View source for COVID-19 Testing, Reporting, and Information Management in the Laboratory/Workflow and information management for COVID-19 (and other respiratory diseases)/Laboratory informatics and workflow management

==4. Workflow and information management for COVID-19 (and other pandemics)==
===4.1 Laboratory informatics and workflow management===

[[File:Molecular diagnostics qia symphony.jpg|right|360px]]Laboratory computing has positively affected clinical service delivery and laboratory management for decades.<ref name="JonesInform14">{{cite journal |title=Informatics and the Clinical Laboratory |journal=The Clinical Biochemist Reviews |author=Jones, R.G.; Johnson, O.A.; Baststone, G. |volume=35 |issue=3 |pages=177–192 |year=2014 |pmid=25336763 |pmc=PMC4204239}}</ref> 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.<ref name="PitkusLab18">{{cite journal |title=Laboratory Informatics: An Increasingly Valuable Commodity Emerging from Today's Laboratories |journal=ASCLS Today |author=Pitkus, A. |volume=32 |issue=2 |year=2018 |url=https://ascls.org/laboratory-informatics-an-increasingly-valuable-commodity-emerging-from-today-s-laboratories/ |accessdate=13 September 2021}}</ref><ref name="RaeenHowLab18">{{cite journal |title=How laboratory informatics has impacted healthcare overall |journal=Applied Research Projects |author=Raeen, M.R. |volume=54 |year=2018 |url=https://dc.uthsc.edu/hiimappliedresearch/54 |doi=10.21007/chp.hiim.0056}}</ref> In the world of [[Epidemiology|epidemiological]] testing, those same [[laboratory informatics]] applications—such as [[laboratory information management system]]s (LIMS), [[laboratory information system]]s (LIS), and [[hospital information system]]s (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."<ref name="WilsonTheNew18">{{cite journal |title=The new informatics of pandemic response: humanitarian technology, efficiency, and the subtle retreat of national agency |journal=Journal of International Humanitarian Action |author=Wilson, C.; Jumbert, M.G. |volume=3 |at=8 |year=2018 |doi=10.1186/s41018-018-0036-5 |pmc=PMC7149122}}</ref> 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 computing|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.<ref name="TWATheEight21">{{cite web |url=https://thirdwaveanalytics.com/blog/8-essential-features-sample-management-lims-in-a-covid-19-testing-lab/ |title=The 8 Essential Features for a Sample Management LIMS in a COVID-19 Testing Lab |author=Third Wave Analytics |publisher=Third Wave Analytics |date=05 September 2021 |accessdate=17 September 2021}}</ref><ref name="TonyCOVID21">{{cite web |url=https://www.labcompare.com/10-Featured-Articles/578098-COVID-19-Testing-Labs-Go-Mobile-by-Leveraging-LIMS/ |title=COVID-19 PCR Testing Labs Go Mobile by Leveraging LIMS |author=Tony, J. |work=Labcompare |date=03 August 2021 |accessdate=17 September 2021}}</ref>

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' ''[[LII:Laboratory Information Systems Project Management: A Guidebook for International Implementations|Laboratory Information Systems Project Management: A Guidebook for International Implementations]]'' or Joe Liscouski's ''[[LII:A Guide for Management: Successfully Applying Laboratory Systems to Your Organization's Work|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.<ref name="WeemaesLab20">{{cite journal |title=Laboratory information system requirements to manage the COVID-19 pandemic: A report from the Belgian national reference testing center |journal=JAMIA |author=Weemaes, M.; Martens, S.; Cuypers, L. et al. |at=ocaa081 |year=2020 |doi=10.1093/jamia/ocaa081 |pmid=32348469 |pmc=PMC7197526}}</ref>

====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.<ref name="TWATheEight21" />

'''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.<ref name="TWATheEight21" />

'''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.<ref name="CAPGuidance20">{{cite web |url=https://www.cap.org/laboratory-improvement/news-and-updates/guidance-for-covid-19-testing-for-cap-accredited-laboratories |title=Guidance for COVID-19 Testing for CAP-Accredited Laboratories |author=College of American Pathologists |publisher=College of American Pathologists |date=07 April 2020 |accessdate=30 April 2020}}</ref>

