|
|
| (60 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| <div class="nonumtoc">__TOC__</div> | | <div class="nonumtoc">__TOC__</div> |
| | {{ombox |
| | | type = notice |
| | | style = width: 960px; |
| | | text = This is sublevel34 of my sandbox, where I play with features and test MediaWiki code. If you wish to leave a comment for me, please see [[User_talk:Shawndouglas|my discussion page]] instead.<p></p> |
| | }} |
|
| |
|
| ==3. Workflow and information management for COVID-19 (and other pandemics)== | | ==Sandbox begins below== |
| | |
| | |
| ===3.1 Laboratory informatics and workflow management===
| |
| | |
| | |
| ===3.2 Laboratory informatics and reporting requirements===
| |
| 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 proving 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>
| |
| | |
| 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>
| |
| | |
| 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>
| |
| | |
| 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.
| |
| | |
| {|
| |
| | STYLE="vertical-align:top;"|
| |
| {| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="90%"
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;" colspan="6"|'''Table 1.''' U.S. state-based COVID-19 reporting requirements
| |
| |-
| |
| ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" |State
| |
| ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" |Electronic file (Y/N)
| |
| ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" |Fax? (Y/N)
| |
| ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" |Forms for reporting
| |
| ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" |Contact
| |
| ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;" |Additional details
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.alabamapublichealth.gov/covid19/healthcare.html Alabama]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|N
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://redcap.link/u0i8heo3 Novel Coronavirus Report Form]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|ALNEDSSsupport@adph.state.al.us
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|"Providers who are either reporting laboratory results for patients tested by a commercial or clinical laboratory (not tested by the BCL) or reporting deaths among patients with positive results must complete" the report form. "Laboratories are required to report all negative and positive COVID-19 virus test results electronically (faxes do not count). If not already enrolled, laboratories will need to manually enter test results directly into the surveillance system." Email the contact to enroll staff access to the system.
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[http://dhss.alaska.gov/dph/Epi/id/Pages/COVID-19/healthcare.aspx Alaska]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[http://dhss.alaska.gov/dph/Epi/Documents/pubs/conditions/frmInfect.pdf Confidential Infectious Disease Report Form]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|COVID Reporting Hotline: 1-877-469-8067<br /> <br />Urgent situation: 907-269-8000 or 800-478-0084 (after-hours)<br /> <br />ELR: megan.tompkins@alaska.gov
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|"Providers must report laboratory-confirmed cases of COVID-19 to SOE by either leaving a message on the COVID Reporting Hotline (1-877-469-8067) or via fax using the standard Infectious Disease Report Form." "[A]ll results both positive and negative must be reported via either integration into existing electronic laboratory reporting (ELR) data feeds or fax (907-563-7868). Please email Megan Tompkins ... to inform us about how your facility will report."
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.azdhs.gov/preparedness/epidemiology-disease-control/infectious-disease-epidemiology/index.php#novel-coronavirus-lab-resources Arizona]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.azdhs.gov/documents/preparedness/epidemiology-disease-control/infectious-disease-epidemiology/novel-coronavirus/lab-resources/sample-aggregate-form.xlsx Sample Aggregate Weekly Submission Form]<br />[https://www.azdhs.gov/documents/preparedness/epidemiology-disease-control/infectious-disease-epidemiology/novel-coronavirus/lab-resources/sample-adhs-csv-file.csv Sample ADHS CSV File]<br />[https://www.azdhs.gov/documents/preparedness/epidemiology-disease-control/infectious-disease-epidemiology/novel-coronavirus/lab-resources/sample-adhs-excel-file.xlsx Sample ADHS Excel File]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Fax: (602) 364-3199<br /> <br />ELR: elr@azdhs.gov
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|"[A] laboratory as defined in A.R.S. § 36-451(4) shall report all COVID-19 test results (positive and negative) to the Arizona Department of Health Services in an electronic format as follows: a. For laboratories reporting to the Arizona Department of Health Services through electronic lab reporting ('ELR'), results of all COVID-19 tests; b. For laboratories not reporting to the Arizona Department of Health Services through ELR, a weekly aggregate number of total COVID-19 tests performed and their results." If reporting is accomplished through mail or fax, use the Sample Aggregate Weekly Submission Form. "Aggregate reporting does NOT replace mandatory laboratory reporting requirements per [https://www.coconino.az.gov/DocumentCenter/View/411/Communicable-Disease-Reporting-Rules- Arizona Administrative Code R9-6-204]."<br /> <br />"ADHS has created a new electronic option for reporting results of COVID-19 in-house testing as an alternative to Health Level Seven (HL7) electronic laboratory reporting or direct entry into MEDSIS. This can now be accomplished through a standardized spreadsheet or comma separated value (CSV) file format."
