LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Workflow and information management for COVID-19 (and other respiratory diseases)

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4. Workflow and information management for COVID-19 (and other pandemics)

4.1 Laboratory informatics and workflow management

Molecular diagnostics qia symphony.jpg

Laboratory computing has positively affected clinical service delivery and laboratory management for decades.[1] These benefits are achieved through automation elements that reduce data entry errors, reduce workloads, collect laboratory instrument data, and check for common errors like duplicate test orders.[2][3] In the world of epidemiological testing, those same laboratory informatics applications—such as laboratory information management systems (LIMS), laboratory information systems (LIS), and hospital information systems (HIS)—provide similar value.

Pandemic response realizes benefits through crisis and risk management systems, syndromic surveillance systems, and medical diagnostic tools. As Norwegian researchers Wilson and Jumbert note about humanitarian technologies and pandemics, "collecting information is central to the implementation of an efficient response, including situational information, needs assessment, and operational information."[4] At the response's core is the valuable reporting of public health data (discussed in the next section). As such, those labs and healthcare systems performing disease testing see numerous benefits in adopting and applying informatics solutions to their workflow: improved operations and positive contributions to disease reporting. If those informatics solutions are cloud-based and mobile-friendly, those labs and healthcare systems may see additional benefits such as being able to test people anywhere, making testing more flexible and rapid as a result.[5][6]

However, just purchasing a random laboratory informatics solution and putting it to use is no guarantee towards realizing the technology's actual benefits. Careful consideration, discussion, training, and policy adjustment are required to get the most of any new system. It would be beyond the scope of this guide to offer complete advice on acquiring and implementing laboratory informatics solutions. That information can be found in the Association of Public Health Laboratories' Laboratory Information Systems Project Management: A Guidebook for International Implementations or Joe Liscouski's A Guide for Management: Successfully Applying Laboratory Systems to Your Organization's Work. What follows instead are considerations to make when selecting a solution to assist your organization with COVID-19 (and other types of disease) testing workflows.

4.1.1 Does the system provide a flexible provider portal?

What types of providers are ordering COVID-19 tests? From surgeons ordering for pre-operation procedures and emergency room physicians for ER patients, to pathology groups and home health care or assisted living centers ordering for their patients, a wide variety of provider types exist. Those provider types and their special needs should be addressed. For example, physicians of record for home health care clients may not only require support for digital signatures in order entry, but additional verbal authorization of the test may also be required. The system should have a means for verifying that these order entry components are entered by the provider.

Healthcare facilities may also require additional flexibility for portal account creation and use. For example, they may find it useful to have portal log-ins tied to a facility rather than a specific physician. An entity may even wish to provide in-house staff or other related workers access to their COVID-19 test report via the portal, requiring role-based permissions to be built into the portal. Be sure to consider who needs access to what information and whether or not the LIMS or LIS can securely meet those needs.

Some healthcare systems will require the order entry portion of the provider portal make disease-specific checks or require disease-specific patient symptoms to be entered as part of the order. In the case of COVID-19, a wide majority of healthcare settings are still requiring the patient to be indicating clinical and/or epidemiological evidence of SARS-CoV-2 infection before testing may begin. Does the system provide checks for testing requirements or, at a minimum, allow documentation of patient aspects such as body temperature, symptoms, travel history, and existing health conditions as part of order entry? This may be implemented through something as simple as comment boxes or through a more refined form with checkboxes and other input areas. These checkboxes and test requirements can further aid with automated triaging.[7]

4.1.2 Does the system allow for the flexible addition of users, providers, and patients?

Providers ordering COVID-19 tests may work at more than one facility, ordering tests at a hospital one day, and ordering tests as a physician of record for a patient in a home health care setting the next. Having one system account for the provider while maintaining the ability to select the location associated with a test order is incredibly useful. In addition, being able to view test orders and reports by location has utility. As such, the system should not only make it easy to add providers and other users, but also allow the assignment of locations to those providers. Of course, the system should also allow for more granular assignments of system roles to users. The system should also allow patients to be added to the system as entities.

4.1.3 Does the system allow for laboratory workflows sympathetic to COVID-19 and other types of respiratory illness testing?

Pre-registration For purposes of both federal reporting and for more rapid reimbursement, having a pre-registration system for patients being tested may prove useful in COVID-19 workflow. A clear preregistration process should capture critical patient and facility information such as name, data of birth, gender, race, ethnicity, demographics, ordering physician or attending health care provider (if applicable), the facility's National Provider Identifier (NPI), and patient insurance information (if insured). Additionally, any national reporting questions should be addressed. For example, in the U.S. federal reporting wants labs to capture whether or not it's the patient's first test, if the patient lives in a congregate care setting, if they are a healthcare worker, and if they are pregnant.

Sample reception and tracking

Sample reception should support single-sample orders as well as sample lots. The system should also allow for multiple sample types to be added. For COVID-19, this has typically involved nasopharyngeal swabs in a sterile viral transport container. However, other sample types such as sputum, blood, or saliva—and other container types such as a sterile container with saline, a sterile dry collection cup, or blood collection tubes—should also be supported. Sometimes samples won't be available at the same time the test order arrives because sampling needs to be scheduled. This requires scheduling of patients to provide samples in intervals of time. Does the informatics system provide a means for providers and laboratory personnel to schedule sample collection associated with test orders? Can it send appointment reminders to scheduled patients, and can it send alerts if the patient doesn't arrive, completes sampling procedures, or views their patient results? The system should also be able to carefully track sample status throughout the workflow. As many COVID-19 testing labs will be dealing with hundreds or even thousands of samples, that tracking should optimally be queue-based, ensuring that no sample leaves a specific queue until it is loaded, tested, and/or reported.[5]

Order and sample management

Viewing and managing test orders specific to COVID-19 and other illnesses should be painless. The system should make it clear in what workflow step a requested test sample is located, from received but not processed, to in-analysis, in-retest, or requiring results approval. If tests for multiple diseases are ordered, the system should allow users to filter tests and related samples by specific test type, such as "SARS-CoV-2 rRT-PCR," or by test result (e.g., "Negative" or "Positive") or testing location (e.g., molecular pathology, serology, "Lab 2-B"). The system should also have the flexibility to show which analyst or instrument is assigned. In the case of retesting, the informatics solution should be able to support testing of both the original sample analysis and one or more associated retests at the same time.[5]

Workflow or "batch" management

Laboratories have their own workflows, and the informatics system they use should be flexible enough to allow users to manage the various steps or "batches" in the workflow. The lab may require a few simple preparation and analysis steps, or it may require a more complex, specific set of steps. This requires system functionality that can readily support the workflow. For example, can specific instruments be assigned to a workflow step? Can the system automatically add quality control (QC) or duplicate samples to a step? Can they be added manually? Despite slightly relaxed quality control frequencies by professional groups such as the College of American Pathologists during the COVID-19 pandemic, they still require quality control tests as described on COVID-19 test kit package inserts.[8]

An example laboratory workflow for molecular detection using one-step real-time reverse transcription PCR (rRT-PCR) of SARS-CoV-2 in one or more samples might look something like this[9][10][11][12]:

  1. Prepare the batching for the ordered rRT-PCR tests, including who is involved, when it is scheduled, and any additional unique identifiers.
  2. Extract, purify, and assess the quality of nucleic acids from a complex biological sample.
  3. Prepare and assemble rRT-PCR components (including reverse transcriptase enzyme, primers, and nucleotides) and reactions to plates or tubes.
  4. Run the analysis using the appropriate quantification method.
  5. Review and take action on the analytical results.

Ensure the laboratory informatics solution developer can explain how that workflow can be further optimized and tracked within the informatics solution.

Results approval

As orders move through the various steps of a lab's workflow, approval processes may be required. With COVID-19 diagnoses in particular, taking appropriate steps to limit the number of false-negative test results is vital[13], requiring careful results review and approval processes. Laboratory analysts may approve the samples through the initial workflow steps, or those steps may be automated. Eventually, however, the analytical steps are completed, and results ready for review.

Depending on the tests being run, the initial default value for a test that hasn't been run should be configurable in the system, either as a "negative" result or an empty or null value. Upon completion of the analysis, the system then should make it abundantly clear which samples in a batch are within and out of test limits, as well as sufficiently easy to manage approval of results. Ideally, tested samples that are within limits will still show the initial default value or, if the initial default was null, show an appropriate value such as "negative." Results that are out of limit should not only show a "positive" or other appropriate result state, but also color coding, flags, or other visual cues that make the outlier status of the sample clear to the analyst.

