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:
- Accula SARS-CoV-2 Test (Mesa Biotech Inc.)
- Linea COVID-19 Assay (Applied DNA Sciences, Inc.)
- TaqPath COVID-19 Assay (Thermo Fisher Scientific, Inc.)
- 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.