User:Shawndouglas/sandbox/sublevel1
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.[1]
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.[1]
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.[2]
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[3][4][5][6]:
- 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[7], 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.
References
- ↑ 1.0 1.1 Third Wave Analytics (5 September 2021). "The 8 Essential Features for a Sample Management LIMS in a COVID-19 Testing Lab". Third Wave Analytics. https://thirdwaveanalytics.com/blog/8-essential-features-sample-management-lims-in-a-covid-19-testing-lab/. Retrieved 17 September 2021.
- ↑ College of American Pathologists (7 April 2020). "Guidance for COVID-19 Testing for CAP-Accredited Laboratories". College of American Pathologists. https://www.cap.org/laboratory-improvement/news-and-updates/guidance-for-covid-19-testing-for-cap-accredited-laboratories. Retrieved 30 April 2020.
- ↑ Life Technologies Corporation (August 2012). "Real-time PCR handbook" (PDF). Life Technologies Corporation. https://www.gene-quantification.de/real-time-pcr-handbook-life-technologies-update-flr.pdf. Retrieved 30 April 2020.
- ↑ Starita, L. (1 April 2020). "COVID-19 SCAN molecular workflow". protocols.io. https://www.protocols.io/view/covid-19-scan-molecular-workflow-bebkjakw. Retrieved 30 April 2020.
- ↑ Udugama, B.; Kadhiresan, P.; Kozlowski, H.N. et al. (2020). "Diagnosing COVID-19: The Disease and Tools for Detection". ACS Nano 14 (4): 3822–3835. doi:10.1021/acsnano.0c02624. PMC PMC7144809. PMID 32223179. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144809.
- ↑ Pendergraph, G.E. (2020). "Reverse Transcriptase PCR (RT-PCR)". HIV: Structure, Replication, and Detection. https://www.labce.com/spg605456_reverse_transcriptase_pcr_rt_pcr.aspx. Retrieved 20 April 2020.
- ↑ Prinzi, A. (27 April 2020). "False Negatives and Reinfections: the Challenges of SARS-CoV-2 RT-PCR Testing". American Society for Microbiology. https://asm.org/Articles/2020/April/False-Negatives-and-Reinfections-the-Challenges-of. Retrieved 30 April 2020.