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<ref name="LTCReal12">{{cite web |url=https://www.gene-quantification.de/real-time-pcr-handbook-life-technologies-update-flr.pdf |format=PDF |title=Real-time PCR handbook |author=Life Technologies Corporation |publisher=Life Technologies Corporation |date=August 2012 |accessdate=30 April 2020}}</ref><ref name="StaritaCOVID20">{{cite web |url=https://www.protocols.io/view/covid-19-scan-molecular-workflow-bebkjakw |title=COVID-19 SCAN molecular workflow |author=Starita, L. |work=protocols.io |date=01 April 2020 |accessdate=30 April 2020}}</ref><ref name="UdugamaDiag20">{{cite journal |title=Diagnosing COVID-19: The Disease and Tools for Detection |journal=ACS Nano |author=Udugama, B.; Kadhiresan, P.; Kozlowski, H.N. et al. |volume=14 |issue=4 |pages=3822–3835 |year=2020 |doi=10.1021/acsnano.0c02624 |pmid=32223179 |pmc=PMC7144809}}</ref><ref name="PendergraphHIV20">{{cite web |url=https://www.labce.com/spg605456_reverse_transcriptase_pcr_rt_pcr.aspx |title=Reverse Transcriptase PCR (RT-PCR) |work=HIV: Structure, Replication, and Detection |author=Pendergraph, G.E. |date=2020 |accessdate=20 April 2020}}</ref>:

#Prepare the batching for the ordered rRT-PCR tests, including who is involved, when it is scheduled, and any additional unique identifiers.
#Extract, purify, and assess the quality of nucleic acids from a complex biological sample.
#Prepare and assemble rRT-PCR components (including reverse transcriptase enzyme, primers, and nucleotides) and reactions to plates or tubes.
#Run the analysis using the appropriate quantification method.
#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<ref name="PrinziFalse20">{{cite web |url=https://asm.org/Articles/2020/April/False-Negatives-and-Reinfections-the-Challenges-of |title=False Negatives and Reinfections: the Challenges of SARS-CoV-2 RT-PCR Testing |author=Prinzi, A. |publisher=American Society for Microbiology |date=27 April 2020 |accessdate=30 April 2020}}</ref>, 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<ref name="John3504HL7_11">{{cite web |url=https://community.spiceworks.com/topic/175107-hl7-interface-cost-and-maintenance |title=HL7 Interface cost and maintenance |author=John3504 |work=Spiceworks |date=07 December 2011 |accessdate=25 April 2020}}</ref> as the developer has to take into account compliance requirements, the required analytical outcomes, and the instrument itself, as well as its available connections.<ref name="StraussConnect18">{{cite web |url=https://www.labmanager.com/laboratory-technology/connecting-lab-instruments-interface-strategies-depend-upon-compliance-requirements-2034 |title=Connecting Lab Instruments: Interface Strategies Depend Upon Compliance Requirements |author=Strauss, D. |work=Lab Manager |date=08 July 2018 |accessdate=30 April 2020}}</ref> 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<ref name="HologicPantherFusion20">{{cite web |url=https://www.hologic.com/coronavirus-test |title=Hologic’s Molecular Test for the Novel Coronavirus, SARS-CoV-2, Receives FDA Emergency Use Authorization |author=Hologic |publisher=Hologic, Inc |date=17 March 2020 |accessdate=30 April 2020}}</ref> and Abbot's RealTime m2000<ref name="AbbottRealTime20">{{cite web |url=https://www.molecular.abbott/us/en/products/infectious-disease/RealTime-SARS-CoV-2-Assay |title=Abbott RealTime SARS-CoV-2 Assay |author=Abbott |publisher=Abbott Laboratories |accessdate=30 April 2020}}</ref> 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.<ref name="WeemaesLab20" /> 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.<ref name="WeemaesLab20" />

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<ref name="FEMACorona20">{{cite web |url=https://www.fema.gov/press-release/20210318/coronavirus-covid-19-pandemic-hhs-letter-hospital-administrators |title=Coronavirus (COVID-19) Pandemic: HHS Letter to Hospital Administrators |author=Azar, A.M. |publisher=FEMA |date=10 April 2020 |accessdate=13 September 2021}}</ref> 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.