The burden and dynamics of hospital-acquired SARS-CoV-2 in England

Abstract Hospital-based transmission played a dominant role in MERS-CoV and SARS-CoV epidemics but large-scale studies of its role in the SARS-CoV-2 pandemic are lacking. Such transmission risks spreading the virus to the most vulnerable individuals and can have wider-scale impacts through hospital-community interactions. Using data from acute hospitals in England we quantify within-hospital transmission, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the wider dynamical consequences. We show that hospital transmission is likely to have been a major contributor to the burden of COVID-19 in England. We estimate that between June 2020 and March 2021 between 95,000 and 167,000 patients acquired SARS-CoV-2 in hospitals with nosocomially-infected patients likely to have been the main sources of transmission to other patients. Increased transmission to patients was associated with hospitals having fewer single rooms and lower heated volume per bed. Moreover, we show that reducing hospital transmission could substantially enhance the efficiency of punctuated lockdown measures in suppressing community transmission. These findings reveal the previously unrecognised scale of hospital transmission, have direct implications for targeting of hospital control measures, and highlight the need to design hospitals better-equipped to limit the transmission of future high consequence pathogens.

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Contrasting SARS-CoV-2 epidemics in Singapore: Cohort studies in migrant workers and the general population

10.21203/rs.3.rs-441527/v1 ◽

2021 ◽

Author(s):

Hannah E Clapham ◽

Wan Ni Chia ◽

Linda Wei Lin Tan ◽

Vishakha Kumar ◽

Jane M Lim ◽

...

Keyword(s):

General Population ◽

Cohort Studies ◽

Migrant Workers ◽

Large Scale ◽

Migrant Worker ◽

Community Dwelling ◽

Control Measures ◽

Preparedness Planning ◽

Community Transmission

Abstract From January 2020, Singapore implemented comprehensive measures to suppress SARS-CoV-2. Community transmission has been limited, although explosive outbreaks have occurred in migrant worker dormitories. We conducted longitudinal SARS-CoV-2 serology studies among 478 residents of a SARS-CoV-2 affected migrant worker dormitory between May and July 2020, and 937 community-dwelling adult Singapore residents with sera collected before September 2019 and in November/December 2020. By end 2020, <2 per 1000 (0.16%, 95% CrI: 0.008% - 0.72%) adult residents in the community were infected with SARS-CoV-2, approximately 4 times higher than the national notified case incidence. In contrast, in the migrant worker cohort, nearly two-thirds 63.8% (95% CrI: 57.9% - 70.3%) had been infected by July 2020; no symptoms were reported in >90% of these infections. SARS-CoV-2 suppression is feasible with rapid implementation of comprehensive control measures. However, the risk of large-scale epidemics in densely-populated environments requires specific consideration in preparedness planning.

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Spatial pattern of invading Dendroctonus micans (Coleoptera: Scolytidae) populations in the United Kingdom

Canadian Journal of Forest Research ◽

10.1139/x02-208 ◽

2003 ◽

Vol 33 (4) ◽

pp. 712-725 ◽

Cited By ~ 21

Author(s):

M Gilbert ◽

N Fielding ◽

H F Evans ◽

J -C Grégoire

Keyword(s):

Spatial Pattern ◽

Large Scale ◽

Spatial Regression ◽

Regional Scale ◽

Management Control ◽

Control Measures ◽

Spatial Gradient ◽

Dendroctonus Micans ◽

Ecological Processes ◽

Using Data

The spatial pattern of Dendroctonus micans (Kug.) attacks on individual spruce stands was analysed at the regional scale in Britain using data collected between 1982 and 1984 by the British Forestry Commission. These survey data reflect at least 10 years of D. micans spread, in the absence of natural enemies and of pest management control measures. A large-scale spatial gradient in the attack density at the stand level was identified and modelled. The large-scale spatial trend model explained 31.3% of the variability, and divided the study area in three separate areas: a zone where the insect was well established and where attack density presented low variations, a transition zone where attack density sharply decreased, and a zone not yet colonized. Attack density was related to site and stand factors, and to landscape neighbourhood in a linear spatial regression model. The factors correlated to attack density and the spatial autocorrelation structure of remaining variability were found to vary according to the zones, reflecting the predominance of different ecological processes occurring in colonized and uncolonized areas. The shape and orientation of the large-scale spatial model was shown to be mostly influenced by the spatial distribution of early attacks.

