scholarly journals Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic

2020 ◽  
Author(s):  
Sureshnee Pillay ◽  
Jennifer Giandhari ◽  
Houriiyah Tegally ◽  
Eduan Wilkinson ◽  
Benjamin Chimukangara ◽  
...  
Keyword(s):  
Real Time ◽  
Control Strategies ◽  
Outbreak Investigation ◽  
Infection Prevention And Control ◽  
Library Preparation ◽  
Large Hospital ◽  
Preparation Methods ◽  
Hospital Outbreak ◽  
Set Up ◽  
And Control

AbstractThe COVID-19 pandemic spread very fast around the world. A few days after the first detected case in South Africa, an infection started a large hospital outbreak in Durban, KwaZulu-Natal. Phylogenetic analysis of SARS-CoV-2 genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. In this manuscript, we outline the obstacles we encountered in order to genotype SARS-CoV-2 in real-time during an urgent outbreak investigation. In this process, we encountered problems with the length of the original genotyping protocol, reagent stockout and sample degradation and storage. However, we managed to set up three different library preparation methods for sequencing in Illumina. We also managed to decrease the hands on library preparation time from twelve to three hours, which allowed us to complete the outbreak investigation in just a few weeks. We also fine-tuned a simple bioinformatics workflow for the assembly of high-quality genomes in real-time. In order to allow other laboratories to learn from our experience, we released all of the library preparation and bioinformatics protocols publicly and distributed them to other laboratories of the South African Network for Genomics Surveillance (SANGS) consortium.

scholarly journals Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 949 ◽  
Author(s):  
Sureshnee Pillay ◽  
Jennifer Giandhari ◽  
Houriiyah Tegally ◽  
Eduan Wilkinson ◽  
Benjamin Chimukangara ◽  
...  
Keyword(s):  
South Africa ◽  
Real Time ◽  
Control Strategies ◽  
Outbreak Investigation ◽  
Infection Prevention And Control ◽  
Library Preparation ◽  
Large Hospital ◽  
Preparation Methods ◽  
Hospital Outbreak ◽  
Set Up

The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.

Effective infection prevention and control strategies in a large accredited psychiatric facility in Singapore

2020 ◽  
Author(s):  
Daniel Poremski ◽  
Sandra Henrietta Subner ◽  
Grace Lam Fong Kin ◽  
Raveen Dev Ram Dev ◽  
Mok Yee Ming ◽  
...  
Keyword(s):  
Mental Health ◽  
Prevention And Control ◽  
Infection Prevention ◽  
Control Strategies ◽  
Infection Prevention And Control ◽  
Psychiatric Facility ◽  
Essential Services ◽  
Community Transmission ◽  
And Control

The Institute of Mental Health in Singapore continues to attempt to prevent the introduction of COVID-19, despite community transmission. Essential services are maintained and quarantine measures are currently unnecessary. To help similar organizations, strategies are listed along three themes: sustaining essential services, preventing infection, and managing human and consumable resources.

scholarly journals Infection Prevention Considerations for a Multi-Mission Convention Center Field Hospital in Baltimore, Maryland during the COVID-19 Pandemic

2021 ◽  
pp. 1-21
Author(s):  
Jennifer A. Jones ◽  
Zishan K. Siddiqui ◽  
Charles Callahan ◽  
Surbhi Leekha ◽  
Sharon Smyth ◽  
...  
Keyword(s):  
Best Practices ◽  
Infection Prevention ◽  
Diagnostic Testing ◽  
The United States ◽  
Infection Prevention And Control ◽  
Field Hospital ◽  
First Case ◽  
Convention Center ◽  
Set Up ◽  
And Control

Abstract The state of Maryland identified its first case of COVID-19 on March 5, 2020. The Baltimore Convention Center (BCCFH) quickly became a selected location to set up a 250-bed inpatient Field Hospital and Alternate Care Site. In contrast to other field hospitals throughout the United States, the BCCFH remained open throughout the pandemic and took on additional COVID-19 missions, including community SARS-CoV-2 diagnostic testing, monoclonal antibody infusions for COVID-19 outpatients, and community COVID-19 vaccinations. At the time of publication, the BCCFH had cared for 1,478 COVID-19 inpatients, performed 108,155 COVID-19 tests, infused 2,166 COVID-19 patients, and administered 115,169 doses of COVID-19 vaccine. To prevent the spread of pathogens during operations, infection prevention and control guidelines were essential to ensure the safety of staff and patients. Through multi-agency collaboration, utilization of infection prevention best practices, and answering what we describe as “PPE-ESP”, an operational framework was established to reduce infection risks for those providing or receiving care at the BCCFH during the COVID-19 pandemic.

scholarly journals Real time surveillance of COVID-19 space and time clusters during the summer 2020 in Spain

