Difference between revisions of "User:Shawndouglas/sandbox/sublevel1"

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[[File:COVID-22 Palmerston North posters MRD.jpg|right|280px]]Since it has started, the [[COVID-19]] [[pandemic]] has brought with it numerous challenges for society to face. How poised is a state and national government to truly lend assistance to its citizens in the face of a crisis? How does the increasing divide between the "haves" and "have nots," and the associated economic structures that lend to them, reveal the fragility of our society? What more can be done to fund epidemiology research? How can we improve our healthcare system to be better equipped to handle communicable disease response and better funded to provide more social services to a broader base of people? And what lessons can be learned from the successes and failures of providing accurate, responsive laboratory testing during pandemics?
* {{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/php/contact-tracing/index.html |title=Contact Tracing |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=16 September 2021}}
 
* {{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/lab/point-of-care-testing.html |title=Guidance for SARS-CoV-2 Point-of-Care and Rapid Testing |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=08 July 2021}}
We've learned that the family of [[coronavirus]]es can be disruptive to humanity, having had past brushes with [[SARS]] and [[MERS]], yet we arguably [https://www.newscientist.com/article/mg24532724-700-we-were-warned-so-why-couldnt-we-prevent-the-coronavirus-outbreak/ haven't done enough] to research these and similar viruses to be more prepared. We were perhaps [https://doi.org/10.1098/rstb.2004.1487 fortunate in some ways] that SARS wasn't worse than it proved to be. However, responses by the World Health Organization (WHO), the Centers for Disease Control and Prevention (CDC), and other organizations and agencies around the world during the SARS and MERS outbreaks laid the foundations for [[laboratory]] testing a novel coronavirus like [[SARS-CoV-2]]. [[Reverse transcription polymerase chain reaction|Reverse transcription PCR]] (RT-PCR) is again proving to be a useful diagnostic tool for identifying the virus in patient specimens. Other methods such as [[Lateral flow test|lateral flow assays]] (LFA) borrow from more rapid methods of identification, and other more rapid methods of testing such as antigen testing and reverse transcription [[loop-mediated isothermal amplification]] (RT-LAMP) lend additional support to testing. And while confusing—particularly given the unknowns surrounding the predictive ability of antibodies conferring immunity—serology antibody tests appear to have their place as well.
* {{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/lab/reporting-lab-data.html |title=How to Report COVID-19 Laboratory Data |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=26 January 2021}}
 
* {{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/lab/pooling-procedures.html |title=Interim Guidance for Use of Pooling Procedures in SARS-CoV-2 Diagnostic and Screening Testing |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=30 June 2021}}
These and related tests can be complex, as evidenced by the CLIA approval status of a strong majority of emergency use authorized (EUA) test kits. Performing these tests on complex instruments and then effectively using the data they provide require clear [[workflow]]s that can be at least partially automated. This is particularly vital given the paltry 13 percent of CLIA-certified U.S labs that are certified to perform moderate- and high-complexity testing. Additionally, given the value of test result data to governments agencies, [[Epidemiology|epidemiological]] researchers, and patients, it's important that reporting is clear, timely, and moderated. Laboratory informatics systems such as [[laboratory information management system]]s (LIMS) and [[laboratory information system]]s (LIS) can go a long way towards ensuring laboratory testing and reporting of communicable diseases goes smoothly.
* {{cite web |url=https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html |title=Interim Guidelines for Collecting and Handling of Clinical Specimens for COVID-19 Testing |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=26 February 2021}}
 
* {{cite web |url=https://www.cdc.gov/coronavirus/2019-nCoV/lab/lab-biosafety-guidelines.html |title=Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19) |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=11 June 2021}}
Choosing just any [[Informatics (academic field)|informatics]] system and implementing it haphazardly in the laboratory doesn't automatically ensure improvements, however. Many elements of the system should be carefully considered. Does the system have a provider portal that is flexible in its ability to handle providers from many different healthcare facility types entering test orders and reviewing results? How well does it address the workflow of COVID-19 and other types of respiratory illness testing? Does it interface with the instruments you're using to test such illnesses, and at a reasonable cost? How well does it handle internal and external reporting requirements, as well as any data visualization and dashboarding you require? During outbreaks and pandemics, the system should improve your laboratory workflow, not slow you down. This includes the element of reporting, which is not only critical but also challenging even in relatively peaceful times of health. And how interoperable is the system with other clinical systems such as [[electronic health record]]s (EHR) and [[radiology information system]]s (RIS)? As we found out, academic and research laboratories wanting to assist with testing have at times been locked out due to their informatics system not interfacing cleanly with a hospital EHR.
* {{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html |title=Overview of Testing for SARS-CoV-2 (COVID-19) |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=02 August 2021}}
 