Finally, can the system handle reflex testing automatically when results are produced? For example, the lab may want a presumptive positive for COVID-19 to trigger the system to automatically add confirmation tests to the test queue for the associated patient. The correct people will also need to be notified of such reflex test creation in the system.

4.1.4 Does the system allow for interfacing with most instruments currently used for testing for COVID-19?

Instrument interfaces (discussed later in this chapter) are typically a non-trivial monetary investment for laboratories[14] as the developer has to take into account compliance requirements, the required analytical outcomes, and the instrument itself, as well as its available connections.[15] Yet a laboratory informatics vendor with experience has likely already set up interfaces to the instruments used in testing COVID-19 and other respiratory illnesses. RT-PCR systems like Hologic's Panther Fusion[16] and Abbot's RealTime m2000[17] represent a few of the systems being used to test for COVID-19 right now. Is the laboratory informatics system able to interface with these and other lab-based and point-of-care (POC) instruments you may require, at a reasonable cost? If so, also ensure the ease of assigning those instruments to specific tests or samples in the system. You should also be able to document well numbers for the analysis, as well as later view which samples are associated with a particular instrument. (In some cases, an instrument may be solely allocated to one specific test type.)

4.1.5 Does the system allow for versatile viewing and reporting of COVID-19 results?

Already mentioned was the process of results approval and the importance of being able to clearly view those results both within and out of test limits. Of course, this information has to be reported for internal and external purposes. Internally, the laboratory or healthcare entity using the informatics system will want to understand their test volume and associated details. If there's any chance the information can be used internally for medical research insights, data mining tools may also be a welcome addition to the system.[7] Additionally, a laboratory results report for SARS-CoV-2 infection will also have to be distributed to the local or state health department along with a case report. Externally, ordering physicians and other external customers—including patients—will require clear and timely results in the form of a report. How does the laboratory informatics solution help with these and other reporting requirements? Can it assist with any external electronic reporting requirements (such as those with the Centers for Medicare & Medicaid Services) you may have?

The system's reporting tools should be configurable to the lab's needs. The reporting itself should provide fields for the addition of comments and consultation notes from the lab and the physician, as the stakeholders need to give clinical and diagnostic guidance based on not only the results but also critical comments. In some cases, a lab or healthcare system may require the addition of comments at different stages of reporting. Perhaps an initial results report is created by the lab and sent to the provider via the provider portal, but a pathologist needs to review the report and add additional commentary concerning future treatment or concerns about the test results. This requires the system be flexible enough to allow additional steps before a report is finalized. Whether or not the system is capable of automating the reporting process may also be worthy of consideration.[7]

Finally, some solutions may include a disease- or test-specific dashboard that can show all samples related to a test, any positives, any negatives, pending results, tests per day, etc. Having this information available in one location can help facilitate reporting to government entities (e.g., reporting statistics to FEMA during emergencies[18] While not strictly necessary, ensure the solution can fulfill your needs with displaying real-time and near-time information to better support rapid decision making.

4.2 Laboratory informatics and reporting requirements

Before we can talk about the details of COVID-19 reporting, we first must briefly discuss the science of epidemiology. The CDC defines epidemiology as "the method used to find the causes of health outcomes and diseases in populations."[19] As we'll soon learn, finding those causes depends on quality data and reporting.

Epidemiology can broadly be split into two categories: descriptive epidemiology and analytical epidemiology. Descriptive epidemiology involves studies and other activities 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.[20] Analytical epidemiology allows for the testing of those hypotheses using both experimental and observational studies, as well as control groups. Similarly, the collection and use of quality experimental and observational data is vital for proving or disproving hypotheses.[21] In both cases, proper reporting of public health data is critical to the success of epidemiologists' response to outbreaks and pandemics, as well as the credibility of their research.[22][23][24] This includes point-of-care and at-home testing results, which are at times more difficult to capture.[24]

The proper reporting of COVID-19 case data is no exception. In the United States, the Centers for Disease Control and Prevention (CDC) has taken a standardized approach to collecting reports on individuals with "lab-confirmed and probable cases of COVID-19,"[25][26] noting that as of April 21, 2021, all state, territorial, and tribal jurisdictions were onboard with electronic laboratory reporting to the CDC.[27] Their COVID-19 Surveillance Worksheet (formerly 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, clinical diagnosis, treatment procedures, and vaccination history. Currently, the CDC is asking healthcare providers and laboratories that are operating as testing sites to "report data for all diagnostic and screening testing completed, which includes molecular, antigen, and antibody testing, for each individual tested" on a daily basis, "within 24 hours of test completion."[28] Local, state, tribal, and territorial public health departments are then asked to submit case reports etc. to the CDC. Electronic reporting using the CDC's system is preferred, but they have a protocol for those areas unable to submit electronically. Recognizing the disparate reporting mechanisms across various state health departments and the problems this causes, particularly during an epidemic, funding efforts are under way to assist the CDC—as well as state, local, and tribal governments—better report disease information through a modernized, centralized public health data management platform.[24][29]

Elsewhere, Canada has similar reporting expectations to the U.S. CDC, with their own case report form and electronic data submission process through the Public Health Agency of Canada.[30] And in the European Union, member countries and the U.K. are asked to report through the Early Warning and Response System, with "additional enhanced surveillance ... established through The European Surveillance System - TESSy."[31]

4.2.1 ICD, CPT, and HCPCS coding


Related are any test reporting and billing requirements in labs and medical facilities. The International Statistical Classification of Diseases and Related Health Problems (ICD) is a commonly used 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. This guide provides basic information about these codes (which should not be considered legally binding advice); however, see the referenced material (and following citations) for more details concerning those codes[32][33][34][35][36]:

  • The CPT code 87635 has the long descriptor of "Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique." The American Medical Association's CPT Assistant fact sheet for SARS-CoV-2 reporting proves useful in supplying assistance on how and when to apply this CPT code in reporting.
  • Since the pandemic has progressed, numerous other CPT codes have become available. This includes a series of parent and child codes for antibody testing, neutralizing antibody screens, antigen testing, and vaccination. Resources for guidance concerning these codes include the American Medical Association and the American Society of Clinical Oncology (PDF).
  • The U.S. government-adopted ICD-10-CM—an authorized version of WHO's ICD-10[37]—has been updated by the CDC and the National Center for Healthcare Statistics. It includes not only codes for conditions associated with COVID-19, but also codes for exposure, screening, and vaccination. The principal diagnosis code "U07.1, COVID-19" is sequenced first for a confirmed COVID-19 diagnosis, followed by any appropriate codes for associated manifestations (though there is an obstetrics exception). CMS's coding guidelines, as well as American Medical Association guidance, may prove useful in choosing the correct codes. The American Society of Clinical Oncology (PDF) is also maintaining a document with ICD-10-CM information.
  • Since the pandemic started, new HCPCS codes have been released by the Centers for Medicare & Medicaid Services (CMS). These are to be used solely for Medicare claims. The American Society of Clinical Oncology (PDF) is maintaining a helpful document with that information.

Laboratories analyzing specimens for SARS-CoV-2 must be equipped to implement and handle analytical testing and test orders using the new test codes. However, they also must be able to quickly and accurately transfer vital case information to the appropriate health authority. This may include using other types of codes such as Logical Observation Identifiers Names and Codes (LOINC) and SNOMED-CT codes, which are briefly discussed in the next subsection.

4.2.2 Reporting to local and regional health departments

Given the valuable nature of case reports during an epidemic[22][23], health care providers, facilities, and laboratories are being held responsible for sending case data to their local and regional health departments. That information then feeds up to the state-level health department, which then makes its way to the national-level entity responsible for handling epidemiology (in the case of the U.S., the CDC). Significant decisions are typically based on that data. For example, the U.S. CDC has been conducting seroprevalance (determination of the "percentages of people who were previously infected with SARS-CoV-2") surveys of various regions of the United States.[38] The insights and decisions the CDC makes depends on cooperation and proper reporting by state and local health departments.

However, acquiring standardized data at the national level can still be challenging. In the case of the U.S., general disease reporting requirements vary from state to state, with many states encouraging full electronic laboratory reporting (ELR), while some still encourage faxed or emailed reports. Add in the urgency and confusion associated with a pandemic, and COVID-19 reporting requirements prove to vary just as much. Some states' health departments have taken a proactive approach to reporting. For example, Iowa's Department of Public Health has issued several mandatory COVID-19 reporting orders meant to supplement existing reporting rules, including an order requiring all Iowa health care providers and public, private, and hospital laboratories "to immediately report all positive and negative Coronavirus Disease 2019 (COVID-19) testing results to the department."[39] Other states have not been as clear on their reporting requirements, in some cases not having any guidance documents or clear information on their health department website for how providers, facilities, and labs should report COVID-19. In those cases, the presumption is that most labs have contacted the health department for advice or are reporting COVID-19 cases as immediately reportable, based upon the state's existing reporting requirements for immediately reportable diseases.