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nicolás Rosillo ◽  
Javier Del-Águila-Mejía ◽  
Ayelén Rojas-Benedicto ◽  
María Guerrero-Vadillo ◽  
Marina Peñuelas ◽  
...  
Keyword(s):  
Real Time ◽  
Scan Statistic ◽  
Cluster Aggregation ◽  
Space And Time ◽  
Spatial Trends ◽  
Community Transmission ◽  
Low Incidence ◽  
Set Up ◽  
And Control ◽  
Time Scan

Abstract Background On June 21st de-escalation measures and state-of-alarm ended in Spain after the COVID-19 first wave. New surveillance and control strategy was set up to detect emerging outbreaks. Aim To detect and describe the evolution of COVID-19 clusters and cases during the 2020 summer in Spain. Methods A near-real time surveillance system to detect active clusters of COVID-19 was developed based on Kulldorf’s prospective space-time scan statistic (STSS) to detect daily emerging active clusters. Results Analyses were performed daily during the summer 2020 (June 21st – August 31st) in Spain, showing an increase of active clusters and municipalities affected. Spread happened in the study period from a few, low-cases, regional-located clusters in June to a nationwide distribution of bigger clusters encompassing a higher average number of municipalities and total cases by end-August. Conclusion STSS-based surveillance of COVID-19 can be of utility in a low-incidence scenario to help tackle emerging outbreaks that could potentially drive a widespread transmission. If that happens, spatial trends and disease distribution can be followed with this method. Finally, cluster aggregation in space and time, as observed in our results, could suggest the occurrence of community transmission.

scholarly journals Effective infection prevention and control strategies in a large, accredited, psychiatric facility in Singapore

2020 ◽  
Vol 41 (10) ◽  
pp. 1238-1240 ◽  
Author(s):  
Daniel Poremski ◽  
Sandra H. Subner ◽  
Grace F.K. Lam ◽  
Raveen Dev ◽  
Yee Ming Mok ◽  
...  
Keyword(s):  
Prevention And Control ◽  
Infection Prevention ◽  
Control Strategies ◽  
Infection Prevention And Control ◽  
Psychiatric Facility ◽  
And Control

scholarly journals When do big problems far away become smaller than the problems closer to home: Lessons for antimicrobial resistance from Father Ted

2019 ◽  
Author(s):  
Tjibbe Donker ◽  
Katie L. Hopkins ◽  
Susan Hopkins ◽  
Berit Muller-Pebody ◽  
Tim E.A. Peto ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Control Strategy ◽  
Prevention And Control ◽  
Infection Prevention ◽  
Control Strategies ◽  
Absolute Number ◽  
Infection Prevention And Control ◽  
Admission Screening ◽  
Imported Cases ◽  
And Control

AbstractInfection prevention and control strategies aimed at reducing the occurrence of Carbapenemase-Producing Enterobacteriaceae (CPE) and other antimicrobial-resistant organisms often include advice about screening patients coming from hospitals with a known resistance problem, to prevent introductions into new hospitals by shared patients. We argue that, despite being an efficient method of identifying cases, admission screening for introduction prevention is only effective if the absolute number of imported cases from other hospitals outnumbers the cases coming from the hospital’s own patient population, and therefore is only a feasible control strategy during the start of an epidemic. When determining whether import screening is still advisable, we therefore need to be continuously reminded of how Father Ted so eloquently summarised the principles of perspective: “These are small, but the ones out there are far away”.

Real-Time Simulation of an Experimental Rig With Pressurized SOFC

2011 ◽  
Author(s):  
Paolo Pezzini ◽  
Francesco Caratozzolo ◽  
Alberto Traverso
Keyword(s):  
Experimental Data ◽  
Real Time ◽  
Control Strategies ◽  
Simulation Models ◽  
Electrical Current ◽  
Cell System ◽  
Time Model ◽  
Transient Behaviour ◽  
Set Up ◽  
Time Required

The availability of reliable simulation models can reduce the time required for commissioning test rigs as well as preventing components from suffering serious damage during testing. The aim of this study is to set up and validate, against experimental data, a real-time model referring to the Rolls-Royce Fuel Cell System Limited (RRFCS) hybrid system concept, based on SOFCs. The dynamic model of the SOFC “block” has been developed, run in real-time, and successfully validated against experiments. Initially, the dynamic evolution of the model is considered under constant inputs at steady-state and is compared against experimental data; secondly, transient behaviour is also considered. Step variations of the main air flow, main fuel flow, syngas flow and electrical current were performed. The model can now be employed to carry out the following: performance analysis, design verification, development of control strategies, on-line analysis and integration with Human Machine Interface.

Sign in / Sign up

Export Citation Format

Share Document