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| ==4. Final thoughts and additional resources== | | <div class="nonumtoc">__TOC__</div> |
| ===4.1 Final thoughts=== | | {{ombox |
| In the relatively brief time 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?
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| We've learned that the family of coronaviruses can be disruptive to humanity with 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 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 assays (LFA) borrow from more rapid methods of identification, lending 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.
| | ==Sandbox begins below== |
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| 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 workflows 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, epidemiological researchers, and patients, it's important that reporting is clear, timely, and moderated. Laboratory informatics systems such as laboratory information management systems (LIMS) and laboratory information systems (LIS) can go a long way towards ensuring laboratory testing and reporting of commmunicable diseases goes smoothly.
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| Choosing just any 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 records (EHR) and radiology information systems (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.
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| 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 we said 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.
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| ===4.2 Key guidance documents=== | |
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| * {{cite web |url=https://www.cdc.gov/coronavirus/2019-nCoV/hcp/clinical-criteria.html |title=Evaluating and Testing Persons for Coronavirus Disease 2019 (COVID-19) |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=24 March 2020}}
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| * {{cite web |url=https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html |title=Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19) |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=24 March 2020}}
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| * {{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=31 March 2020}}
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| * {{cite web |url=https://www.osha.gov/Publications/OSHA3990.pdf |format=PDF |title=Guidance on Preparing Workplaces for COVID-19 |work=OSHA 3990-03 2020 |author=Occupational Safety and Health Administration |publisher=Occupational Safety and Health Administration |date=March 2020}}
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| * {{cite web |url=https://www.paho.org/en/file/61863/download?token=4nO-2lxQ |format=PDF |title=Laboratory Guidelines for the Detection and Diagnosis of COVID-19 Virus Infection |author=Pan American Health Organization |publisher=Pan American Health Organization |date=30 March 2020}}
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| * {{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=03 April 2020}}
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| * {{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=01 April 2020}}
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| * {{cite web |url=https://www.fda.gov/regulatory-information/search-fda-guidance-documents/enforcement-policy-face-masks-and-respirators-during-coronavirus-disease-covid-19-public-health |title=Enforcement Policy for Face Masks and Respirators During the Coronavirus Disease (COVID-19) Public Health Emergency |work=FDA-2020-D-1138-0013 |author=U.S. Food and Drug Administration |publisher=U.S. Food and Drug Administration |date=25 March 2020}}
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| * {{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}}
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| * {{cite web |url=https://www.fda.gov/regulatory-information/search-fda-guidance-documents/policy-diagnostic-tests-coronavirus-disease-2019-during-public-health-emergency |title=Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency |work=FDA-2020-D-0987-0012 |author=U.S. Food and Drug Administration |publisher=U.S. Food and Drug Administration |date=16 March 2020}}
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| * {{cite web |url=https://apps.who.int/iris/handle/10665/331500 |title=Laboratory biosafety guidance related to coronavirus disease (COVID-19): Interim guidance, 19 March 2020 |work=WHO/WPE/GIH/2020.2 |author=World Health Organization, et al. |publisher=World Health Organization |date=19 March 2020}}
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| * {{cite web |url=https://apps.who.int/iris/handle/10665/331501 |title=Laboratory testing for coronavirus disease (COVID-19) in suspected human cases: Interim guidance, 19 March 2020 |work=WHO/COVID-19/laboratory/2020.5 |author=World Health Organization, et al. |publisher=World Health Organization |date=19 March 2020}}
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| ===4.3 Web portals===
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| ====4.3.1 U.S. agency portals====
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| * [https://www.cdc.gov/coronavirus/2019-ncov/hcp/index.html Coronavirus Disease 2019 (COVID-19) - Information for Healthcare Professionals] (CDC)
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| * [https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html Coronavirus Disease 2019 (COVID-19) - Information for Laboratories] (CDC)
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| * [https://www.fda.gov/emergency-preparedness-and-response/coronavirus-disease-2019-covid-19/covid-19-related-guidance-documents-industry-fda-staff-and-other-stakeholders COVID-19-Related Guidance Documents for Industry, FDA Staff, and Other Stakeholders] (FDA)
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| * [https://www.fema.gov/coronavirus Coronavirus (COVID-19) Response] (FEMA)
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| ====4.3.2 U.S. state and territory portals====
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| * [https://governor.alabama.gov/newsroom/covid-19/ Alabama]
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| * [http://dhss.alaska.gov/dph/Epi/id/Pages/COVID-19/default.aspx Alaska]
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| * [https://az.gov/government-0 Arizona]
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| * [https://govstatus.egov.com/ar-covid-19 Arkansas]
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| * [https://covid19.ca.gov/ California]
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| * [https://covid19.colorado.gov/ Colorado]
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| * [https://portal.ct.gov/coronavirus Connecticut]
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| * [https://coronavirus.delaware.gov/ Delaware]
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| * [https://coronavirus.dc.gov/ District of Columbia]
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| * [https://floridahealthcovid19.gov/ Florida]
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| * [https://georgia.gov/covid-19-state-services-georgia Georgia]
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| * [https://hawaiicovid19.com/ Hawaii]
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| * [https://coronavirus.idaho.gov/ Idaho]
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| * [https://coronavirus.illinois.gov/ Illinois]
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| * [https://coronavirus.in.gov/ Indiana]
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| * [https://coronavirus.iowa.gov/ Iowa]
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| * [https://govstatus.egov.com/coronavirus Kansas]
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| * [https://govstatus.egov.com/kycovid19 Kentucky]
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| * [https://gov.louisiana.gov/coronavirus/ Louisiana]
