With the emergence of new SARS-CoV-2 mutants from time to time and the slow rate of vaccination in many parts of the world, COVID-19 testing laboratories may have to continue testing samples for many more years to come. COVID-19 diagnostic laboratories need to quickly turnaround samples and report accurate test results to enable quick decision-making for quarantine, isolation, and treatment of COVID-19 patients.

COVID-19 diagnostic laboratories should leverage modern technology for sample and data management and secure result delivery to patients and physicians. With a large number of samples coming in, COVID-19 testing laboratories should have a robust COVID-19 sample management system, also known as a COVID LIMS, to accelerate the testing throughput and meet the testing demand.

Following are some essential features to consider when deciding on a COVID LIMS for your laboratory:

1. Secure and Easy Access

A COVID LIMS should be easily accessible to all authorized staff involved in the laboratory process. It should be securely accessible on any device with an active internet connection irrespective of the physical location of staff. An ideal solution to fulfill these requirements is a cloud-based Laboratory Information Management System (LIMS).

A LIMS should be able to manage and securely store all kinds of Protected Health Information (PHI). A good LIMS should have the ability to protect the PHI of patients and healthcare providers by assigning role-based access rights to authorized staff. A LIMS should enforce two-factor authentication if anyone tries to access PHI to ensure foolproof security.

2. Patient Portal and Physician Portal

Several laboratories manage sample information manually using paper test request forms. However, the request forms are usually poorly written and are difficult for the laboratory staff to read clearly. This creates room for errors and delays testing. Furthermore, the laboratory staff may take days to deliver test reports to patients due to cumbersome manual processes.

A LIMS can automate the entire process, right from patient registration to report delivery. A COVID LIMS should have a secure patient portal to enable faster patient registration and secure delivery of test results.

How Does the Patient Portal Work?

Once a patient registers on the patient portal present on a laboratory’s website, the patient receives a QR code which can be scanned at the sample collection site to confirm the patient’s identity. Subsequently, the sample is collected, associated with the patient’s record, and sent to the laboratory for testing. As soon as the laboratory releases the test report, the patient can securely download it from the patient portal. The patient can have the digital test report scanned at airports or workplaces through a QR code, removing the hassle of carrying hard copies of the test report.

Physician Portal

A physician portal works similarly. A physician can also request a COVID-19 test for a patient from the physician portal and can access the test report in real-time as soon as it is released by the laboratory. This enables the physician to commence the treatment regimen without any delay.

3. Automated Sample, Data, and Result Management

A COVID LIMS should be able to record and store every data associated with all samples. Data collected and stored should always be associated with the correct sample. A LIMS should be capable of storing re-testing results along with the original test results if a sample was tested multiple times. A LIMS also enables laboratories to process samples and report results in a batch.

4. Instrument Integration

COVID-19 testing laboratories test a large number of specimens daily. They conduct different types of tests, such as RT-PCR and serological tests. It is inefficient for the laboratory staff to manually transfer the analytical data from instruments to a LIMS as it is error-prone and time-consuming. A LIMS should be configurable to support varied test methods. Furthermore, a LIMS should facilitate integration with diagnostic instruments, such as RT-PCR machines, for bi-directional data transfer. This automated data transfer process ensures data integrity and reduces the test turnaround time.

5. Formula Configuration

A LIMS should support the configuration of complex formulas for calculating final test results. Once the results are imported in a LIMS from diagnostic instruments, the LIMS should be able to quickly determine the final test results based on the results of control samples, test samples, and preset formulas.

6. Integration with Public Health Department Systems

All CLIA certified COVID-19 testing laboratories need to share the final test results with the appropriate state or local Department of Public Health (DPH), irrespective of whether the test results are positive or negative. Laboratories that report results directly to the Centers for Disease Control and Prevention (CDC) should continue sending test results to the CDC. A LIMS can help laboratories share this data with DPH in a requested time frame and required format. A LIMS should support integration with the DPH systems to securely send the final test results to the appropriate public health department.

7. Regulatory Compliance Support

COVID-19 testing laboratories face challenges in meeting regulatory requirements such as CLIA, ISO 15189:2012, HIPAA, GCP, and EU GDPR. A LIMS should enable testing laboratories to meet all these requirements with ease. A LIMS should be able to streamline quality control (QA) and quality assurance (QC) processes in a laboratory. It should be capable of managing training and competency records of laboratory personnel and monitoring their performance. Monitoring staff training can help laboratory managers assign COVID-19 tests to personnel with the appropriate skills, experience, and knowledge of biosafety protocols.

A good COVID LIMS should be capable of managing all laboratory documents, including standard operating procedures (SOPs) for standardized laboratory workflows. A LIMS should also be able to maintain the confidentiality of important documents by allowing role-based access to authorized personnel. A COVID LIMS should help laboratory managers manage all laboratory instruments, schedule calibration and maintenance of instruments to prevent analytical errors.