The CDC, however, maintains a page concerning how to report COVID-19 laboratory data. It's important to note their take on using standard terminology, which is based on their mapping tool LOINC In Vitro Diagnostic (LIVD) Test Code Mapping for SARS-CoV-2 Tests[28]:

This specification supports the use of standardized LOINC and SNOMED Clinical Terms (CT) codes to improve the accuracy of reporting tests for the SARS-CoV-2 virus. Using these harmonized LOINC and SNOMED-CT codes helps ensure that the same type of test is represented uniformly across the United States ... LOINC codes must be used to represent the “question” a test asks of a specimen (e.g., does this specimen have SARS-CoV-2 RNA?), and SNOMED-CT codes must be used to represent the diagnostic “answer” (e.g., what was detected?).

The CDC's Excel-based mapping tool lists the current (and previous) FDA EUAed diagnostic tests with codes for LOINC test order, LOINC test result, SNOMED-CT test description, SNOMED-CT specimen source, and Device Identifier. Ensure that your laboratory is using these LOINC and SNOMED-CT codes for reporting to your local and state health departments.

Table 1 addresses the reporting requirements for the United States' 50 states, while Table 2 covers U.S. territories. If clear reporting guidance specific to COVID-19 could be found, it was described. If no such guidance could be found, then the state's existing guidance and rules regarding disease reporting were referenced. In some cases, the state health departments don't clearly spell out whether a faxed or mailed report is required after immediately phoning in a report. In other cases, it's not clear if ELR—though it exists—is an acceptable form of reporting COVID-19 cases. This ambiguity is stated in the form of a "(?)" found next to the "Y" and "N" for electronic filing and faxing. In all cases, if there is any doubt about reporting requirements, call your local health department to confirm.

Table 1. U.S. state-based COVID-19 reporting requirements
State Electronic, including email? (Y/N) Fax? (Y/N) Forms for reporting Contact Additional details
Alabama Y N Novel Coronavirus Report Card Use the Report Card "to submit laboratory-confirmed (or pre-approved epidemiologically-linked) cases or deaths of Novel Coronavirus (COVID-19) to the Alabama Department of Public Health." (Though long-term care facilities and correctional facilities should used different forms.) "Performing 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.
Alaska Y Y Confidential Infectious Disease Report Form COVID Reporting Hotline: 1-877-469-8067
Urgent situation: 907-269-8000 or 800-478-0084 (after-hours)
"Providers must report laboratory-confirmed cases of COVID-19 to SOE via fax (907-563-7868) using the standard Infectious Disease report form or via electronic means. The reporting hotline has been discontinued." "All results (i.e., positive, negative, indeterminate, etc.) must be reported via either integration into existing electronic laboratory reporting (ELR) data feeds, submission of a standard format CSV via SFTP, or fax (907-563-7868). Please email Megan Tompkins ... to inform us about how your facility will report." (See Guidance for Coronavirus Disease 2019 (COVID-19) Testing in Alaska for more.)
Arizona Y N Sample ADHS CSV File
Sample ADHS Excel File
ELR: "Facilities performing laboratory tests for COVID-19 are required to report both positive and negative results for COVID-19 directly to ADHS pursuant to Executive Order 2021-14. Laboratory is defined in A.R.S. § 36-451(4). Facilities shall report using an electronic format, described below." Consult the laboratory information page for details of all reporting options.
Arkansas Y Y (?) Communicable Disease Reporting Form Phone: (501) 537-8969 or 1-800-554-5738 after-hours Arkansas Department of Health doesn't appear to have published any information about specific COVID-19 reporting requirements. As of September 2021, the DoH still hasn't updated its list of mandatory reportable diseases. The state is presumably treating "suspected or confirmed" COVID-19 cases as an immediately reportable event that "are to be reported immediately to the ADH." The language used on its reportable disease instructions suggests that a follow-up fax of the case report isn't required; however, call and confirm with the DoH. The only mention of ELR is a plain page labelled "Public Health Reporting." It would appear users can submit reports via this tool, though registration may be required if new to the tool.
California Y N (?) Confidential Morbidity Report Contact: Local health officers
CalREDIE: or (866) 866-1428
The DPH added COVID-19 to its Reportable Diseases and Conditions lists for health care providers and laboratories early in the pandemic. This health care provider document indicates that a "case or suspected case" of COVID-19 should be reported immediately by phone. The document makes no mention of requiring a follow-up fax or digital report by health care providers. The laboratory document indicates "[l]aboratories must report any initial findings as well as any subsequent findings. ”Any laboratories approved to test for SARS-CoV-2 must report all positive and non-positive (negative, indeterminate, and specimen unsatisfactory) test results from both antigen/molecular and antibody/serology tests for SARS-CoV-2." Laboratory findings are "are reportable to the local health officer of the health jurisdiction where the patient resides by telephone within one (1) hour ... from the time that the laboratory notifies the health care provider or other person authorized to receive the report." Labs are asked to also subsequently report results electronically (ELR) to the California Reportable Disease Information Exchange (CalREDIE) "within one working day of identification."
Colorado Y N None CEDRS:
"All test results (e.g., positive, negative, and inconclusive) for rapid point-of-care COVID-19 tests must be reported to public health" officials by providers. Additionally, "[a]ll positive, negative, and inconclusive SARS-CoV-2 test results must be reported electronically by laboratories." The disease reporting form and fax methods should not be used. A list of required reporting components and descriptions of digital reporting options are available on the state's COVID-19 reporting page.
Connecticut Y Y 2019 Novel Coronavirus (COVID-19) Case Report Form
Reportable Laboratory Findings, Form OL-15C
Fax: (860) 629-6962
Presumably, laboratories are reporting COVID-19 as is required for any communicable disease. This has traditionally been done using Form OL-15C sent through mail or fax, as well as ELR, which appears to be the preferred method. As for other healthcare providers, per the DPH's COVID-19 response portal: "Providers can now submit a COVID-19 case report online. This is the preferred way to submit COVID-19 case reports."
Delaware Y N None Call: 1-888-295-5156
"The Department of Health and Social Service’s March 10, 2020 order requiring all labs to immediately report all tests and all results to the Division of Public Health (DPH) remains in effect. All COVID results, positive AND negative are reportable." "All COVID-19 test results from any laboratory must be reported to DPH via the

Delaware Electronic Reporting Surveillance System (DERSS). Providers must confirm with their designated laboratories that they have the ability to transmit results to DERSS through approved methods." Review the provider lab reporting requirements for further details.

