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| ==3. Workflow and information management for COVID-19 (and other pandemics)== | | ==Sandbox begins below== |
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| ===3.1 Laboratory informatics and workflow management===
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| ===3.2 Laboratory informatics and reporting requirements===
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| Epidemiology can broadly be split into two categories: descriptive epidemiology and analytical epidemiology. Descriptive epidemiology involves studies and other activites that deal with geographical comparisons and temporal trend descriptions of disease. As such, the collection and use of quality incidence data is vital to developing hypotheses.<ref name="NaitoUtil14">{{cite journal |title=Utilization and application of public health data in descriptive epidemiology |journal=Journal of Epidemiology |author=Naito, M. |volume=24 |issue=6 |pages=435–6 |year=2014 |doi=10.2188/jea.je20140182 |pmid=25327184 |pmc=PMC4213216}}</ref> Analytical epidemiology allows for the testing of those hypotheses using both experimental and obsevational studies, as well as control groups. Similarly, the collection and use of quality experimental and observational data is vital for providing or disproving hypotheses.<ref name="CDCPrinc12">{{cite book |url=https://www.cdc.gov/csels/dsepd/ss1978/SS1978.pdf |format=PDF |title=Principles of Epidemiology in Public Health Practice |author=Centers for Disease Control and Prevention |edition=3rd |publisher=Centers for Disease Control and Prevention |year=2012 |accessdate=11 April 2020}}</ref> In both cases, proper reporting of data is critical to the success of epidemiologists' response to outbreaks and pandemics, as well as the credibility of their research.<ref name="HamiltonUsing19">{{cite book |chapter=Chapter 5: Using Technologies for Data Collection and Management |title=The CDC Field Epidemiology Manual |author=Hamilton, J.J.; Hopkins, R.S. |editor=Rasmussen, S.A.; Goodman, R.A. |publisher=Oxford University Press |edition=4th |pages=71–104 |year=2019 |isbn=9780190933692}}</ref><ref name="vonElmTheStren07">{{cite journal |title=The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: Guidelines for reporting observational studies |journal=PLoS Medicine |author=von Elm, E.; Altman, D.G.; Egger, M. et al. |volume=4 |issue=10 |at=e296 |year=2007 |doi=10.1371/journal.pmed.0040296 |pmid=17941714 |pmc=PMC2020495}}</ref>
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| The proper reporting of COVID-19 case data is no exception. In the United States, the CDC has taken a standardized approach to collecting reports on "individuals with at least one respiratory specimen that tested positive for the virus that causes COVID-19."<ref name="CDCInformRepo20">{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/php/reporting-pui.html |title=Information for Health Departments on Reporting Cases of COVID-19 |author=Centers for Disease Control and Prevention |work=Coronavirus Disease 2019 (COVID-19) |publisher=Centers for Disease Control and Prevention |date=21 March 2020 |accessdate=21 March 2020}}</ref> Their COVID-19 Case Report Form is designed to collect a wide variety of information about a COVID-19 case, including patient demographics, epidemiological characteristics, exposure and contact history, and clinical diagnosis and treatment procedures. Currently, the CDC is asking local and state health departments to submit case reports, and asking healthcare providers to contact those health departments when "concerned that a patient may have COVID-19." The CDC has also slimmed its reporting requirements, limiting reporting of "persons under investigation" to areas where testing must be forwarded to the CDC due to insufficient capacity to test locally.<ref name="CDCInformRepo20" /> Electronic reporting using the CDC's system is preferred, but they have a protocol for those areas unable to submit electronically. Canada has similar reporting expectations, with their own case report form and electronic data submission process through the Public Health Agency of Canada.<ref name="CanadaInterim20">{{cite web |url=https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/health-professionals/interim-guidance-surveillance-human-infection.html |title=Interim national surveillance guidelines for human infection with Coronavirus disease (COVID-19) |author=Government of Canada |publisher=Government of Canada |date=10 February 2020 |accessdate=11 April 2020}}</ref> And in the European Union, member countries and the U.K. are asked to report through the Early Warning and Response System.<ref name="ECDCCaseDef20">{{cite web |url=https://www.ecdc.europa.eu/en/case-definition-and-european-surveillance-human-infection-novel-coronavirus-2019-ncov |title=Case definition and European surveillance for COVID-19, as of 2 March 2020 |author=European Centre for Disease Prevention and Control |publisher=European Centre for Disease Prevention and Control |work=COVID-19 Portal |date=02 March 2020 |accessdate=11 April 2020}}</ref>
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| Somewhat related are any internal reporting requirements, particularly for test reporting in labs and medical facilities. The [[International Statistical Classification of Diseases and Related Health Problems]] (ICD) is a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease. Their ICD-10-CM code set has been modified to include lab testing codes for COVID-19, as has the [[Current Procedural Terminology]] (CPT) code set. [https://www.mgma.com/data/data-stories/coding-guidance-for-new-icd-10-cm-and-lab-testing Green and Bradley] provide insight into these additions<ref name="GreenCoding20">{{cite web |url=https://www.mgma.com/data/data-stories/coding-guidance-for-new-icd-10-cm-and-lab-testing |title=Coding guidance for new ICD-10-CM and lab testing codes for COVID-19 |work=MGMA Stat |author=Green, C.; Bradley, V. |date=01 April 2020 |accessdate=11 April 2020}}</ref>, as does the [https://www.aappublications.org/news/2020/03/12/coding031220 American Academy of Pediatrics].<ref name="AAPHowTo20">{{cite web |url=https://www.aappublications.org/news/2020/03/12/coding031220 |title=How to use ICD-10-CM, new lab testing codes for COVID-19 |author=AAP Division of Health Care Finance |publisher=American Academy of Pediatrics |date=12 March 2020 |accessdate=11 April 2020}}</ref>
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| Laboratories analyzing specimens for SARS-CoV-2 therefore must be equipped to not only handle analytical testing and test orders using the new test codes, but they also must be able to quickly and accurately transfer vital case information to the appropriate health authority. TO BE CONTINUED...
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| ===3.3 Additional benefits of laboratory informatics in disease testing===
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| ====3.3.1 Bioinformatics====
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| ==References==
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| {{Reflist|colwidth=30em}}
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