Conclusion

COVID-19 testing laboratories have been playing a critical role in controlling COVID-19 right from the onset of the pandemic. All COVID-19 testing laboratories need to quickly test samples and report results. COVID-19 testing laboratories face many operational challenges on a day-to-day basis. It is challenging for laboratories to manage a large number of specimens and associated data, generate test reports in a batch, manage patient records, record laboratory activities, safeguard the PHI of patients, manage documents, instruments, and staff training records, and meet compliance. A COVID-19 LIMS should have all the essential features listed above to enable laboratories to manage data seamlessly and automate processes, thus preventing manual errors. Furthermore, a LIMS system should enable laboratories to meet their regulatory and reporting requirements. By leveraging a COVID-19 sample management system, COVID-19 testing laboratories can reduce the test turnaround time and assure the accuracy of test results.

The evolution of highly transmissible SARS-CoV-2 variants has concerned health officials worldwide. It is important to accelerate the vaccination rollout to prevent the spread of SARS-CoV-2 and reduce the rate of viral mutations. The new variants of SARS-CoV-2 may affect the accuracy of COVID-19 test results, however, with an unknown degree of impact. With the emergence of SARS-CoV-2 variants, COVID-19 diagnostic laboratories need to adapt to new assays to ensure accurate reporting of test results.

SARS-CoV-2 Variants and Their Origin

SARS-CoV-2 constantly evolves through mutation, with new variants emerging with time. Although numerous SARS-CoV-2 variants have been detected, only four variants are of public health concern because they are highly transmissible, cause more severe illness, and elude the immune system. These four SARS-CoV-2 variants are listed in the table below.

Variant Type	Pango Lineages	Country of Origin
Alpha	B.1.1.7	United Kingdom
Beta	B.1.351 B.1.351.2 B.1.351.3	South Africa
Gamma	P.1 P.1.1 P.1.2	Brazil
Delta	B.1.617.2 AY.1 AY.2 AY.3	India

Apart from the variants of concern mentioned above, the following new variants are of interest according to the World Health Organization (WHO).

SARS-CoV-2 Variant Type	Pango Lineages	Country of Origin
Eta	B.1.525	Multiple countries
Iota	B.1.526	United States of America
Kappa	B.1.617.1	India
Lambda	C.37	Peru

Which Molecular Tests are Affected by SARS-CoV-2 Viral Mutations?

A COVID-19 test may produce a false-negative result if a part of the SARS-CoV-2 genome that is targeted by RT-PCR tests is mutated. The Food and Drug Administration (FDA) has identified the following tests that could be impacted by new SARS-CoV-2 viral mutations:

1. Accula SARS-CoV-2 Test (Mesa Biotech Inc.)
2. Linea COVID-19 Assay (Applied DNA Sciences, Inc.)
3. TaqPath COVID-19 Assay (Thermo Fisher Scientific, Inc.)
4. Xpert Xpress SARS-CoV-2, Xpert Xpress SARS-CoV-2 DoD, Xpert Omni SARS-CoV-2 (Cepheid)

The presence of viral mutations tends to reduce the sensitivity of these tests. Diagnostic tests that leverage a single genetic target of SARS-CoV-2 are more likely to be impacted by variants. Contrarily, tests that detect multiple genetic targets of SARS-CoV-2 are more foolproof and are less likely to be impacted by variants.

How COVID-19 Testing Laboratories can Address the Challenges Posed by SARS-CoV-2 Variants

Continuously emerging variants of SARS-CoV-2 are likely to affect the current diagnostic tests. Laboratories must adopt new methods to overcome the risk of reporting false negatives. As the pandemic continues, there is a possibility of further genetic changes in the genome of SARS-CoV-2 that may significantly impact the accuracy of COVID-19 tests. Hence, COVID-19 testing laboratories should support new assays and test methods that can detect SARS-CoV-2 variants.

Laboratories should perform in silico analysis of the primer binding to assess the impact of new variants on current RT-PCR tests. Laboratories can also implement a screening process for the identification of emerging SARS-CoV-2 variants. For this, they need to work coherently with public health authorities and genome sequencing surveillance networks. Laboratories conducting genome sequencing-based assays may consider including variant monitoring in their routine quality assessment program to identify new variants. Whole-genome sequencing should be done for patients with prolonged COVID-19 positivity to monitor new emerging variants.

Role of a COVID-19 Laboratory Management Software

A COVID-19 LIMS supports testing workflows, assays and also generates custom test reports that comply with FDA, CDC, and local reporting guidelines. A LIMS also aids in the validation of new methods for COVID-19 testing. A configurable LIMS helps in complex data management, workflow automation and minimizes operational errors. Furthermore, a configurable COVID-19 laboratory management software enables COVID-19 testing laboratories to accommodate new workflows or update existing workflows to easily adapt to new assays.

Conclusion

The quick spread of COVID-19 has threatened public health and the economy and demands advanced strategies to arrest the spread of COVID-19. Scientists are progressively developing antiviral therapies and vaccines to fight the virus. It is necessary to identify new emerging variants to prevent inaccurate reporting of test results that may undermine the current efforts to control the coronavirus. A configurable COVID-19 laboratory management software can help COVID-19 testing laboratories support new test methods, assays and meet reporting requirements with ease.