ABSTRACT
Population scale sweeps of viral pathogens, such as SARS-CoV-2, that incorporate large numbers of asymptomatic or mild symptom patients present unique challenges for public health agencies trying to manage both travel and local spread. Physical distancing is the current major strategy to suppress spread of the disease, but with enormous socio-economic costs. However, modelling and studies in isolated jurisdictions suggest that active population surveillance through systematic molecular diagnostics, combined with contact tracing and focused quarantining can significantly suppress disease spread1-3 and has significantly impacted disease transmission rates, the number of infected people, and prevented saturation of the healthcare system4-7. However, reliable systems allowing for parallel testing of 10-100,000s of patients in larger urban environments have not yet been employed. Here we describe "COVID-19 screening using Systematic Parallel Analysis of RNA coupled to Sequencing" (C19-SPAR-Seq), a scalable, multiplexed, readily automated next generation sequencing (NGS) platform8 that is capable of analyzing tens of thousands of COVID-19 patient samples in a single instrument run. To address the strict requirements in clinical diagnostics for control of assay parameters and output, we employed a control-based Precision-Recall and predictive Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of over 600 patients performed with a specificity of 100% and sensitivity of 91% on samples with low viral loads and a sensitivity of > 95% on high viral loads associated with disease onset and peak transmissibility. Our study thus establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.
ABSTRACT
BACKGROUND: Pharmacy curriculum change was made from a 4-year program to a 2+4 year program in year 2009 in Korea. The change has resulted in more educational exposures on patient-centered practice environments for about 1,400 hours in the last year of the professional pharmacy program. When the Middle East Respiratory Syndrome (MERS) outbreak hit Seoul and suburban areas and propagated to other provinces in Korea, emergency response to avoid student infection in the pharmacy practice sites became an urgent issue. While other health professional programs such as medicine and nursing had activated emergency preparedness manuals, timely and clear guidelines were not disseminated to all pharmacy programs and protective measures largely relied on individual pharmacy program. METHODS: A survey was developed by the Committee on Pharmacy Practice Experience Programs in the Korean College of Clinical Pharmacy to document the status of pharmacy programs during the Korea MERS outbreak in 2015. The 10-question survey was distributed to the pharmacy practice experience coordinators to 34 out of 35 pharmacy schools in Korea by emails. RESULTS: Our findings showed that 82.4% of the program coordinators (28/34) responded to the survey, 96.4% of the programs did not have emergency preparedness manuals, administrative meetings were held in 89.3% of the pharmacy programs, the rotation schedules were modified or withheld in 53.6% of schools, and the changes were mostly observed from the programs classified as MERS outbreak regions. CONCLUSION: Further needs in establishing the emergency preparedness manual should be explored for pharmacy education stakeholders.