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1.
PLoS Comput Biol ; 17(2): e1008618, 2021 02.
Article in English | MEDLINE | ID: covidwho-2109274

ABSTRACT

For practical reasons, many forecasts of case, hospitalization, and death counts in the context of the current Coronavirus Disease 2019 (COVID-19) pandemic are issued in the form of central predictive intervals at various levels. This is also the case for the forecasts collected in the COVID-19 Forecast Hub (https://covid19forecasthub.org/). Forecast evaluation metrics like the logarithmic score, which has been applied in several infectious disease forecasting challenges, are then not available as they require full predictive distributions. This article provides an overview of how established methods for the evaluation of quantile and interval forecasts can be applied to epidemic forecasts in this format. Specifically, we discuss the computation and interpretation of the weighted interval score, which is a proper score that approximates the continuous ranked probability score. It can be interpreted as a generalization of the absolute error to probabilistic forecasts and allows for a decomposition into a measure of sharpness and penalties for over- and underprediction.


Subject(s)
COVID-19/epidemiology , Communicable Diseases/epidemiology , Pandemics , COVID-19/virology , Forecasting , Humans , Probability , SARS-CoV-2/isolation & purification
2.
Nature ; 611(7936): 570-577, 2022 11.
Article in English | MEDLINE | ID: covidwho-2106425

ABSTRACT

Expanding our global testing capacity is critical to preventing and containing pandemics1-9. Accordingly, accessible and adaptable automated platforms that in decentralized settings perform nucleic acid amplification tests resource-efficiently are required10-14. Pooled testing can be extremely efficient if the pooling strategy is based on local viral prevalence15-20; however, it requires automation, small sample volume handling and feedback not available in current bulky, capital-intensive liquid handling technologies21-29. Here we use a swarm of millimetre-sized magnets as mobile robotic agents ('ferrobots') for precise and robust handling of magnetized sample droplets and high-fidelity delivery of flexible workflows based on nucleic acid amplification tests to overcome these limitations. Within a palm-sized printed circuit board-based programmable platform, we demonstrated the myriad of laboratory-equivalent operations involved in pooled testing. These operations were guided by an introduced square matrix pooled testing algorithm to identify the samples from infected patients, while maximizing the testing efficiency. We applied this automated technology for the loop-mediated isothermal amplification and detection of the SARS-CoV-2 virus in clinical samples, in which the test results completely matched those obtained off-chip. This technology is easily manufacturable and distributable, and its adoption for viral testing could lead to a 10-300-fold reduction in reagent costs (depending on the viral prevalence) and three orders of magnitude reduction in instrumentation cost. Therefore, it is a promising solution to expand our testing capacity for pandemic preparedness and to reimagine the automated clinical laboratory of the future.


Subject(s)
Automation , COVID-19 Testing , Magnets , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , Robotics , SARS-CoV-2 , Humans , COVID-19/diagnosis , COVID-19/virology , COVID-19 Testing/methods , Molecular Diagnostic Techniques/economics , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/economics , Nucleic Acid Amplification Techniques/methods , Pandemics/prevention & control , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Algorithms , Automation/economics , Automation/methods , Robotics/methods , Indicators and Reagents/economics
4.
Infect Control Hosp Epidemiol ; 42(2): 228-229, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-2096442

ABSTRACT

Coronavirus disease 2019 (COVID-19) has migrated to regions that were initially spared, and it is likely that different populations are currently at risk for illness. Herein, we present our observations of the change in characteristics and resource use of COVID-19 patients over time in a national system of community hospitals to help inform those managing surge planning, operational management, and future policy decisions.


Subject(s)
COVID-19/epidemiology , COVID-19/therapy , Hospitalization/statistics & numerical data , Adult , Age Factors , Aged , Aged, 80 and over , COVID-19/ethnology , COVID-19/mortality , Female , Hospitals, Community , Humans , Male , Middle Aged , SARS-CoV-2/isolation & purification , Virginia/epidemiology , Young Adult
5.
Infect Control Hosp Epidemiol ; 42(1): 75-83, 2021 01.
Article in English | MEDLINE | ID: covidwho-2096434

