/transmission , Fomites/virology , Infection Control/methods , Patients' Rooms , Pneumonia, Viral/transmission , Adolescent , Adult , Aerosols , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/prevention & control , Female , Hospitalization , Humans , Male , Middle Aged , Pandemics/prevention & control , Pneumonia, Viral/diagnosis , Pneumonia, Viral/prevention & control , SARS-CoV-2 , Viral Load
16.
Infect Control Hosp Epidemiol ; 41(7): 820-825, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-2096308

ABSTRACT

OBJECTIVES: Patients with COVID-19 may present with respiratory syndromes indistinguishable from those caused by common viruses. Early isolation and containment is challenging. Although screening all patients with respiratory symptoms for COVID-19 has been recommended, the practicality of such an effort has yet to be assessed. METHODS: Over a 6-week period during a SARS-CoV-2 outbreak, our institution introduced a "respiratory surveillance ward" (RSW) to segregate all patients with respiratory symptoms in designated areas, where appropriate personal protective equipment (PPE) could be utilized until SARS-CoV-2 testing was done. Patients could be transferred when SARS-CoV-2 tests were negative on 2 consecutive occasions, 24 hours apart. RESULTS: Over the study period, 1,178 patients were admitted to the RSWs. The mean length-of-stay (LOS) was 1.89 days (SD, 1.23). Among confirmed cases of pneumonia admitted to the RSW, 5 of 310 patients (1.61%) tested positive for SARS-CoV-2. This finding was comparable to the pickup rate from our isolation ward. In total, 126 HCWs were potentially exposed to these cases; however, only 3 (2.38%) required quarantine because most used appropriate PPE. In addition, 13 inpatients overlapped with the index cases during their stay in the RSW; of these 13 exposed inpatients, 1 patient subsequently developed COVID-19 after exposure. No patient-HCW transmission was detected despite intensive surveillance. CONCLUSIONS: Our institution successfully utilized the strategy of an RSW over a 6-week period to contain a cluster of COVID-19 cases and to prevent patient-HCW transmission. However, this method was resource-intensive in terms of testing and bed capacity.


Subject(s)
Coronavirus Infections/transmission , Cross Infection/transmission , Infection Control/methods , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Occupational Diseases/prevention & control , Patient Isolation , Pneumonia, Viral/transmission , Population Surveillance/methods , Adult , Aged , Aged, 80 and over , Betacoronavirus , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/prevention & control , Cross Infection/diagnosis , Cross Infection/prevention & control , Early Diagnosis , Female , Humans , Length of Stay , Male , Middle Aged , Pandemics/prevention & control , Patients' Rooms/organization & administration , Personal Protective Equipment , Pneumonia/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/prevention & control , SARS-CoV-2 , Singapore , Symptom Assessment , Tertiary Care Centers
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