District of Columbia Y N Notifiable Disease and Condition Case Report Form ELR:
Reporting questions:
"... healthcare providers must report negative and positive test results for all COVID-19 diagnostic and serologic testing, including point-of-care testing. Reports should be submitted electronically using DC Reporting and Surveillance Center (DCRC), our online reporting system." "Laboratories are recommended to submit COVID-19 results via Electronic Lab Reporting. Please email to initiate the process. Hospitals, skilled nursing facilities, and assisted living facilities should report cases in patients/residents via daily line lists to DC Health."
Florida Y N None ELR: "Mandatory reporting requirements are outlined by Florida Department of Health Executive Order 20-013, section 381.0031, Florida Statutes, and Florida Administrative Code Chapter 64D-3, and state all health care practitioners, laboratories and facilities, including long-term care facilities, must report both negative and positive COVID-19 test results, including point-of-care rapid test results, within 24 hours of the result being known." As of September 2021, the documentation found on appears outdated, however, as the links to the report portal that are indicated are broken. A site,, was found, and it appears to be the current report portal for health care providers and facilities.
Georgia Y Y Notifiable Disease Report Form Fax: Based on District Health Office
Call: 1-866-782-4584
Georgia lists COVID-19 as an immediately reportable disease condition. "All Georgia physicians, laboratories, and other health care providers" are encouraged to call their District Health Office or the main number. The state is also accepting COVID-19 reports through its SendSS online application.
Hawaii Y N (?) Human Infection with 2019 Novel Coronavirus Short Form Fax: (808) 586-4595
Per the Director of Health: "Pursuant to section 325-2, Hawaii Revised Statutes, every physician or health care professional having a client affected by or suspected of being affected by COVID-19 (SARS-CoV-2) and every laboratory director having laboratory data regarding an individual affected by or suspected of being affected by COVID-19 (SARS-CoV-2) shall report the incidence or suspected incidence of COVID-19 (SARS-CoV-2) to the Department of Health in the manner specified by the Department of Health. At this time, all test results shall be reported via the electronic laboratory reporting system." That system is presumed to be this portal. Faxing may no longer be an option; confirm with the Department of Health.
Idaho N Y No standardized COVID-19 reporting form Phone: (208) 334-5939
Fax: (208) 332-7307
The Idaho Department of Health and Welfare doesn't appear to have published any information about COVID-19 reporting requirements. As of September 2021, the state has not added COVID-19 to its mandatory reportable diseases list. They simply state that "Labs report their test results to the state, and the number of tests done and the number of people who test positive are posted on this website each day." Presumably this means that labs should be following the state's reportable diseases protocol for reporting "within one working day of identification or suspicion" using phone or fax. No standardized reporting form appears to exist. It's not clear if ELR is being used to report COVID-19 cases.
Illinois Y Y IDPH Coronavirus Novel 2019 Case Report Form Fax: Based on Local Health Department
"All providers and testing sites must report to Public Health all individuals tested for COVID-19, in accordance with the Illinois Control of Communicable Diseases Code (77 Ill. Adm. Code 690.200(a)(5)). Mandated reporters, such as health care providers, hospitals and laboratories, by law must report probable or confirmed cases of COVID-19 electronically through Illinois’ National Electronic Disease Surveillance System (I-NEDSS) within 24 hours. If they do not have access to I-NEDSS, they can report by mail, telephone or fax to the local health department ... or, if no local health department is available, to the Illinois Department of Public Health Division of Infectious Diseases at 217-785-7165, TTY (hearing impaired use only) 800-547-0466."
Indiana Y Y Confidential Report of Communicable Diseases ELR: (317) 233-7684 or
Fax: (317) 233-7747
"CDC requires every COVID-19 testing site to report every diagnostic and screening test performed to detect SARS-CoV-2 or to diagnose a possible case of COVID-19 (e.g., molecular, antigen, antibody) to the appropriate state or local public health department, based on the individual’s residence. All testing sites must report diagnostics and screening tests within 24 hours of test completion to the appropriate state or local public health department." Their guidance suggest three reporting methods: ELR, REDCap, and Fax. Examine the guidance for further information.
Iowa Y N None ELR: Jill Newland "All Iowa health care providers and public, private, and hospital laboratories are required to immediately report all positive and negative SARS-CoV-2 testing results to the department. Immediate reporting is defined as reporting within one day of the test being performed, a standard utilized by the department since its initial March 19, 2020, Mandatory Reporting Order. Reports must be made electronically through the Iowa Disease Surveillance System (IDSS) or other electronic means as directed by the department."
Kansas Y N (?) Kansas Reportable Disease Portal Phone: (877) 427-7317
Fax: (877) 427-7318
"Report antigen or PCR point of care results, positive and negative, directly to KDHE via the Kansas Reportable Disease Portal within 24 hours ... For facilities that do not perform point of care antigen or PCR testing, for antigen or PCR testing done through a reference laboratory or in-hospital laboratory, your facility does not need to report result to KDHE. The laboratory conducting the SARS-CoV-2 test is required to report results to KDHE." Faxing forms appears to be discouraged: "Clinics/hospital systems: if possible, please modify electronic health record systems to cease sending notifiable disease forms to KDHE via email and fax. If your facility uses Epic for its electronic medical records, you may be able to submit reports to KDHE automatically."
Kentucky Y N None Email: "If you are a healthcare organization resulting any type of COVID-19 test, you are required to report both positive and negative results to the Kentucky Department for Public Health (KDPH) ... If you are resulting labs at your facility, KDPH requires you to report results through Kentucky Health Information Exchange (KHIE), either electronically through an interface connection or by manually entering results. If you are not currently electronically connected to KHIE, you must manually report these results through KHIE's Direct Data Entry (Lab) feature located in the ePartnerViewer ... You are required to report all positive results within 24 hours of resulting ... You are required to report all negative results within 7 days of resulting."
Louisiana Y N None Phone: (504) 568-8295
"All facilities performing testing for COVID-19/SARS-CoV-2 are required to report all COVID-19/SARS-CoV-2 results to LDH. This includes rapid testing, point-of-care testing, antibody testing, or any other testing performed for COVID-19. Electronic laboratory reporting (ELR) in HL7 or CSV format is the preferred mechanism for reporting results ... Note: COVID-19 test results sent via ELR should include all results of testing (i.e., positive, negative, indeterminate, etc.)." Also, if you do not have ELR set up or for some reason can't report electronically: "The ELR team will work with you to set up ELR or an alternative reporting method."
Maine Y N (?) None Phone: 800-821-5821
A February 2021 update to the state's Control of Notifiable Conditions and Notifiable Conditions List mandates that health care providers and labs must report COVID-19 test results. It mandates that "[l]aboratory reporting must be done electronically through HL7 messaging as specified in this subsection. Electronic reporting required for laboratories is in addition to other reporting requirements specified in this rule." Consult the "New Rules for the Control of Notifiable Conditions" PDF on the disease reporting page for details. It appears COVID-19 should no longer be reported by fax.
Maryland Y N (?) Confidential Report: Laboratory Evidence of Certain Communicable Diseases Contact: Local health department The only reporting requirement to be found are in a PDF, item No. MDH 2020-10-01-01, which largely addresses point-of-care testing. Presumably this extends to other types of testing, but it's not clear what other types of testing. It mentions that "[p]ositive, negative, and inconclusive point of care test results shall be reported." The document goes on to explain that electronic reporting is preferred, especially for those labs that are already set up to so do so. Some other electronic format like a CSV file is next preferred, and then, "[i]f the results cannot be sent by HL-7 format or another approved electronic format, they must be immediately submitted to the appropriate local health officer in a manner designated by MDH."
Massachusetts N Y No standardized COVID-19 reporting form Contact: Local health departments
MDPH phone: (617) 983-6800
MDPH fax: (617) 983-6813
The State of Massachusetts doesn't appear to have published any collection of information about specific COVID-19 reporting requirements. The state is presumably treating COVID-19 "suspected and confirmed cases" as an immediately reportable event that "should be reported to your local board of health" by phone, or if unavailable, to the Massachusetts Department of Public Health by phone or fax. The MDPH disease reporting web page makes no mention of ELR.
Michigan Y Y No standardized COVID-19 reporting form MDSS: Support contacts
Contact: Local health department list in reporting guide
The Michigan Department of Health & Human Services has updated its Health Care Professional's Guide to Disease Reporting in Michigan to include detections of SARS-CoV-2. They note that "if the agent is identified by clinical or laboratory diagnosis," the detection (by both healthcare providers and laboratories) "must be reported to the Michigan Disease Surveillance System (MDSS) or local health department within 24 hours." As for how: "Mandatory reporting of communicable diseases can (and, whenever possible, should) be accomplished via the MDSS. The MDSS is a web-based communicable disease reporting system developed for the state of Michigan." If unable to electronically report, contact the local health department using the directory in the disease reporting guide.
Minnesota Y Y COVID-19 Case Report Form Fax: (651) 201-5743
Phone: (651) 201-5414 or (877) 676-5414
"The Minnesota Department of Health (MDH) is requiring all mandated reporters to report any cases and deaths due to SARS-CoV-2 to MDH within one working day." This includes health care facilities, medical laboratories, and in special cases veterinary laboratories. Case report forms can be faxed or case reports submitted by phone. On a separate page discussing laboratories, the DoH further discusses ELR. Read that for more details.
Mississippi Y (?) N Reportable Diseases and Conditions form Phone: (601) 576-7725 or 1-800-556-0003; for weekends, holidays and after 5pm: (601) 576-7400; Email: The Mississippi State Department of Health states: "All COVID-19 results must be reported to the Mississippi State Department of Health at this time." However, it gives no further guidance specifically for commercial laboratories or health care providers testing for SARS-CoV-2. Presumably the MSDH is considering COVID-19 a Class 1A disease, required to be "reported directly to the Department of Health by telephone within 24 hours of first knowledge or suspicion." The MSDH also has an online disease reporting tool (account required); however, it's not clear if it is equipped to received COVID-19 reports.
Missouri Y Y sFTP Excel template
Disease Case Report form
sFTP: (573) 526-5271
Fax: (573) 751-6417
The Missouri Department of Health and Senior Services has officially added COVID-19 to its list of immediately reportable conditions, including a waiver "to require that all positive and negative results for COVID-19 are sent directly to DHSS. Now, all laboratories must report directly to DHSS." They add that "[l]aboratories are encouraged to report via electronic means." Alternatively, labs may also submit a report to the Bureau of Reportable Disease Informatics (BRDI) via fax. "[M]edical providers (non-laboratories) also have an obligation to submit disease case reports (form CD-1) to DHSS. However, under the current suspension, providers do not have to report negative results if those results are being reported by an outside lab. Providers are expected to submit a case report on any non-negative results as the additional information on the case report is required for public health intervention."
Montana N Y (?) No standardized COVID-19 reporting form Contact: Local health department
DPHHS phone: (406) 444-0273
The Montana Department of Public Health and Human Services doesn't appear to have published any information about specific COVID-19 reporting requirements. The state is presumably treating COVID-19 like its other reportable diseases: "whether suspected or confirmed" the case "must be reported immediately to your local health jurisdiction as required by the Administrative Rules of Montana." If the local public health jurisdiction is unavailable, a call can be placed to the MDPHHS. It is not clear if laboratories should report both positive and negative results, though news reports have shown that the DPHHS is reporting both positive and negatives. The disease reporting web page makes no mention of ELR.
Nebraska N N Health Care Provider Confidential Communication form
Laboratory Summary of Reportable Diseases, Poisonings and Organisms
Phone: Based on county The Nebraska Department of Health and Human Services provides little in the way of specific guidance for reporting COVID-19. They simply state: "Any patient (+) for COVID-19 virus should be immediately reported to local/state public health office." They define "immediate notification" as "required to call by telephone to a live public health surveillance official within 24 hours of detection." This apparently includes providers currently on ELR. Labs and healthcare providers should verify if any additional reporting (fax, ELR) is required. As the pandemic has progressed, reporting transparency and requirements have also changed, becoming more controversial; contact your local health department for the latest requirements.
Nevada N Y Confidential Disease Reporting Form Contact: Local health department list in reporting form Nevada DHHS guidance states "all in-state and out-of-state laboratories who are processing and testing samples from Nevada residents are required under severe penalties to report all COVID-19 test results to the Division of Public and Behavioral Health within 24 hours from analysis." Its guidance appears to suggest a phone call for such notification. According to the state's disease reporting form, this phone call should be done in addition to faxing a report. "All cases, suspect cases, and carriers