ABSTRACT

BACKGROUND: Shortages of personal protective equipment during the coronavirus disease 2019 (COVID-19) pandemic have led to the extended use or reuse of single-use respirators and surgical masks by frontline healthcare workers. The evidence base underpinning such practices warrants examination. OBJECTIVES: To synthesize current guidance and systematic review evidence on extended use, reuse, or reprocessing of single-use surgical masks or filtering face-piece respirators. DATA SOURCES: We used the World Health Organization, the European Centre for Disease Prevention and Control, the US Centers for Disease Control and Prevention, and Public Health England websites to identify guidance. We used Medline, PubMed, Epistemonikos, Cochrane Database, and preprint servers for systematic reviews. METHODS: Two reviewers conducted screening and data extraction. The quality of included systematic reviews was appraised using AMSTAR-2. Findings were narratively synthesized. RESULTS: In total, 6 guidance documents were identified. Levels of detail and consistency across documents varied. They included 4 high-quality systematic reviews: 3 focused on reprocessing (decontamination) of N95 respirators and 1 focused on reprocessing of surgical masks. Vaporized hydrogen peroxide and ultraviolet germicidal irradiation were highlighted as the most promising reprocessing methods, but evidence on the relative efficacy and safety of different methods was limited. We found no well-established methods for reprocessing respirators at scale. CONCLUSIONS: Evidence on the impact of extended use and reuse of surgical masks and respirators is limited, and gaps and inconsistencies exist in current guidance. Where extended use or reuse is being practiced, healthcare organizations should ensure that policies and systems are in place to ensure these practices are carried out safely and in line with available guidance.


Subject(s)
COVID-19 , Equipment Reuse/standards , Infection Control/instrumentation , Masks/virology , N95 Respirators/virology , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/prevention & control , Humans , Infection Control/methods , Practice Guidelines as Topic , Risk Management/methods , Risk Management/standards
6.
Infect Control Hosp Epidemiol ; 42(1): 89-92, 2021 01.
Article in English | MEDLINE | ID: covidwho-2096391
16.
Sci Rep ; 12(1): 17221, 2022 Oct 14.
Article in English | MEDLINE | ID: covidwho-2077104

ABSTRACT

For SARS-CoV-2, R0 calculations in the range of 2-3 dominate the literature, but much higher estimates have also been published. Because capacity for RT-PCR testing increased greatly in the early phase of the Covid-19 pandemic, R0 determinations based on these incidence values are subject to strong bias. We propose to use Covid-19-induced excess mortality to determine R0 regardless of RT-PCR testing capacity. We used data from the Robert Koch Institute (RKI) on the incidence of Covid cases, Covid-related deaths, number of RT-PCR tests performed, and excess mortality calculated from data from the Federal Statistical Office in Germany. We determined R0 using exponential growth estimates with a serial interval of 4.7 days. We used only datasets that were not yet under the influence of policy measures (e.g., lockdowns or school closures). The uncorrected R0 value for the spread of SARS-CoV-2 based on RT-PCR incidence data was 2.56 (95% CI 2.52-2.60) for Covid-19 cases and 2.03 (95% CI 1.96-2.10) for Covid-19-related deaths. However, because the number of RT-PCR tests increased by a growth factor of 1.381 during the same period, these R0 values must be corrected accordingly (R0corrected = R0uncorrected/1.381), yielding 1.86 for Covid-19 cases and 1.47 for Covid-19 deaths. The R0 value based on excess deaths was calculated to be 1.34 (95% CI 1.32-1.37). A sine-function-based adjustment for seasonal effects of 40% corresponds to a maximum value of R0January = 1.68 and a minimum value of R0July = 1.01. Our calculations show an R0 that is much lower than previously thought. This relatively low range of R0 fits very well with the observed seasonal pattern of infection across Europe in 2020 and 2021, including the emergence of more contagious escape variants such as delta or omicron. In general, our study shows that excess mortality can be used as a reliable surrogate to determine the R0 in pandemic situations.


Subject(s)
Basic Reproduction Number , COVID-19 , COVID-19/epidemiology , COVID-19/mortality , COVID-19 Nucleic Acid Testing , Germany/epidemiology , Humans , Pandemics , Reproducibility of Results , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
17.
Cir Cir ; 90(4): 497-502, 2022.
Article in English | MEDLINE | ID: covidwho-2067556

ABSTRACT

BACKGROUND: The onset of the SARS-Cov-2 pandemic brought with it important changes in the hospital care for all diseases. According to the international literature, since the beginning of the pandemic there has been an impact in the incidence, etiology, and severity of head trauma, all these changes as a direct consequence of lockdown. OBJECTIVE: In this article we analyzed the characteristics of craniofacial trauma in patients admitted to a private hospital in Mexico City during the SARS-CoV-2 pandemic. METHOD: Medical records from patients admitted in Medica Sur between March 2020 and June 2021. In this study, incidence, etiology, severity of the injuries and the SARS-CoV-2 PCR result performed upon admission were analyzed. RESULTS: Although there is no study in Mexico like ours, the results were similar to those reported by other hospital centers worldwide, presenting a greater number of cases classified as mild craniofacial trauma, in addition to finding that the main age group affected were older adults. CONCLUSIONS: The reported information in our study provides a general view of craniofacial trauma characteristics during SARS-CoV-2 pandemic.