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Arkansas
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|California
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.colorado.gov/pacific/cdphe/report-a-disease Colorado]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://drive.google.com/file/d/151OUa9o2vPG32tSx_eqlMVP86zkTv3Yw/view?usp=sharing General Communicable Disease Reporting Form]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Fax: (303) 782-0338<br /> <br />CEDRS: lavelle.fernandez@state.co.us<br /> <br />ELR: andrew.horvath@state.co.us
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|The state doesn't appear to have specific rules or a reporting form for laboratory reporting of COVID-19. Presumably labs are reporting COVID-19 as is required for any communicable disease. The state lists multiple ways to report a case: calling, faxing a General Communicable Disease Reporting Form, through CEDRS, or by using ELR. The also offers guidance for healthcare providers. "Any suspected or confirmed case or outbreak of COVID-19 should immediately be reported to the local or state public health agency. To report, utilize the [Outbreak COVID-19 Outbreak Report Form]. Send this form to your local public health agency OR to CDPHE by securely emailing a completed form to: cdphe_haioutbreak@state.co.us."
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://portal.ct.gov/DPH/Epidemiology-and-Emerging-Infections/Laboratory-Reporting Connecticut]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://portal.ct.gov/-/media/DPH/EEIP/Forms/nCoV_-PUI_Form.pdf?la=en 2019 Novel Coronavirus (COVID-19) Case Report Form]<br /> <br />[https://portal.ct.gov/-/media/Departments-and-Agencies/DPH/dph/infectious_diseases/pdf_forms_/OL15C_Form.pdf?la=en Reportable Laboratory Findings, Form OL-15C]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Fax: (860) 629-6962<br /> <br />ELR: dph.elr@ct.gov
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Presumably labs are reporting COVID-19 as is required for any communicable disease. This has traditionally been done using Form OL-15C sent through [https://portal.ct.gov/DPH/Epidemiology-and-Emerging-Infections/Laboratory-Reporting mail or fax], as well as [https://portal.ct.gov/DPH/Epidemiology-and-Emerging-Infections/Electronic-Laboratory-Reporting ELR]. "Providers can now submit a COVID-19 case report [https://dphsubmissions.ct.gov/Covid/InitiateCovidReport online]. This is the preferred way to submit COVID-19 case reports."
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.dhss.delaware.gov/dhss/dph/php/alerts/dhan421.html Delaware]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|N
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|No standardized COVID-19 reporting form
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Call: 1-888-295-5156<br /> <br />Email: reportdisease@delaware.gov
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|"COVID-19 is a reportable condition to the DPH. Any positive test results from any laboratory must be reported to DPH via the Delaware Electronic Reporting Surveillance System (DERSS). If you have a strong clinical suspicion that a patient may be infected with COVID-19 based on clinical symptoms and epidemiological factors (e.g., close contact with a confirmed case, recent travel to an area with sustained transmission), contact the DPH Office of Infectious Disease Epidemiology at 1-888-295-5156, or report through reportdisease@delaware.gov within 24 hours leading to submission of test samples to a commercial lab to allow for surveillance and monitoring as appropriate." The state makes no mention of reporting negative COVID-19 test results.
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[http://www.floridahealth.gov/diseases-and-conditions/disease-reporting-and-management/disease-reporting-and-surveillance/surveillance-and-investigation-guidance/index.html Florida]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Y
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|No standardized COVID-19 reporting form
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|Fax: (850) 414-6894<br /> <br />ELR: MUElectronicLabReporting@flhealth.gov or ELR@flhealth.gov
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|"Commercial laboratory results for COVID-19 will either be reported through electronic laboratory reporting (ELR), faxing, or phone calls from laboratories. Results received at the Bureau of Epidemiology will be sent to counties via Merlin. Bureau of Public Health Laboratories test results are reported to [county health departments] through
| |
| Merlin and they are mailed to the ordering providers." In separate documentation, the state notes that both positive and negative COVID-19 laboratory results should be reported. As for health care providers and facilities, they must report a [[http://www.floridahealth.gov/diseases-and-conditions/disease-reporting-and-management/disease-reporting-and-surveillance/_documents/novel-coronavirus-reporting-hcp.pdf specific set of persons related to COVID-19] to the County Health Departments.