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Modelling diverse sources of Clostridium difficile in the community: importance of animals, infants and asymptomatic carriers

Epidemiology and Infection ◽

10.1017/s0950268819000384 ◽

2019 ◽

Vol 147 ◽

Cited By ~ 3

Author(s):

A. McLure ◽

A. C. A. Clements ◽

M. Kirk ◽

K. Glass

Keyword(s):

Clostridium Difficile ◽

Human Population ◽

Reproduction Number ◽

Relative Importance ◽

Community Transmission ◽

Hospital Acquired ◽

Animal Reservoirs ◽

Community Onset ◽

Hospital Transmission

AbstractClostridium difficile infections (CDIs) affect patients in hospitals and in the community, but the relative importance of transmission in each setting is unknown. We developed a mathematical model of C. difficile transmission in a hospital and surrounding community that included infants, adults and transmission from animal reservoirs. We assessed the role of these transmission routes in maintaining disease and evaluated the recommended classification system for hospital- and community-acquired CDIs. The reproduction number in the hospital was <1 (range: 0.16–0.46) for all scenarios. Outside the hospital, the reproduction number was >1 for nearly all scenarios without transmission from animal reservoirs (range: 1.0–1.34). However, the reproduction number for the human population was <1 if a minority (>3.5–26.0%) of human exposures originated from animal reservoirs. Symptomatic adults accounted for <10% transmission in the community. Under conservative assumptions, infants accounted for 17% of community transmission. An estimated 33–40% of community-acquired cases were reported but 28–39% of these reported cases were misclassified as hospital-acquired by recommended definitions. Transmission could be plausibly sustained by asymptomatically colonised adults and infants in the community or exposure to animal reservoirs, but not hospital transmission alone. Under-reporting of community-onset cases and systematic misclassification underplays the role of community transmission.

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Assessment of quality of life in patients with the effects of transient ischemic stroke

East European Journal of Neurology ◽

10.33444/2411-5797.2016.6(12).37-39 ◽

2016 ◽

pp. 37-39

Author(s):

A. Babirad

Keyword(s):

Quality Of Life ◽

Ischemic Stroke ◽

Large Scale ◽

Cerebrovascular Diseases ◽

Control Measures ◽

Sociological Research ◽

Cerebrovascular Events ◽

Sf 36 ◽

Angioplasty And Stenting

Cerebrovascular diseases are a problem of the world today, and according to the forecast, the problem of the near future arises. The main risk factors for the development of ischemic disorders of the cerebral circulation include oblique and aging, arterial hypertension, smoking, diabetes mellitus and heart disease. An effective strategy for the prevention of cerebrovascular events is based on the implementation of large-scale risk control measures, including the use of antiagregant and anticoagulant therapy, invasive interventions such as atheromectomy, angioplasty and stenting. In this connection, the efforts of neurologists, cardiologists, angiosurgery, endocrinologists and other specialists are the basis for achieving an acceptable clinical outcome. A review of the SF-36 method for assessing the quality of life in patients with the effects of transient ischemic stroke is presented. The assessment of quality of life is recognized in world medical practice and research, an indicator that is also used to assess the quality of the health system and in general sociological research.

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Student Perceptions of Community: A Different Perspective

NASPA Journal ◽

10.2202/0027-6014.1064 ◽

1998 ◽

Vol 35 (4) ◽

Author(s):

Jackie Clark ◽

Joan Hirt

Keyword(s):

Student Perceptions ◽

Large Scale ◽

Research University ◽

Small Scale ◽

Social Environments ◽

Common Assumption ◽

Small Communities ◽

Public Research University ◽

The Common ◽

Using Data

The creation of small communities has been proposed as a way of enhancing the educational experience of students at large institutions. Using data from a survey of students living in large and small residences at a public research university, this study does not support the common assumption that small-scale social environments are more conducive to positive community life than large-scale social environments.

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Modeling Fused Filament Fabrication using Artificial Neural Networks

Production Engineering ◽

10.1007/s11740-021-01020-y ◽

2021 ◽

Author(s):

Paul Oehlmann ◽

Paul Osswald ◽

Juan Camilo Blanco ◽

Martin Friedrich ◽

Dominik Rietzel ◽

...

