Matthew Scotch PhD MPH Associate Professor of Biomedical Informatics Assistant Director Biodesign Center for Environmental Health Engineering Key Concepts Epidemiology Surveillance Epidemiology ID: 1045074
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1. Surveillance of COVID-19Matthew Scotch, PhD, MPHAssociate Professor of Biomedical InformaticsAssistant Director, Biodesign Center for Environmental Health Engineering
2. Key ConceptsEpidemiologySurveillance
3. Epidemiology“the study of the distribution and determinants (causes, risk factors) of health-related states and events (not just diseases) in specified populations”https://www.cdc.gov/careerpaths/k12teacherroadmap/epidemiology.html
4. Public Health Surveillance“ongoing systematic collection, analysis, and interpretation of data, closely integrated with the timely dissemination of these data to those responsible for preventing and controlling disease and injury”Nsubuga P, White ME, Thacker SB, et al. Public Health Surveillance: A Tool for Targeting and Monitoring Interventions. In: Jamison DT, Breman JG, Measham AR, et al., editors. Disease Control Priorities in Developing Countries. 2nd edition. Washington (DC): The International Bank for Reconstruction and Development / The World Bank; 2006. Chapter 53. Available from: https://www.ncbi.nlm.nih.gov/books/NBK11770/ Co-published by Oxford University Press, New York.
5. Surveillance for COVID-19Traditional Passive Reportable Disease SurveillanceNew ApproachesDigital epidemiologyGenomic epidemiologyWastewater-based epidemiology
6. Digital EpidemiologyUse of digital data for epidemiologySocial mediaOnline news reportsSmartphone dataOnline blogs and other Web resourcesData often not generated for public health purposesSalathe, M., et al., Digital epidemiology. PLoS Comput Biol, 2012. 8(7): p. e1002616.
7. JHU Web-based Dashboardhttps://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6https://systems.jhu.edu/research/public-health/2019-ncov-map-faqs/
8. MethodologyText mining / NLP / Manual Annotation of News Reports“semi-automated living data stream strategy” pg. 1Multiple LanguagesCommunication with authoritative sources Geospatial mapping and graphing functionsDong, E., H. Du, and L. Gardner, An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis, 2020.
9. Genomic EpidemiologyUse of virus sequences to inform understanding on transmission and spreadPhylodynamics/phylogeneticsPopulation geneticsRequires Next Generation Sequencing (NGS) and reliable sequence metadata
10. https://nextstrain.org/ncov
11. https://nextstrain.org/ncov
12. What we have learned through GEOne introduction from animal reservoirNo repeated introductions from animal hosts like MERSWildtype virus: not engineered in a labMutations as we would expect for an RNA virus1. Zhang, Y.Z. and E.C. Holmes, A Genomic Perspective on the Origin and Emergence of SARS-CoV-2. Cell, 2020.2. Grubaugh, N.D., M.E. Petrone, and E.C. Holmes, We shouldn't worry when a virus mutates during disease outbreaks. Nat Microbiol, 2020. 5(4): p. 529-530.
13. SARS-CoV-2 Work atWastewater-based epidemiologyRolf Halden, Arvind Varsani, Matthew ScotchClinical surveillance from NP swabs of ILI Matthew Scotch, Brenda Hogue, Efrem LimTesting at ASU Health ClinicJosh LaBaer, Center for Personalized Diagnostics, and others
14. Surveillance through ASU Health ServicesNP swab specimens collected since Jan 24th to NowBuilds on NIH-funded flu surveillance study at ASU (R01LM013129, PIs: Scotch, Halden, Varsani) qRT-PCR assays for SARS-CoV-2 (N, E and RdRp genes)Current capacity: 48 samples in 4 hrs (from sample to result)ASU SARS-CoV-2 Surveillance
15. 5 ASU positives plus 1 ADHS positivePending next generation sequencing (NGS)
16.