must be reported within 24 hours." It's not clear if ELR is being accepted for COVID-19 reporting.

New Hampshire N Y COVID-19 Case Report Form Phone: (603) 271-4496
Fax: (603) 271-0545
Health care providers and laboratories should immediately report suspect and confirmed cases of COVID-19 to the New Hampshire Department of Health and Human Services. It seems likely the DPHHS prefers both a phone call and a faxed report, though it's not explicitly stated. The case should likely be "reported within 24 hours of diagnosis or suspicion of diagnosis." The NHDHHS disease reporting web page makes no mention of ELR. An online test result reporting form is available, per the state's General Provider COVID-19 Resources page.
New Jersey Y N (?) No standardized COVID-19 reporting form ELR: See quick-start guide
Local health departments
"[T]he New Jersey Domestic Security Preparedness Task Force hereby directs that commercial laboratories operating in New Jersey report all COVID-19 test results to the New Jersey Department of Health beginning March 23, 2020. The results of all COVID-19 tests performed before this date shall be included in the initial report. Subsequently, results shall be sent daily, and included results not previously reported. Information shall be transmitted no later than 8:00 p.m. each day through the Department of Health’s CDRSS platform. Specific data reported shall include positive, negative, and inconclusive test results. This directive shall supplement, not supplant, any other existing reporting requirements." From that statement, it's not clear if laboratories should also be immediately phoning their results to the health department in addition to ELR over CDRSS.
New Mexico N Y (?) Notifiable Condition Report Form Phone: (505) 827-0006
Fax: (505) 827-0013
The New Mexico Department of Health doesn't appear to have published any information about specific COVID-19 reporting requirements. The DoH is presumably treating "confirmed or suspected" COVID-19 cases as an immediately reportable event that "require immediate reporting by telephone to Epidemiology and Response Division." It's not clear if a faxed report is also required. The DoH disease reporting web page makes no mention of ELR.
New York Y N Confidential Case Report - DOH-389
Universal Reporting Form - PD-16
Contact: Local health departments
The New York Department of Health states: "Positive results must be immediately reported to the local Department of Health by the laboratory performing the test, per established guidance, and all test results should be reported by the laboratories into New York State Department of Health’s Electronic Clinical Laboratory Reporting System (ECLRS) four times a day." The established guidance appears to be found in the state's updated reporting instructions, which now includes COVID-19 as a disease that "should be reported immediately to local health departments by phone followed by submission of the confidential case report form (DOH-389). In NYC use case report form PD-16." This means "within 24 hours of diagnosis." The instructions indicate case reports should be mailed. Both health care facilities and laboratories should report.
North Carolina Y Y COVID-19 Confidential Communicable Disease Report Contact: Local health departments
Fax: (919) 733-0490
Per NCDHHS's clinical diagnostic laboratory guidance: "each person in charge of a laboratory providing diagnostic service in this State and any other health care provider licensed in this State that provides diagnostic service [is required] to report the results of all COVID-19 testing to the Department of Health and Human Services." An electronic reporting process appears to have been added later in 2020.
Ohio Y Y Ohio Confidential Reportable Disease form Contact: Local health districts
In March 2020, the Ohio Department of Health ordered "confirmed cases of COVID-19 be reported immediately as a Class A disease pursuant to Ohio Adm. Code 3701-3-02(A) to the local health district in which the person resides (or the local health district wherein the person is being medically evaluated if the person's residence is unknown or not in Ohio)." Physicians, medical care facilities, and laboratories are encouraged to report positive cases. Per the state's communicable disease requirements, Class A diseases should be reported immediately by phone, with a follow-up HEA 3334 Ohio Confidential Reportable Disease form. That requirements doc also states "follow-up reports can also be made electronically through direct entry into the Ohio Disease Reporting System (ODRS) or through Electronic Laboratory Reporting."
Oklahoma Y Y Reportable Disease Card for Healthcare Providers (Blue Card)
Reportable Disease Card for Laboratories (Yellow Card)
Phone: (405) 271-4060
Fax: (405) 271-6680
According the DoH's COVID-19 reporting page, COVID-19 cases should optimally be reported by some digital means (HL7, manually entered CSV, exported CSV from information system). The DoH is presumably treating "laboratory results indicating" (i.e., "upon suspicion, diagnosis, or positive test") COVID-19 as an immediately reportable event. This also holds true for healthcare providers. The Public Health Investigation and Disease Detection of Oklahoma (PHIDDO) system is apparently the preferred method.
Oregon Y Y COVID-19 Report Form Contact: Local public health authority
Fax: (971) 673-1100
Oregon COVID-19 Reporting Portal or ELR: (971) 673-1111
"The Oregon Health Authority (OHA), Public Health Division, is temporarily adopting OAR 333-017-0800 and OAR 333-018-900, which add a definition of COVID-19 and adds COVID-19 to the list of diseases reportable to public health authorities within 24 hours. Positive test results for COVID-19 must be reported within 24 hours and negative COVID-19 results within one working day." "Both medical laboratories and health care providers are required to report COVID-19 test results to the state and local public health authorities." According to state law, reports should be initially submitted by phone call, with a follow-up report either through the Oregon COVID-19 Reporting Portal or a fax. ELR is also an option.
Pennsylvania Y N No standardized COVID-19 reporting form (use PA-NEDDS) PA-NEDSS: 1-877-724-3258 From the Pennsylvania Department of Health: "All entities conducting testing to identify SARS-CoV-2, the virus that causes COVID-19, are required to report positive, inconclusive/indeterminate, and negative results to PA-NEDSS within 24 hours of test completion. PA-NEDSS is a secure, web-based system used in Pennsylvania for disease reporting and surveillance."
Rhode Island Y Y None Phone: (401) 222-2577 or (401) 276-8046 after hours
Fax: (401) 222-2488
Per the Rhode Island Department of Health: "For reporting positive results from testing you have ordered and sent out through a laboratory system, report positive results only." You may report by secure email or fax. "For reporting point-of-care and rapid test results performed at your site, report all positive and negative results." Note the specific email addresses depending on the test type. ELR is not mentioned.
South Carolina Y Y (?) No standardized COVID-19 reporting form Contact: Local public health office
ELR: or
Per the South Carolina Department of Health and Environmental Control: "Please notify DHEC of positive results. COVID-19 cases and deaths are urgently reportable per the South Carolina List of Reportable Conditions. They must be reported by phone within 24 hours to the appropriate regional health department." Supplemental guidance: "Positive and negative test results for COVID-19 must be reported to DHEC urgently within 24 hours by all entities performing testing, including testing at point-of-care or at-home specimen collections processed by laboratories." That guidance adds: "Facilities that are not already submitting results via Electronic Lab Reporting (ELR) or DHEC's secure reporting portal (SCIONx) should contact to inquire about ELR submission, or to inquire about other reporting options."
South Dakota Y Y South Dakota Confidential Disease Report (online/HTML) Phone: (605) 773-3737 or 800-592-1861
Fax: (605) 773-5509
"SD-DOH would like to remind medical providers, hospitals, and laboratories that cases of COVID-19, caused by the SARS-CoV-2 virus, are considered immediately reportable in South Dakota (under Coronavirus Respiratory syndromes)." The SD-DOH and the state laws don't make clear what reporting method is best for Category I diseases, only that they should be reported immediately. Under "how to report," they list, in order, online reporting, phone, fax, and mail. The SD-DOH disease reporting web page makes no mention of ELR.