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| * [https://www.maine.gov/governor/mills/covid-19 Maine]
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| * [https://coronavirus.maryland.gov/ Maryland]
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| * [https://www.mass.gov/info-details/covid-19-updates-and-information Massachusetts]
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| * [https://www.michigan.gov/coronavirus/ Michigan]
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| * [https://www.health.state.mn.us/diseases/coronavirus/index.html Minnesota]
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| * [https://www.coronavirus.ms.gov/ Mississippi]
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| * [https://health.mo.gov/living/healthcondiseases/communicable/novel-coronavirus/ Missouri]
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| * [https://covid19.mt.gov/ Montana]
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| * [http://dhhs.ne.gov/Pages/Coronavirus.aspx Nebraska]
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| * [https://nvhealthresponse.nv.gov/ Nevada]
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| * [https://www.nh.gov/covid19/ New Hampshire]
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| * [https://covid19.nj.gov/ New Jersey]
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| * [https://www.newmexico.gov/ New Mexico]
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| * [https://coronavirus.health.ny.gov/home New York]
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| * [https://www.ncdhhs.gov/divisions/public-health/coronavirus-disease-2019-covid-19-response-north-carolina North Carolina]
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| * [https://ndresponse.gov/covid-19-resources North Dakota]
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| * [https://coronavirus.ohio.gov/wps/portal/gov/covid-19/home Ohio]
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| * [https://coronavirus.health.ok.gov/ Oklahoma]
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| * [https://govstatus.egov.com/or-covid-19 Oregon]
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| * [https://www.pa.gov/guides/responding-to-covid-19/ Pennsylvania]
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| * [https://health.ri.gov/covid/ Rhode Island]
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| * [https://www.scdhec.gov/infectious-diseases/viruses/coronavirus-disease-2019-covid-19 South Carolina]
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| * [https://covid.sd.gov/ South Dakota]
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| * [https://www.tn.gov/governor/covid-19.html Tennessee]
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| * [https://texas.gov/#covid19 Texas]
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| * [https://coronavirus.utah.gov/ Utah]
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| * [https://www.healthvermont.gov/response/infectious-disease/2019-novel-coronavirus Vermont]
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| * [https://www.virginia.gov/coronavirus/ Virginia]
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| * [https://coronavirus.wa.gov/ Washington]
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| * [https://dhhr.wv.gov/COVID-19/Pages/default.aspx West Virginia]
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| * [https://www.dhs.wisconsin.gov/covid-19/index.htm Wisconsin]
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| * [https://covid19.wyo.gov/ Wyoming]
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| '''U.S. territories'''
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| * [https://www.americansamoa.gov/ American Samoa]
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| * [http://dphss.guam.gov/covid-19/ Guam]
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| * [https://www.chcc.gov.mp/coronavirusinformation.php Northern Mariana Islands]
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| * [http://salud.gov.pr/Pages/coronavirus.aspx Puerto Rico]
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| * [https://doh.vi.gov/covid19usvi Virgin Islands]
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| ====4.3.3 Other national and multinational portals====
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| * [https://www.australia.gov.au/ Australian Government]
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| * [https://www.ecdc.europa.eu/en/novel-coronavirus/laboratory-support European CDC]
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| * [https://www.canada.ca/en/public-health/services/diseases/coronavirus-disease-covid-19.html Government of Canada]
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| * [https://www.mhlw.go.jp/stf/seisakunitsuite/bunya/newpage_00032.html Government of Japan]
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| * [https://coronavirus.gob.mx/ Government of México]
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| '''World Health Organization (WHO) and regionals'''
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| * [https://www.who.int/emergencies/diseases/novel-coronavirus-2019 WHO]
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| * [https://www.afro.who.int/health-topics/coronavirus-covid-19 WHO Africa]
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| * [https://www.paho.org/en/topics/coronavirus-infections/coronavirus-disease-covid-19 WHO Americas]
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| * [http://www.emro.who.int/health-topics/corona-virus/index.html WHO Eastern Mediterranean]
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| * [http://www.euro.who.int/en/health-topics/health-emergencies/coronavirus-covid-19 WHO Europe]
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| * [https://www.who.int/southeastasia/outbreaks-and-emergencies/novel-coronavirus-2019 WHO South-East Asia]
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| * [https://www.who.int/westernpacific/emergencies/covid-19 WHO Western Pacific]
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| ===4.4 Key journal articles===
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| * {{cite journal |title=Testing Individuals for Coronavirus Disease 2019 (COVID-19) |journal=JAMA |author=Hadaya, J.; Schumm, M.; Livingston, E.H. |year=2020 |doi=10.1001/jama.2020.5388 |pmid=32236503}}
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| * {{cite journal |title=Safety considerations in the laboratory testing of specimens suspected or known to contain the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |journal=American Journal of Clinical Pathology |author=Iwen, P.C.; Stiles, K.L.; Pantella, M.A. |at=aqaa047 |year=2020 |doi=10.1093/ajcp/aqaa047 |pmid=32190890}}
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| * {{cite journal |title=Laboratory diagnosis of emerging human coronavirus infections – The state of the art |journal=Emerging Microbes & Infections |author=Loeffelholz, M.J.; Tang, T.-W. |volume=9 |issue=1 |pages=747–56 |year=2020 |doi=10.1080/22221751.2020.1745095 |pmid=32196430}}
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| https://www.ecdc.europa.eu/sites/default/files/documents/Overview-rapid-test-situation-for-COVID-19-diagnosis-EU-EEA.pdf
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| ===4.5 Public health lab directory===
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| * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846798/
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| * https://www.aphl.org/membership/Pages/memberlabs.aspx
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| ===4.6 National and global resources===
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| * http://www.centerforhealthsecurity.org/resources/COVID-19/Serology-based-tests-for-COVID-19.html
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| ===4.7 Public health laboratory informatics solutions===
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