INTRODUCCIÓN: El inicio de la pandemia provocada por SARS-CoV-2 trajo consigo importantes cambios en los cuidados hospitalarios para todas las enfermedades. De acuerdo con la literatura internacional, desde el comienzo, y a consecuencia del aislamiento, ha existido un impacto en la incidencia, la etiología y la gravedad del trauma craneomaxilofacial. OBJETIVO: Estudiar las características del trauma craneofacial en los pacientes ingresados a un hospital privado en la Ciudad de México durante la pandemia por SARS-CoV-2. MÉTODO: Se revisaron los expedientes clínicos de los pacientes ingresados a Médica Sur, entre marzo de 2020 y junio de 2021. Se analizaron la incidencia, la etiología, la gravedad de las lesiones y el resultado de la prueba de reacción en cadena de la polimerasa para SARS-CoV-2 que se realizó durante la atención hospitalaria. RESULTADOS: En México no existe un estudio semejante al nuestro, pero los resultados fueron similares a los reportados por otros centros hospitalarios en el mundo, presentando un mayor número de casos clasificados como traumatismo craneofacial leve, además de encontrar que el principal grupo de edad afectado fueron los adultos mayores. CONCLUSIONES: La información reportada en nuestro estudio brinda un panorama general sobre las características del trauma craneofacial durante la pandemia por SARS-CoV-2.


Subject(s)
COVID-19 , Craniocerebral Trauma , Facial Injuries , Hospitals, Private , Pandemics , Aged , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , Cities/epidemiology , Communicable Disease Control , Craniocerebral Trauma/epidemiology , Craniocerebral Trauma/etiology , Craniocerebral Trauma/therapy , Facial Injuries/epidemiology , Facial Injuries/etiology , Facial Injuries/therapy , Humans , Injury Severity Score , Mexico/epidemiology , SARS-CoV-2/isolation & purification
18.
PLoS One ; 17(2): e0262515, 2022.
Article in English | MEDLINE | ID: covidwho-1688746

ABSTRACT

BACKGROUND: Following the full re-opening of schools in England and emergence of the SARS-CoV-2 Alpha variant, we investigated the risk of SARS-CoV-2 infection in students and staff who were contacts of a confirmed case in a school bubble (school groupings with limited interactions), along with their household members. METHODS: Primary and secondary school bubbles were recruited into sKIDsBUBBLE after being sent home to self-isolate following a confirmed case of COVID-19 in the bubble. Bubble participants and their household members were sent home-testing kits comprising nasal swabs for RT-PCR testing and whole genome sequencing, and oral fluid swabs for SARS-CoV-2 antibodies. RESULTS: During November-December 2020, 14 bubbles were recruited from 7 schools, including 269 bubble contacts (248 students, 21 staff) and 823 household contacts (524 adults, 299 children). The secondary attack rate was 10.0% (6/60) in primary and 3.9% (4/102) in secondary school students, compared to 6.3% (1/16) and 0% (0/1) among staff, respectively. The incidence rate for household contacts of primary school students was 6.6% (12/183) and 3.7% (1/27) for household contacts of primary school staff. In secondary schools, this was 3.5% (11/317) and 0% (0/1), respectively. Household contacts were more likely to test positive if their bubble contact tested positive although there were new infections among household contacts of uninfected bubble contacts. INTERPRETATION: Compared to other institutional settings, the overall risk of secondary infection in school bubbles and their household contacts was low. Our findings are important for developing evidence-based infection prevention guidelines for educational settings.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Adolescent , Adult , Antibodies, Viral/analysis , COVID-19/virology , Child , Contact Tracing , England/epidemiology , Female , Humans , Incidence , Male , Nasopharynx/virology , Prospective Studies , RNA, Viral/analysis , RNA, Viral/metabolism , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Schools/statistics & numerical data , Students/statistics & numerical data
19.
Pharmacol Rep ; 72(6): 1446-1478, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-2060162

ABSTRACT

The viral infection due to the new coronavirus or coronavirus disease 2019 (COVID-19), which was reported for the first time in December 2019, was named by the World Health Organization (WHO) as Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV2), because of the very similar genome and also its related symptoms to SARS-CoV1. The ongoing COVID-19 pandemic with significant mortality, morbidity, and socioeconomic impact is considered by the WHO as a global public health emergency. Since there is no specific treatment available for SARS-CoV2 infection, and or COVID-19, several clinical and sub-clinical studies are currently undertaken to find a gold-standard therapeutic regimen with high efficacy and low side effect. Based on the published scientific evidence published to date, we summarized herein the effects of different potential therapies and up-to-date clinical trials. The review is intended to help readers aware of potentially effective COVID-19 treatment and provide useful references for future studies.


Subject(s)
COVID-19/drug therapy , SARS-CoV-2/isolation & purification , Animals , COVID-19/virology , Clinical Trials as Topic , Humans
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