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4. Final thoughts and additional resources

4.1 Final thoughts

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?

We've learned that the family of coronaviruses can be disruptive to humanity with past brushes with SARS and MERS, yet we arguably haven't done enough to research these and similar viruses to be more prepared. We were perhaps 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.

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.

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.

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.

4.2 Key guidance documents

• Centers for Disease Control and Prevention (27 April 2020). "Evaluating and Testing Persons for Coronavirus Disease 2019 (COVID-19)". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-nCoV/hcp/clinical-criteria.html. 

• Centers for Disease Control and Prevention (29 April 2020). "Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19)". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html. 

• Centers for Disease Control and Prevention (31 March 2020). "Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19)". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-nCoV/lab/lab-biosafety-guidelines.html. 

• Occupational Safety and Health Administration (March 2020). "Guidance on Preparing Workplaces for COVID-19" (PDF). OSHA 3990-03 2020. Occupational Safety and Health Administration. https://www.osha.gov/Publications/OSHA3990.pdf. 

• Pan American Health Organization (30 March 2020). "Laboratory Guidelines for the Detection and Diagnosis of COVID-19 Virus Infection" (PDF). Pan American Health Organization. https://www.paho.org/en/file/61863/download?token=4nO-2lxQ. 

• Public Health England (1 May 2020). "COVID-19: Guidance for sampling and for diagnostic laboratories". U.K Government. https://www.gov.uk/government/publications/wuhan-novel-coronavirus-guidance-for-clinical-diagnostic-laboratories. 

• Public Health Laboratory Network (29 April 2020). "PHLN guidance on laboratory testing for SARS-CoV-2 (the virus that causes COVID-19)". Department of Health, Australian Government. https://www.health.gov.au/resources/publications/phln-guidance-on-laboratory-testing-for-sars-cov-2-the-virus-that-causes-covid-19. 

• U.S. Food and Drug Administration (2 April 2020). "Enforcement Policy for Face Masks and Respirators During the Coronavirus Disease (COVID-19) Public Health Emergency". FDA-2020-D-1138-0013. U.S. Food and Drug Administration. https://www.fda.gov/regulatory-information/search-fda-guidance-documents/enforcement-policy-face-masks-and-respirators-during-coronavirus-disease-covid-19-public-health. 

• U.S. Food and Drug Administration (30 March 2020). "Enforcement Policy for Gowns, Other Apparel, and Gloves During the Coronavirus Disease (COVID-19) Public Health Emergency". FDA-2020-D-1138-0023. U.S. Food and Drug Administration. https://www.fda.gov/regulatory-information/search-fda-guidance-documents/enforcement-policy-gowns-other-apparel-and-gloves-during-coronavirus-disease-covid-19-public-health. 

• U.S. Food and Drug Administration (16 March 2020). "Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency". FDA-2020-D-0987-0012. U.S. Food and Drug Administration. https://www.fda.gov/regulatory-information/search-fda-guidance-documents/policy-diagnostic-tests-coronavirus-disease-2019-during-public-health-emergency. 

• World Health Organization, et al. (19 March 2020). "Laboratory biosafety guidance related to coronavirus disease (COVID-19): Interim guidance, 19 March 2020". WHO/WPE/GIH/2020.2. World Health Organization. https://apps.who.int/iris/handle/10665/331500. 

• World Health Organization, et al. (19 March 2020). "Laboratory testing for coronavirus disease (COVID-19) in suspected human cases: Interim guidance, 19 March 2020". WHO/COVID-19/laboratory/2020.5. World Health Organization. https://apps.who.int/iris/handle/10665/331501. 

4.3 Web portals

4.3.1 U.S. agency portals

• Coronavirus Disease 2019 (COVID-19) - Information for Healthcare Professionals (CDC)
• Coronavirus Disease 2019 (COVID-19) - Information for Laboratories (CDC)
• COVID-19-Related Guidance Documents for Industry, FDA Staff, and Other Stakeholders (FDA)
• Coronavirus (COVID-19) Response (FEMA)

4.3.2 U.S. state and territory portals

• Alabama
• Alaska
• Arizona
• Arkansas
• California
• Colorado
• Connecticut
• Delaware
• District of Columbia
• Florida
• Georgia
• Hawaii
• Idaho
• Illinois
• Indiana
• Iowa
• Kansas
• Kentucky
• Louisiana
• Maine
• Maryland
• Massachusetts
• Michigan
• Minnesota
• Mississippi
• Missouri
• Montana
• Nebraska
• Nevada
• New Hampshire
• New Jersey
• New Mexico
• New York
• North Carolina
• North Dakota
• Ohio
• Oklahoma
• Oregon
• Pennsylvania
• Rhode Island
• South Carolina
• South Dakota
• Tennessee
• Texas
• Utah
• Vermont
• Virginia
• Washington
• West Virginia
• Wisconsin
• Wyoming