Keyword(s):

Real Time ◽

Large Scale ◽

Cost Effective ◽

Print Quality ◽

Ann Model ◽

Production Environment ◽

Fused Filament Fabrication ◽

Artificial Neural ◽

Using Data ◽

Artificial Neural Network Ann

AbstractWith industries pushing towards digitalized production, adaption to expectations and increasing requirements for modern applications, has brought additive manufacturing (AM) to the forefront of Industry 4.0. In fact, AM is a main accelerator for digital production with its possibilities in structural design, such as topology optimization, production flexibility, customization, product development, to name a few. Fused Filament Fabrication (FFF) is a widespread and practical tool for rapid prototyping that also demonstrates the importance of AM technologies through its accessibility to the general public by creating cost effective desktop solutions. An increasing integration of systems in an intelligent production environment also enables the generation of large-scale data to be used for process monitoring and process control. Deep learning as a form of artificial intelligence (AI) and more specifically, a method of machine learning (ML) is ideal for handling big data. This study uses a trained artificial neural network (ANN) model as a digital shadow to predict the force within the nozzle of an FFF printer using filament speed and nozzle temperatures as input data. After the ANN model was tested using data from a theoretical model it was implemented to predict the behavior using real-time printer data. For this purpose, an FFF printer was equipped with sensors that collect real time printer data during the printing process. The ANN model reflected the kinematics of melting and flow predicted by models currently available for various speeds of printing. The model allows for a deeper understanding of the influencing process parameters which ultimately results in the determination of the optimum combination of process speed and print quality.

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Nebula: ultra-efficient mapping-free structural variant genotyper

Nucleic Acids Research ◽

10.1093/nar/gkab025 ◽

2021 ◽

Author(s):

Parsoa Khorsand ◽

Fereydoun Hormozdiari

Keyword(s):

Large Scale ◽

Structural Variants ◽

Sequencing Technologies ◽

Generic Framework ◽

Common Genetic Variants ◽

Order Of Magnitude ◽

Complex Events ◽

Comparable Accuracy ◽

Using Data ◽

Computational Resources

Abstract Large scale catalogs of common genetic variants (including indels and structural variants) are being created using data from second and third generation whole-genome sequencing technologies. However, the genotyping of these variants in newly sequenced samples is a nontrivial task that requires extensive computational resources. Furthermore, current approaches are mostly limited to only specific types of variants and are generally prone to various errors and ambiguities when genotyping complex events. We are proposing an ultra-efficient approach for genotyping any type of structural variation that is not limited by the shortcomings and complexities of current mapping-based approaches. Our method Nebula utilizes the changes in the count of k-mers to predict the genotype of structural variants. We have shown that not only Nebula is an order of magnitude faster than mapping based approaches for genotyping structural variants, but also has comparable accuracy to state-of-the-art approaches. Furthermore, Nebula is a generic framework not limited to any specific type of event. Nebula is publicly available at https://github.com/Parsoa/Nebula.

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Universal Masking to Control Healthcare-Associated Transmission of SARS-CoV-2

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2021.127 ◽

2021 ◽

pp. 1-24

Author(s):

Eliza R. Thompson ◽

Faith S. Williams ◽

Pat A. Giacin ◽

Shay Drummond ◽

Eric Brown ◽

...

Keyword(s):

Large Scale ◽

Infection Prevention ◽

Index Patient ◽

Field Investigation ◽

Point Prevalence ◽

Control Measures ◽

Prevention Measures ◽

Infection Control Measures ◽

Va Health Care System ◽

Healthcare Associated

Abstract Objective: To assess extent of a healthcare-associated outbreak of SARS-CoV-2 and evaluate effectiveness of infection control measures, including universal masking Design: Outbreak investigation including 4 large-scale point-prevalence surveys Setting: Integrated VA Health Care System with 2 facilities and 330 beds Participants: Index patient and 250 exposed patients and staff Methods: We identified exposed patients and staff and classified them as probable and confirmed cases based on symptoms and testing. We performed a field investigation and assessment of patient and staff interactions to develop probable transmission routes. Infection prevention interventions implemented included droplet and contact precautions, employee quarantine, and universal masking with medical and cloth facemasks. Four point-prevalence surveys of patient and staff subsets were conducted using real-time reverse-transcriptase polymerase chain reaction for SARS-CoV-2. Results: Among 250 potentially exposed patients and staff, 14 confirmed cases of Covid-19 were identified. Patient roommates and staff with prolonged patient contact were most likely to be infected. The last potential date of transmission from staff to patient was day 22, the day universal masking was implemented. Subsequent point-prevalence surveys in 126 patients and 234 staff identified 0 patient cases and 5 staff cases of Covid-19, without evidence of healthcare-associated transmission. Conclusions: Universal masking with medical facemasks was effective in preventing further spread of SARS-CoV-2 in our facility in conjunction with other traditional infection prevention measures.