| |
| |-
| |
|
| |
| |-
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://dph.georgia.gov/epidemiology/disease-reporting Georgia]
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| | style="background-color:white; padding-left:10px; padding-right:10px;"|
| |
| |-
| |
|
| |
| |}
| |
| |}
| |
| | |
| | |
| ===3.3 Additional benefits of laboratory informatics in disease testing and public health===
| |
| In a 2013 research paper published in the journal ''BMJ Quality & Safety'', El-Kareh ''et al.'' analyzed and described the state of diagnostic health information technology (HIT). They noted that without the aid of HIT, clinicians are more error-prone, leaving them "vulnerable to fallible human memory, variable disease presentation, clinical processes plagued by communication lapses, and a series of well-documented ‘heuristics,’ biases, and disease-specific pitfalls."<ref name="El-KarehUseOf13">{{cite journal |title=Use of health information technology to reduce diagnostic errors |journal=BMJ Quality & Safety |author=El-Kareh, R.; Hasan, O.; Schiff, G.D. |volume=22 |issue=Suppl. 2 |pages=ii40–ii51 |year=2013 |doi=10.1136/bmjqs-2013-001884 |pmid=23852973 |pmc=PMC3786650}}</ref> Appropriate, well-designed HIT systems are capable of helping clinicians and laboratorians by providing more timely access to information, improved communication, better clinical reasoning and decision making, and improved workflows, as well as a reduction in diagnostic errors, and, as a result, improved patient safety and health outcomes.<ref name="NASEMImprov15">{{cite book |url=https://www.nap.edu/read/21794/chapter/7 |chapter=Chapter 5: Technology and Tools in the Diagnostic Process |title=Improving Diagnosis in Health Care |author=National Academies of Sciences, Engineering, and Medicine |publisher=The National Academies Press |pages=217–62 |year=2015 |doi=10.17226/21794 |isbn=9780309377720}}</ref>
| |
| | |
| From a public health perspective, the application of informatics to disease surveillance, reporting, and health promotion is also vital. Winters-Miner ''et al.'' note in particular the value of using informatics tools and methods to implement predictive analytics and data mining into public health. They use disease prevention and biosurveillance as major examples. We could, for example "analyze large populations of people to quantify risks related to public health, and help physicians to develop intervention programs for those patients at highest risk of some ailment or medical condition."<ref name="Winters-MinerBiomedical15">{{cite book |chapter=Chapter 3: Biomedical Informatics |title=Practical Predictive Analytics and Decisioning Systems for Medicine |author=Winters-Miner, L.A.; Bolding, P.S.; Hilbe, J.M. et al. |publisher=Academic Press |pages=42–59 |year=2015 |doi=10.1016/B978-0-12-411643-6.00003-X |isbn=9780124116436}}</ref> Additionally, through the use of syndromic surveillance systems (tools aiding in the detection of indicators leading up to disease diagnosis for individuals and populations<ref name="MandlImplement04">{{cite journal |title=Implementing syndromic surveillance: A practical guide informed by the early experience |journal=JAMIA |author=Mandl, K.D.; Overhage, J.M.; Wagner, M.M. et al. |volume=11 |issue=2 |pages=141–50 |year=2004 |doi=10.1197/jamia.M1356 |pmid=14633933 |pmc=PMC353021}}</ref>), they suggest that outbreaks can be better detected at local and national levels, and public health measures can be better implemented, increasing public awareness and hindering the spread of disease.<ref name="Winters-MinerBiomedical15" />
| |
| | |
| https://www.nature.com/articles/s41746-019-0110-4
| |
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4204239/
| |
| https://www.nap.edu/read/21794/chapter/7#241
| |
| https://www.mlo-online.com/home/article/13017228/poct-made-easier-with-informatics
| |
| | |
| ====3.3.1 Bioinformatics====
| |
| | |
| | |
| ==References==
| |
| {{Reflist|colwidth=30em}}
| |