Tennessee Y Y PH-1600 Case Report Form Fax: (615) 741-3857
Phone: (615) 741-7247
"Healthcare providers who receive positive COVID-19 test results on their patients or patients in their facility [should report]." "Laboratories performing COVID-19 testing should be reporting these results electronically via ELR or our emergency spreadsheet template. If you are a laboratory that needs to report via one of these methods, please email" These entities "should report within 24 hours of receiving a COVID-19 diagnosis, positive lab report on a patient, and/or becoming aware of a suspected or confirmed COVID-19 associated death." Please submit a case report by filling out the PH-1600 form on all NAAT, PCR and antigen positive COVID-19 test results from facility or commercial labs (this includes any NAAT, PCR or antigen positive patients tested via Point of Care testing); you do not need to submit further information on a lab result from the TDH Public Health Laboratory." The Tennessee Department of Health lists two reporting options: faxing the PH-1600 form and positive lab report or sending it electronically (via Morbidity Report or ELR).
Texas Y Y Infectious Disease Report (Single case)
Infectious Disease Report (Multiple cases)
Contact: Local health department
"On July 29, 2021, Governor Greg Abbott ordered every public or private entity that is utilizing an FDA-approved test, including an emergency use authorization test, for human diagnostic purposes of COVID-19, shall continue to submit to DSHS, as well as to the local health department, daily reports of all test results." This includes positive, negative, and indeterminate results. "To comply with the Governor’s orders, DSHS is expediting an alternative method of accepting specific CSV formatted files for submitters who are unable to submit via HL7 format." ELR registration can be performed online.
Utah Y Y Utah Public Health Confidential Morbidity Report Fax: (801) 538-9923
Phone: 1-888-EPI-UTAH
The Utah Department of Health added COVID-19 to its reportable conditions in May 2020 for both manual and electronic reporters. "All test results are reportable. This includes positive/reactive, indeterminate, equivocal, and negative/non-reactive." "Electronic reporters must report laboratory results within 24 hours of finalization. Manual reporters must report immediately notifiable conditions within 24 hours of identification and standard notifiable conditions within three business days of identification." Details on ELR are limited, though an ELR guide for hospitals can be found here.
Vermont Y (?) Y No standardized COVID-19 reporting form Phone: (802) 863-7240
Fax: (802) 951-4061
ELR: (802) 651-1619 or
The Vermont Department of Health states: "All COVID-19 results (positive, negative, etc.) are required to be reported to the Vermont Department of Health within 24 hours of test report completion" Its April 2021 guidance adds: "The report shall be made by telephone, in writing, or electronically to the Department of Health, Epidemiology Program." Additional details can be found here.
Virginia Y N See portals linked below Contact: Local health department The VDH states: "All COVID-19 reports from clinicians or facilities based on point-of-care tests should be reported using the VDH Point-of-Care (POC) Portal, not the Confidential Morbidity Portal. For other reports not involving POC testing, healthcare providers should continue to report patients with suspected or confirmed COVID-19 through the Confidential Morbidity Portal." They add that "[a]ll COVID-19 test results should be reported to VDH within 24 hours."
Washington Y N None Contact: Local health jurisdiction The Washington State Department of Health has adopted several emergency rules to ensure reporting compliance. The DoH notes: "Facilities administering point-of-care (POC) testing for COVID-19 must report all their COVID-19 testing results to the Washington State Department of Health." (See here for more about POC reporting requirements.) "Washington State (under WAC 246-101) requires laboratories to report all COVID-19 results (including positive, negative, inconclusive; and other results based on State Health Officer Letters) to the LHJ of the patient's residence. ELR, national flat file, and electronic case reporting options are available for labs.
West Virginia N (?) Y 2019 Novel Coronavirus (COVID-19) Case Report Form Contact: Local health departments "Report suspect or confirmed cases immediately to the local health department by phone and follow up with written report." "Providers and LHDs should submit this report to the Division of Infectious Disease Epidemiology by fax at 304-558-8736 for all cases of COVID-19." It's not clear if ELR is an acceptable form of reporting COVID-19 cases.
Wisconsin Y Y Wisconsin COVID-19 Patient Information F-02700 Contact: [h Local health department]
"The state epidemiologist declared COVID-19 a Category I reportable disease per a memo issued on Feb. 4, 2020. Health care providers and laboratories must report confirmed or suspected cases to the Department of Health Services (DHS) within 24 hours of detection. To relieve the reporting burden, DHS waived the requirement (April 6 Memo) for notifying local health departments by telephone of suspected and confirmed cases as long as cases are reported to the Wisconsin Electronic Disease Surveillance System (WEDSS)." Additional rules apply. See "Reporting and surveillance guidance" here.
Wyoming N Y Confidential Disease Report form Phone: 1-888-996-9104
Fax: (307) 777-5573
"Providers and laboratories must report positive [SARS-CoV-2] laboratory tests from commercial reference laboratories to WDH by faxing copies of the laboratory report form to 307-777-5573." According to Wyoming's Reportable Diseases and Conditions List, this faxed report would be in addition to immediate notification by phone. Additionally, "[h]ospital and reference labs with ELR capacity must report positive and negative results," as well as viral detection and serology results. According to that document, COVID-19 isn't a disease preferred for ELR. Confirm with the health department.
Table 2. U.S. territory-based COVID-19 reporting requirements
Territory Electronic, including email? (Y/N) Fax? (Y/N) Forms for reporting Contact Additional details
American Samoa N N (?) Can't locate the AMS COVID-19 Investigation Form Contact: Facebook page
Phone: (684) 633-5871 or (684) 633-5872
According to American Samoa's report Territory of American Samoa's Response and Action Plan to Combat the Cornoavirus Pandemic, resources for testing are unfortunately thin. It makes mention that the American Samoa Department of Health should be notified "immediately of probable or confirmed cases of COVID-19." It also mentions completing an "AMS COVID-19 Investigation Form." "If there is more than one case of novel coronavirus in a household, local area or facility, or an outbreak is suspects, notify Command Post immediately at (684) 633-5871 or (684) 633-5872."
Guam N Y (?) No standardized COVID-19 reporting form Contact: Office of Epidemiology and Research - Phone: (671) 735-7289, Fax: (671) 734-2066 It's clear that Guam is having laboratories report cases of COVID-19, but no reporting requirements for COVID-19 (or any other diseases) can be located on the Department of Public Health and Social Services website. Perhaps contact the Office of Epidemiology and Research for more information.
Northern Mariana Islands N N No standardized COVID-19 reporting form Contact: CHCC laboratory The CNMI Department of Public Health has indicated that laboratory testing has been primarily been performed by the Guam Public Health Laboratory, but due to them not being able to meet demand, the CNMI DPH will ship samples to Diagnostic Laboratory Services in Honolulu, Hawaii. Presumably those labs are responsible, in part, for reporting results back to the CNMI.
Puerto Rico Unknown Unknown Unknown Phone: (787) 765-2929
The Departamento de Salud de Puerto Rico has a relevant document OA 440 Sobre la distribución, manejo, administración y reporte de los resultados de las pruebas de COVID-19 concerning reporting results.
U.S. Virgin Islands N Y Notification of Infectious Disease Form Phone: (340) 626-1654
Territorial fax: 1-888-400-8620
"Make an IMMEDIATE telephone report to the USVI Department of Health at 626-1654 then send the completed

form IMMEDIATELY (within 24 hrs) by fax to 1-888-400-8620. If an immediate report is required after regular working hours, please call 626-1654." Additional COVID-19 information here.

