LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Final thoughts and additional resources
- 1 5. Final thoughts and additional resources
- 1.1 5.1 Final thoughts
- 1.2 5.2 Key guidance documents
- 1.3 5.3 Web portals
- 1.4 5.4 Key journal articles
- 1.5 5.5 Public health lab directory
- 1.6 5.6 Test kit and other resources
- 1.7 5.7 Public health laboratory informatics vendors
- 2 Citation information for this chapter
5. Final thoughts and additional resources
5.1 Final thoughts
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, 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.
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 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.
5.2 Key guidance documents
- Centers for Disease Control and Prevention (20 November 2020). "Guidance for SARS-CoV-2 Point-of-Care Testing". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/lab/point-of-care-testing.html.
- Centers for Disease Control and Prevention (02 November 2020). "How to Report COVID-19 Laboratory Data". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/lab/reporting-lab-data.html.
- Centers for Disease Control and Prevention (01 October 2020). "ICD-10-CM Official Guidelines for Coding and Reporting - FY 2021" (PDF). Centers for Disease Control and Prevention. https://www.cdc.gov/nchs/data/icd/10cmguidelines-FY2021.pdf.
- Centers for Disease Control and Prevention (05 November 2020). "Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens for 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 (19 September 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.
- Centers for Disease Control and Prevention (21 October 2020). "Overview of Testing for SARS-CoV-2 (COVID-19)". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html.
- Centers for Disease Control and Prevention (17 May 2020). "Preliminary Criteria for the Evaluation of Digital Contact Tracing Tools for COVID-19". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/downloads/php/prelim-eval-criteria-digital-contact-tracing.pdf.
- European Commission (19 October 2020). "Coronavirus: EU interoperability gateway for contact tracing and warning apps – Questions and Answers". European Union. https://ec.europa.eu/commission/presscorner/detail/en/QANDA_20_1905.
- European Data Protection Board (April 2020). "Guidelines 04/2020 on the use of location data and contact tracing tools in the context of the COVID-19 outbreak" (PDF). European Union. https://edpb.europa.eu/sites/edpb/files/files/file1/edpb_guidelines_20200420_contact_tracing_covid_with_annex_en.pdf.
- 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 (16 July 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 (12 November 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 (May 2020). "Enforcement Policy for Face Masks and Respirators During the Coronavirus Disease (COVID-19) Public Health Emergency (Revised)". FDA-2020-D-1138. 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 (15 May 2020). "Policy for Coronavirus Disease-2019 Tests During the Public Health Emergency (Revised)". FDA-2020-D-0987-0049. 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. (02 October 2020). "Assessment tool for laboratories implementing SARS-CoV-2 testing: Interim guidance, 2 October 2020". WHO/2019-nCoV/Lab_Assessment_Tool/2020.2. World Health Organization. https://apps.who.int/iris/handle/10665/335843.
- World Health Organization, et al. (11 September 2020). "Diagnostic testing for SARS-CoV-2: Interim guidance, 11 September 2020". WHO/2019-nCoV/laboratory/2020.6. World Health Organization. https://apps.who.int/iris/handle/10665/334254.
- World Health Organization, et al. (13 May 2020). "Laboratory biosafety guidance related to coronavirus disease (COVID-19): Interim guidance, 13 May 2020". WHO/WPE/GIH/2020.3. World Health Organization. https://apps.who.int/iris/handle/10665/332076.
5.3 Web portals
5.3.1 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)
5.3.2 U.S. state and territory portals
- District of Columbia
- New Hampshire
- New Jersey
- New Mexico
- New York
- North Carolina
- North Dakota
- Rhode Island
- South Carolina
- South Dakota
- West Virginia
5.3.3 Other national and multinational portals
World Health Organization (WHO) and regionals
- WHO Africa
- WHO Americas
- WHO Eastern Mediterranean
- WHO Europe
- WHO South-East Asia
- WHO Western Pacific
5.4 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.
- Richter, A.; Plant, T.; Kidd, M. et al. (2020). "How to establish an academic SARS-CoV-2 testing laboratory". Nature Microbiology 5: 1452–54. doi:10.1038/s41564-020-00818-3. PMID 33139885.
- 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=PMC7144809.
- Weemaes, M.; Martens, S.; Cuypers, L. et al. (2020). "Laboratory information system requirements to manage the COVID-19 pandemic: A report from the Belgian national reference testing center". JAMIA: ocaa081. doi:10.1093/jamia/ocaa081. PMC PMC7197526. PMID 32348469. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=PMC7197526.
- West, C.P.; Montori, V.M.; Sampathkumar, P. (2020). "COVID-19 Testing: The Threat of False-Negative Results". Mayo Clinic Proceedings 95 (6): 1127–29. doi:10.1016/j.mayocp.2020.04.004. PMC PMC7151274. PMID 32376102. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=PMC7151274.
- 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=PMC7074995.
5.5 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
- Massachusetts State Public Health Laboratory
- 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
- New York State Department of Health, Wadsworth Center
- 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
- Vermont Department of Health Laboratory
- Virginia Division of Consolidated Laboratory Services
- Washington State Public Health Laboratories
- West Virginia Office of Laboratory Services
- Wisconsin State Laboratory of Hygiene
- Wyoming Public Health Laboratory
- American Samoa Department of Public Health
- Commonwealth of the Northern Mariana Islands, Commonwealth Healthcare Corporation Laboratory
- Guam Department of Public Health and Social Services Laboratory Services
- Puerto Rico Public Health Laboratory
- United States Virgin Islands Department of Health
5.6 Test kit and other resources
- COVID-19 Diagnostics in Context - Harvard Center for Systems Biology
- COVID-19 Emergency Use Authorizations - U.S. FDA
- SARS-CoV-2 Test & Controls Database - AdVeritasDx
- SARS-CoV-2 Diagnostic Pipeline - Foundation for Innovative New Diagnostics
- Serology-based tests for COVID-19 - Johns Hopkins
5.7 Public health laboratory informatics vendors
This is not a complete list but rather a representative sampling of vendors who explicitly discuss how their laboratory informatics solution helps public health laboratories.
- Abbott Informatics Corporation
- BGASoft, Inc.
- CliniSys Group Limited
- Common Cents Systems, Inc.
- Deutsche Telekom Healthcare
- Eusoft Srl
- LabLynx, Inc.
- LabWare, Inc.
- Orchard Software Corporation
- Polisystem Informatica Srl
- Promium, LLC
- Sunquest Information Systems, Inc.
Citation information for this chapter
Chapter: 5. Final thoughts and additional resources
Edition: Fall 2020
Title: COVID-19 Testing, Reporting, and Information Management in the Laboratory
Author for citation: Shawn E. Douglas
License for content: Creative Commons Attribution-ShareAlike 4.0 International
Publication date: November 2020