* {{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/sars-cov2-testing-strategies.html |title=Testing Strategies for SARS-CoV-2 |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=13 August 2021}}
Hopefully this guide has provided important background in several areas, from COVID-19's historical impact and challenging health issues, to the current state of laboratory testing, reporting, and informatics applications being applied to fight its spread. As noted in the beginning, this pandemic and how humanity is dealing with it is rapidly changing us, as we try to keep up with ways to fend it off. That means information changes rapidly. An effort will be made to update this content as new information comes to light. In the meantime, stay safe and consider your informatics solutions with care.
* {{cite web |url=https://www.cms.gov/files/document/fy-2022-icd-10-cm-coding-guidelines.pdf |format=PDF |title=ICD-10-CM Official Guidelines for Coding and Reporting - FY 2022 |author=Centers for Medicare & Medicaid Services |publisher=Centers for Medicare & Medicaid Services |date=August 2021}}
* {{cite web |url=https://ec.europa.eu/commission/presscorner/detail/en/QANDA_20_1905 |title=Coronavirus: EU interoperability gateway for contact tracing and warning apps – Questions and Answers |author=European Commission  |publisher=European Union |date=19 October 2020}}
* {{cite web |url=https://edpb.europa.eu/sites/default/files/files/file1/edpb_guidelines_20200420_contact_tracing_covid_with_annex_en.pdf |format=PDF |title=Guidelines 04/2020 on the use of location data and contact tracing tools in the context of the COVID-19 outbreak |author=European Data Protection Board |publisher=European Union |date=21 April 2020}}
* {{cite web |url=https://www.osha.gov/coronavirus/safework |title=Protecting Workers: Guidance on Mitigating and Preventing the Spread of COVID-19 in the Workplace |author=Occupational Safety and Health Administration |publisher=Occupational Safety and Health Administration |date=13 August 2021}}
* {{cite web |url=https://iris.paho.org/handle/10665.2/52458 |title=Laboratory Guidelines for the Detection and Diagnosis of COVID-19 Virus Infection |author=Pan American Health Organization |publisher=Pan American Health Organization |date=08 July 2020}}
* {{cite web |url=https://www.gov.uk/government/publications/wuhan-novel-coronavirus-guidance-for-clinical-diagnostic-laboratories |title=COVID-19: Guidance for sampling and for diagnostic laboratories |author=Public Health England |publisher=U.K Government |date=29 March 2021}}
* {{cite web |url=https://www.health.gov.au/resources/publications/phln-guidance-on-laboratory-testing-for-sars-cov-2-the-virus-that-causes-covid-19 |title=PHLN guidance on laboratory testing for SARS-CoV-2 (the virus that causes COVID-19) |author=Public Health Laboratory Network |publisher=Department of Health, Australian Government |date=22 June 2021}}
* {{cite web |url=https://www.fda.gov/regulatory-information/search-fda-guidance-documents/enforcement-policy-face-masks-barrier-face-coverings-face-shields-surgical-masks-and-respirators |title=Enforcement Policy for Face Masks, Barrier Face Coverings, Face Shields, Surgical Masks, and Respirators During the Coronavirus Disease (COVID-19) Public Health Emergency (Revised) |work=FDA-2020-D-1138 |author=U.S. Food and Drug Administration |publisher=U.S. Food and Drug Administration |date=September 2021}}
* {{cite web |url=https://www.fda.gov/regulatory-information/search-fda-guidance-documents/enforcement-policy-gowns-other-apparel-and-gloves-during-coronavirus-disease-covid-19-public-health |title=Enforcement Policy for Gowns, Other Apparel, and Gloves During the Coronavirus Disease (COVID-19) Public Health Emergency |work=FDA-2020-D-1138-0023 |author=U.S. Food and Drug Administration |publisher=U.S. Food and Drug Administration |date=30 March 2020}}
* {{cite web |url=https://www.fda.gov/regulatory-information/search-fda-guidance-documents/policy-coronavirus-disease-2019-tests-during-public-health-emergency-revised |title=Policy for Coronavirus Disease-2019 Tests During the Public Health Emergency (Revised) |work=FDA-2020-D-0987-0049 |author=U.S. Food and Drug Administration |publisher=U.S. Food and Drug Administration |date=15 May 2020}}
* {{cite web |url=https://apps.who.int/iris/handle/10665/335843 |title=Assessment tool for laboratories implementing SARS-CoV-2 testing: Interim guidance, 2 October 2020 |work=WHO/2019-nCoV/Lab_Assessment_Tool/2020.2 |author=World Health Organization, et al. |publisher=World Health Organization |date=02 October 2020}}
* {{cite web |url=https://apps.who.int/iris/handle/10665/334254 |title=Diagnostic testing for SARS-CoV-2: Interim guidance, 11 September 2020 |work=WHO/2019-nCoV/laboratory/2020.6 |author=World Health Organization, et al. |publisher=World Health Organization |date=11 September 2020}}
* {{cite web |url=https://apps.who.int/iris/handle/10665/332076 |title=Laboratory biosafety guidance related to coronavirus disease (COVID-19): Interim guidance, 13 May 2020 |work=WHO/WPE/GIH/2020.3 |author=World Health Organization, et al. |publisher=World Health Organization |date=13 May 2020}}

Revision as of 20:49, 3 February 2022

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