4.3 Additional benefits and challenges of laboratory informatics in disease testing and public health

COVID-19 is at the forefront of the consciousness of humanity, by and large, and the informatics tools we implement for managing, treating, and surveilling the disease are of great import. From disease databases to electronic health records, from bioinformatics tools for peptide and protein modeling to laboratory tools such as LIMS and LIS, we continue to fight back against the threat of the SARS-CoV-2 virus. Yet despite the gravity of the pandemic, this is neither the first nor the last time laboratory and scientific informatics will play a positive role in testing for disease and improving public health outcomes.

Health informatics technology, when used responsibly, has already proven to be useful in studying and treating contagious diseases. 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."[40] 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.[41]

From a public health perspective, the application of informatics to disease surveillance, reporting, and health habit 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."[42] Additionally, through the use of syndromic surveillance systems (tools aiding in the detection of indicators leading up to disease diagnosis for individuals and populations[43]), 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.[42]

In the clinical laboratory, informatics systems have been influencing workflow improvements and improved service delivery for more than five decades.[1] And while improvements have been seen in the laboratory from not only the introduction of computerized systems[40][41][3] but also the realization of quality control[44] and point-of-care testing[45], more challenges remain. For example, quality management in the laboratory is still often a manual, time-consuming activity. While the LIMS and LIS have some tools to assist with this task, the inclusion of laboratory analytics and business intelligence tools into those systems may lead to even further improvements in quality and efficiency in the lab.[46] And in the realm of point-of-care testing, oversight and control of instruments can be lost when connectivity and training is lacking. Proper interfacing of these lab instruments could lead to improvements in those areas, says Siemens Healthineers' Daniel Gundler. "Maintaining POC instruments and overseeing the operators performing POC tests would be much easier if all the information and data from each instrument were accessible through one user interface in which coordinators could manage both the instruments and operators."[47]

4.3.1 System interoperability

Electronic medical record.jpg

System interoperability also poses benefits and challenges to clinical disease testing and prevention. Interoperability is defined as “the ability of different information systems, devices and applications (‘systems’) to access, exchange, integrate and cooperatively use data in a coordinated manner” to ensure timely, portable information and improved health outcomes.[48] Improving interoperability among clinical informatics systems is recognized as an important step towards improving health outcomes.[49][50] The National Academies of Sciences, Engineering, and Medicine had much to say on this topic in their 2015 publication Improving Diagnosis in Health Care[41]:

Improved interoperability across different health care organizations—as well as across laboratory and radiology information systems—is critical to improving the diagnostic process. Challenges to interoperability include the inconsistent and slow adoption of standards, particularly among organizations that are not subject to EHR certification programs, as well as a lack of incentives, including a business model that generates revenue for health IT vendors via fees associated with transmitting and receiving data.

In particular, they discuss an additional concern, one that still causes issues today: interfaces between electronic health records (EHR) and the laboratory and other clinical information systems that feed medical diagnostic information into the EHRs[41]:

Additionally, the interface between EHRs and laboratory and radiology information systems typically has limited clinical information, and the lack of sufficiently detailed information makes it difficult for a pathologist or radiologist to determine the proper context for interpreting findings or to decide whether diagnostic testing is appropriate. For example, one study found that important non-oncological conditions (such as Crohn’s disease, human immunodeficiency virus, and diabetes) were not mentioned in 59 percent of radiology orders and the presence of cancer was not mentioned in 8 percent of orders, demonstrating that the complete patient context is not getting received. Insufficient clinical information can be problematic as radiologists and pathologists often use this information to inform their interpretations of diagnostic testing results and suggestions for next steps. In addition, the Centers for Disease Control and Prevention’s Clinical Laboratory Improvement Advisory Committee (CLIAC) expressed concern over the patient safety risks regarding the interoperability of laboratory data and display discrepancies in EHRs. They recommended that laboratory health care professionals collaborate with other stakeholders to “develop effective solutions to reduce identified patient safety risks in and improve the safety of EHR systems” regarding laboratory data.

In fact, interoperability issues have come up during the global laboratory response to the COVID-19 pandemic. In early April 2020, a report from Nature revealed that academic research laboratories wanting to assist with COVID-19 testing efforts have at times been stymied by the incompatibility between academic informatics systems and hospital EHRs. Not only do hospitals use EHRs of differing types, but many of those EHRs were not designed to talk to other EHRs, let alone to academic and research laboratories' informatics systems. Combine this with strict account procedures and the costs of developing interfaces on-the-fly, more than a few medical systems have turned away the offer of help from academic and research labs.[51] As it turns out, HL7- and other standard-based interfaces have long been expensive for many vendors to implement[14], the cost justified typically when high volumes of samples are involved. Additionally, in more normal, non-pandemic circumstances, the requirement to interface with EHRs and hospital information systems (HIS) is almost exclusively found in the LIS and LIMS used in patient settings, i.e., in the hospitals, medical offices, and laboratories catering to diagnosing disease in patients. Academic labs have not been equipped at any level (software, hardware, or personnel) to do high volume clinical testing, nor have they had reason to ensure their informatics systems can interface with clinical systems.

Interoperability benefits and challenges show up elsewhere too. Take for example the value of phenotypes, a representation of the genetic analysis of the collective observable traits of an organism, traits caused by the interaction of its genome with the environment. The value of patient phenotyping data is increasingly useful in the fight against known and novel viruses, as well as a broad variety of non-viral diseases. As Ausiello and Shaw note, in order for medicine to advance and produce improved patient outcomes, "traditional clinical information must be combined with genetic data and non-traditional phenotypes and analyzed in a manner that yields actionable insights into disease diagnosis, prevention, or treatment."[52] Whether it's identifying "the measurable phenotypic characteristics of patients that are most predictive of individual variation" in treatment outcomes for chronic pain[53] or COVID-19[54][55], phenotypes have utility in the clinical sector.

Here again interoperability between EHRs and laboratory informatics systems comes into play. In a 2019 paper published by Zhang et al. in nph Digital Medicine, the topic of extracting patient phenotypes from laboratory test results fed into EHRs is addressed.[56] The authors state that one of the more difficult aspects of their research is that while "[l]aboratory tests have broad applicability for translational research ... EHR-based research using laboratory data have been challenging because of their diversity and the lack of standardization of reporting laboratory test results." They add[56]:

Despite the great potential of EHR data, patient phenotyping from EHRs is still challenging because the phenotype information is distributed in many EHR locations (laboratories, notes, problem lists, imaging data, etc.) and since EHRs have vastly different structures across sites. This lack of integration represents a substantial barrier to widespread use of EHR data in translational research.

The answer to the clinical and laboratory interoperability question is unclear. A 2019 article in the American Association for Clinical Chemistry's CLN Stat addressed remaining roadblocks, including lack of standards development, data quality issues, clinical data matching, lack of incentivizing health IT optimization, text-based reporting formats, differences in terminology, and HL7 messaging issues. They add that proposals from the Office of the National Coordinator for Health Information Technology (ONC) and the Centers for Medicare and Medicaid Services include possible fixes such as standardized application programming interfaces (API). They also note that middleware may pick up the slack in connecting more laboratory devices, rather than depending on the LIS to handle all the interfacing.[57] On a more positive note, the Office of the National Coordinator for Health Information Technology (ONC) updated its Interoperability Standards Advisory (ISA) Vocabulary/Code Set/Terminology page in November to better "highlight critical public health interoperability needs on COVID-19 in an easily accessible way." Replying to the ONC, HIMSS's Senior Director Jeff Coughlin goes on to add[58]:

There is a growing need to consider data exchange for home settings and considerations around device interoperability. There are a number of applications in use and this setting requires work across a number of systems (emergency medical services, hospital electronic health records, telemedicine system [synchronous and asynchronous] and, remote patient monitoring and device management). ISA should provide guidance on specific standards to assist in exchange with this setting."

Even so, it remains obvious that more work needs to be done in the development and standard use of clinical and laboratory informatics applications if the promise of personalized medicine and the need for improved disease testing and response are to be fulfilled. In particular, how we responsibly protect personal health information while putting its anonymized variants to beneficial use for disease testing and prevention remains a critical question that must be solved in order to better prepare for the next COVID-19.