U.S. territories

• American Samoa
• Guam
• Northern Mariana Islands
• Puerto Rico
• Virgin Islands

4.3.3 Other national and multinational portals

• Australian Government
• European CDC
• Government of Canada
• Government of Japan
• Government of México

World Health Organization (WHO) and regionals

• WHO
• WHO Africa
• WHO Americas
• WHO Eastern Mediterranean
• WHO Europe
• WHO South-East Asia
• WHO Western Pacific

4.4 Key journal articles

• Hadaya, J.; Schumm, M.; Livingston, E.H. (2020). "Testing Individuals for Coronavirus Disease 2019 (COVID-19)". JAMA. doi:10.1001/jama.2020.5388. PMID 32236503. 

• Iwen, P.C.; Stiles, K.L.; Pantella, M.A. (2020). "Safety considerations in the laboratory testing of specimens suspected or known to contain the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)". American Journal of Clinical Pathology: aqaa047. doi:10.1093/ajcp/aqaa047. PMID 32190890. 

• Loeffelholz, M.J.; Tang, T.-W. (2020). "Laboratory diagnosis of emerging human coronavirus infections – The state of the art". Emerging Microbes & Infections 9 (1): 747–56. doi:10.1080/22221751.2020.1745095. PMID 32196430. 

• Udugama, B.; Kadhiresan, P.; Kozlowski, H.N. et al. (2020). "Diagnosing COVID-19: The Disease and Tools for Detection". ACS Nano 14 (4): 3822–3835. doi:10.1021/acsnano.0c02624. PMC PMC7144809. PMID 32223179. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144809. 

• Yuen, K.-S.; Fung, S.-Y.; Chan, C.-P.; Jin, D.-Y. (2020). "SARS-CoV-2 and COVID-19: The most important research questions". Cell & Bioscience 10: 40. doi:10.1186/s13578-020-00404-4. PMC PMC7074995. PMID 32190290. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074995. 

4.5 Public health lab directory

• Alabama Bureau of Clinical Laboratories
• Alaska Division of Public Health Laboratories
• Arizona Bureau of State Laboratory Services
• Arkansas Public Health Laboratory
• California Department of Public Health Laboratory
• Colorado Laboratory Services Division
• Connecticut Department of Public Health, Dr. Katherine A. Kelley Public Health Laboratory
• Delaware Public Health Laboratory
• District of Columbia Public Health Laboratory
• Florida Bureau of Public Health Laboratories
• Georgia Public Health Laboratory
• Hawaii State Laboratories Division
• Idaho Bureau of Laboratories
• Illinois Department of Public Health Laboratory
• Indiana State Department of Health Laboratories
• Iowa, The University of, State Hygienic Laboratory
• Kansas Health & Environmental Laboratories
• Kentucky Division of Laboratory Services
• Louisiana Office of Public Health Laboratories
• Maine Health & Environmental Testing Laboratory
• Maryland Department of Health Laboratories Administration
• Michigan Bureau of Laboratories
• Minnesota Public Health Laboratory
• Mississippi Public Health Laboratory
• Missouri State Public Health Laboratory
• Montana Laboratory Services Bureau
• Nebraska Public Health Laboratory
• Nevada State Public Health Laboratory
• New Hampshire Public Health Laboratories
• New Jersey Public Health and Environmental Laboratories
• New Mexico Department of Health Scientific Laboratory Division
• North Carolina State Laboratory of Public Health
• North Dakota Division of Laboratory Services
• Ohio Bureau of Public Health Laboratory
• Oklahoma Public Health Laboratory
• Oregon State Public Health Laboratory
• Pennsylvania Bureau of Laboratories
• Rhode Island Division of State Laboratories and Medical Examiners
• South Carolina Public Health Laboratory
• South Dakota State Public Health Laboratory
• Tennessee Department of Health Laboratory Services
• Texas Department of State Health Services Lab
• Utah Public Health Laboratory

United States Virgin Islands Department of Health Vermont Department of Health Laboratory Virginia Division of Consolidated Laboratory Services Wadsworth Center, New York State Department of Health Washington Public Health Laboratories West Virginia Department of Health & Human Services William A. Hinton State Laboratory Institute Wisconsin State Laboratory of Hygiene Wyoming Public Health Laboratory

• Commonwealth of the Northern Mariana Islands, Commonwealth Healthcare Corporation Laboratory
• Puerto Rico Public Health Laboratory

4.6 National and global resources

• http://www.centerforhealthsecurity.org/resources/COVID-19/Serology-based-tests-for-COVID-19.html