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COVID-19 Community Transmission among Healthcare Workers at a Tertiary Care Cardiac Center

Medical Sciences ◽

10.3390/medsci9030049 ◽

2021 ◽

Vol 9 (3) ◽

pp. 49

Author(s):

Mazin Barry ◽

Asirvatham Alwin Robert ◽

Mohamad-Hani Temsah ◽

Syed Abdul Bari ◽

Muhammad Yasin Akhtar ◽

...

Keyword(s):

Healthcare Workers ◽

Tertiary Care ◽

Transmission Risk ◽

Mitigation Measures ◽

Age Group ◽

Community Transmission ◽

Mode Of Transmission ◽

Healthcare Associated ◽

Female Nurses ◽

Cardiac Center

Aim: To determine the frequency, mode of transmission, and outcome of Coronavirus Disease 2019 (COVID-19) among healthcare workers (HCWs) in a tertiary care cardiac center in the Kingdom of Saudi Arabia (KSA). Methods: This is a retrospective study of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infected HCWs and was conducted from 2 March to 31 December 2020. Data related to the presence of COVID-19 symptoms, mode of transmission, hospitalization, and mortality were collected from the patients’ medical records. Results: Of the 4462 patients tested for COVID-19 by real-time reverse transcriptase polymerase chain reaction (RT-PCR), 203 (4.5%) HCWs were positive; of these, 125 (61.6%) were males, and the most common age group was <40 years. The most commonly encountered health professionals were nurses (74, 36.4%), followed by therapists/technicians (48, 23.6%), housekeepers (25, 12.3%), and physicians (21, 10.4%). The majority (184, 90.6%) of the HCWs contracted COVID-19 in the community, and only 19 (9.4%) were healthcare-associated infections. Of the infected HCWs, 169 (83.3%) had mild symptoms and were managed in home isolation. The most common symptoms were fever (128, 63.1%), body ache (124, 61.8%), headache (113, 55.7%), dry cough (123, 60.6%), sore throat (97, 47.8%), body weakness (97, 47.8%), and fatigue (94, 46.3%). Comparing males and females, there was a significantly higher number of female nurses; in contrast, there was a higher number of male physicians, housekeepers, therapists/technicians, and other specialty HCWs. A significantly lower number of nurses, therapists/technicians were infected in the ≥40 years age group compared to <40 years. Furthermore, a significantly higher difference was observed among non-Saudi nurses compared to Saudi nurses. No mortality was documented among the included HCWs. Conclusions: In the largest tertiary cardiac center in KSA, most HCWs who contracted COVID-19 developed mild symptoms; nurses and those aged <40 years were most commonly infected, and most infections were acquired in the community. HCWs’ adherence to mitigation measures outside of the workplace is vital to curb the current pandemic and decrease nosocomial transmission risk.

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Heterogeneity and effectiveness analysis of COVID-19 prevention and control in major cities in China through time-varying reproduction number estimation

Scientific Reports ◽

10.1038/s41598-020-79063-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Qing Cheng ◽

Zeyi Liu ◽

Guangquan Cheng ◽

Jincai Huang

Keyword(s):

Prevention And Control ◽

Large Scale ◽

Reproduction Number ◽

Correlation Method ◽

Control Measures ◽

Time Varying ◽

Short Period ◽

Significant Difference ◽

Prevention And Control Measures ◽

And Control

AbstractBeginning on December 31, 2019, the large-scale novel coronavirus disease 2019 (COVID-19) emerged in China. Tracking and analysing the heterogeneity and effectiveness of cities’ prevention and control of the COVID-19 epidemic is essential to design and adjust epidemic prevention and control measures. The number of newly confirmed cases in 25 of China’s most-affected cities for the COVID-19 epidemic from January 11 to February 10 was collected. The heterogeneity and effectiveness of these 25 cities’ prevention and control measures for COVID-19 were analysed by using an estimated time-varying reproduction number method and a serial correlation method. The results showed that the effective reproduction number (R) in 25 cities showed a downward trend overall, but there was a significant difference in the R change trends among cities, indicating that there was heterogeneity in the spread and control of COVID-19 in cities. Moreover, the COVID-19 control in 21 of 25 cities was effective, and the risk of infection decreased because their R had dropped below 1 by February 10, 2020. In contrast, the cities of Wuhan, Tianmen, Ezhou and Enshi still had difficulty effectively controlling the COVID-19 epidemic in a short period of time because their R was greater than 1.

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