4.3.2 Contact tracing

What is contact tracing COVID-19.png

Contact tracing is a public health process that involves the determination of who a patient had specific contact with while infectious, then informing, supporting, and maintaining contact with those effected individuals in order to reduce the spread of an infection.[59] The seeds of contact tracing may go as far back as late fifteenth and early sixteenth century efforts to control infection rates of syphilis among prostitutes in part of Europe.[60] However, the practice was adopted more vigorously in the late nineteenth and early twentieth century in Great Britain for tracking cases of communicable diseases such as measles[61] and sexually transmitted diseases like syphilis and gonorrhea.[62] Further inroads were made in the United States in the early 1930s with its efforts to reduce sexually transmitted diseases among U.S. troops.[63]

Throughout it all, contract tracing has been predominately a manual effort. However, the technological age has brought with it both social promise and privacy questions in regards to the application of informatics to contact tracing. In the mid-2000s, the use of Wi-Fi and RFID technology in Singapore hospital settings "to provide an alternative to tedious and error-prone manual contact tracing" was being reported in academic literature.[64] Since then, the use of informatics tools in contact tracing has increased, seeing practical application in combating severe acute respiratory syndrome (SARS)[65], Ebola[66], and tuberculosis.[67] As such, it should not be surprising that early in the COVID-19 pandemic, contract tracing was also being discussed within the context of both manual and digital tracing efforts.[59][68][69][70]

Contact tracing using digital tools, however, comes with both benefits and challenges.[71][72] Digital contact tracing tools have the potential to make contract tracing quicker and more efficient than manual processes. People can forget who they may have been in close contact with, for example, but with digital tracing, past location data can be mined to provide a clearer picture. As a result, with more accurate data, local and state policy-making efforts can be more nimbly tailored to current needs, and the effectiveness of those efforts can be better monitored.[67][64][71][73] However, several challenges also exist, primarily with social and cultural perceptions of the technology's acceptability and the privacy concerns surrounding it.

Social acceptability and trust around the world

The social acceptability and trust put into contact tracing applications and the governments that use them is of significant concern. An April 2020 "blitz" survey of the Flemish Region of Belgium showed that only 51 percent of respondents had "no objection to a CORONA-app, under strict conditions."[74] As legal researcher Domenico Orlando points out, many contact tracing applications like Italy's Immuni app, however, require at least 60 percent of the population to participate for it to be effective.[75] He adds that while whether or not "trust and social acceptance will follow is an unknown variable" when it comes to digital contact tracing, having a strong set of legal protections in place—such as those found with E.U. data protection law and the efforts of the European Data Protection Board (EDPB) to create data protection guidelines for digital surveillance tools[76]—at least makes the technology more feasible.[75] Political and cultural context also plays a role in social acceptance. Countries like South Korea and states like Taiwan—in comparison to mainland China—arguably have seen greater adoption of digital surveillance due to a more relaxed political context[77], though attempts by the citizenry to be vigilantes who shame and discriminate others based on contact tracing data may work counter to that overall adoption rate.[71] Recent past experiences with digitally tracing MERS and SARS outbreaks in both cases, however, have probably played an even greater role in the success of convincing those governments' citizenry to voluntarily participate.[73] Similar adoption success can be seen in a Singapore poll that showed 70 percent of respondents were open to installing its government's voluntary TraceTogether app, which is based on the privacy-preserving protocol BlueTrace.[73]

Challenges in the U.S.

In the United States, adopted use of contract tracing apps has been much more sporadic. Several cultural factors contribute. First and foremost, Americans' reluctance to answer calls from unknown numbers is continuing to increase. A First Orion 2019 Spam Call Trends and Projections Report found that more than 40 percent of calls received are spam calls, and 70 percent of Americans do not answer calls from an unknown number.[78] A December 2019 TrueCaller report found that robocalls in the U.S. "increased from 7% [in 2018] to a staggering 35% – which means that more than every third spam call a user gets is a robocall."[79] This issues get complicated even further by lack of enforcement on "spoofing," the practice of making a phone number appear to originate locally, or from a specific business. Even if a call looks legitimate, it may actually not be.[78][80] As Vice writer Casey Johnston suggests, given spam and spoofing practices and the related lack of enforcement, "until the United States takes its scam and spam call problem seriously, we’re probably going to be in the contact-tracing dark ages for a very long time."[80]

Second, overall trust in the federal government to do what's best and resolve problems has some catching up to do. September 2020 polls by the Pew Research Center[81] and Gallup[82] showed faith in overall federal government near all-time lows. As Lydia Saad of Gallup concluded in her 2020 analysis: "As the country is engaged in critical efforts to combat the medical, economic and societal effects of the global coronavirus pandemic, Americans' trust in the federal government to handle domestic issues is near its lowest point in Gallup trends since 1972, as is their trust in the executive and legislative branches, public officials generally, and the American people themselves."[82] A few positive signs have shown, with overall public trust in government making a small uptick and "trust in the federal government to provide accurate information about COVID-19" rising with the January 2021 presidency change.[83][84] Yet as long as overall trust in the federal government remains low, it will continue to be difficult to roll out any significant contract tracing efforts across the nation.

Third, the ebbs and flows of case numbers—with surges in November 2020 and again in the summer of 2021 with the delta variant[85][86]—make the number of cases to track tough to overcome. This is often compounded by the time it takes to get results, often too long to stem the flow of new infections.[87] A lack of a clear and organized national strategy for contract tracing, unlike the European Union[88], punctuates the challenges of getting more people to use contact tracing apps.[89]

Privacy and other issues

The preservation of user privacy and sensitive identifying data are also vital considerations in digital tracing apps. The previously mentioned BlueTrace protocol and its open-source reference implementation OpenTrace strive to address most of those concerns when "logging Bluetooth encounters between participating devices to facilitate contact tracing, while protecting the users’ personal data and privacy." More specifically, it strives to limit collection of personally-identifiable information, locally store and lock down encounter history, prevent third-party tracking, and provide revocable consent to store and allow use of encounter data.[90] Ultimately, these and other such solutions must ensure the anonymity of tracing data doesn't become compromised. Lew and Anderson also note that "[c]loud-based storage of anonymous identifier beacons may also threaten security, given that any centralized list of identifiers could theoretically be hacked and re-identified."[72] As noted previously, re-identified data, let alone leaked anonymized data, could lead to shaming and discrimination against individuals identified as being infected.[71]

Privacy is not solely a concern of application developers, however. Government entities should also be held responsible for better ensuring how informatics solutions are created and used for epidemiological tracking. The European Union's EDPB and its contact tracing guidelines, adopted in April 2020, offer a compromise between the societal needs of contact tracing and the individual needs of privacy. The EDPB addresses the topics of location data sources and anonymized use, as well as the recommendations and functional requirements of applications employing those data sources, concluding "that one should not have to choose between an efficient response to the current crisis and the protection of our fundamental rights: we can achieve both."[76] The U.S. CDC is less eloquent with its COVID-19 digital contact tracing guidelines, though they still stress the preference for secure data transfer mechanisms, open-source architecture, need-to-know-only access to data for public health authorities, and the ability for users to revoke data access consent at any time.[68]

Finally, most digital tracing solutions also suffer from a few additional downsides. Several researchers have expressed concerns about data accuracy and actionability issues in mobile devices that lead to false positives. These issues include[72][90]:

  • inaccurate inter-device distance detection
  • inaccurate exposure detection in high-density buildings with multiple walls
  • inability to track duration of exposure (i.e., seconds or hours)
  • failures with the underlying technology itself, including BlueTooth or the operating system

The future

Despite these and other drawbacks, various governments around the world have found greater success at managing the COVID-19 pandemic with digital contact tracing. Huang et al. in the Harvard Business Review wonder if the successes reported in South Korea, Taiwan, and other parts of the East could be replicated in the United States and other Western democracies[73]:

Can Western democracies achieve the results seen in East Asia without emulating their means? Probably not. There is likely a fundamental conflict between these requirements and deeply entrenched Western liberal values, such as the expectation of privacy, consent, and the sanctity of individual rights ... At the time of publication, at least three local governments in the United States are considering adoption of a contact-tracing app developed in a project led by MIT, Reuters reports ... But for such technologies to be effective, compliance must be nearly universal. Without a government mandate in the U.S., it’s hard to imagine universal voluntary adoption of even a privacy-protecting tracing app.
Maybe Covid-19 is a sign of our future steady state. Different societies will make different choices about how to respond to the next pandemic. For Western democracies the time has come to either rethink our values around the tradeoff between personal privacy and public safety in a pandemic or to accelerate technology innovation and policy development that can preserve both.


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Citation information for this chapter

Chapter: 4. Workflow and information management for COVID-19 (and other respiratory diseases)

Edition: Fall 2021

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: September 2021