Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) possesses a positive-sense single-stranded RNA genome. Mutations of this genome may occur over time, and while these changes are not unexpected, specific mutations may alter important characteristics of the virus. When viral genomic changes are associated with potential altered transmission, virulence, or vaccine efficacy, they may be identified as a particular SARS-CoV-2 Variant of Concern (VOC). Currently, there are three commonly discussed VOCs.

The three VOCs that are currently monitored include the B.1.1.7 lineage, first identified in the UK; B.1.351 lineage, first identified in South Africa; and P.1 lineage, first identified in Brazil. While nomenclature continues to evolve, Pango lineage nomenclature is the current CanCOGen recommendation.¹

Given the particular importance of molecular assays in the detection of SARS-CoV-2, it is also essential to monitor the viral genomic sequences to ensure that molecular based diagnostic assay performance characteristics have not changed to ensure ongoing accurate, sensitive detection of the VOCs. Various genetic targets may be used in diagnostic assays, including the E gene, RdRp gene, ORF1ab, S gene, and N gene.

Among commonly used diagnostic assays, a change in the sensitivity has only been identified with the B.1.1.7 VOC. In this particular VOC, a deletion in residues 69-70 in the S-gene is present, which may cause a negative S-gene result (S-gene target failure, SGTF) in some assays.² Overall, sensitivity of assays with SGTF are unaffected due to alternative targets.

Ongoing vigilance and monitoring for genome mutations which may affect assay performance, irrespective of their association with VOCs, is important. For example, recently there have been described N gene mutations that may affect N gene based assays.^3,4

The inability of some assays to detect certain targets highlights the importance of potentially incorporating multiple targets in an assay or a different-target assay for redundancy. It underscores the need to monitor for viral genome changes that may affect assay performance and ensure that a timely review of target sequence with viral genomes is performed.

References

1. National Collaborative Centre for Infectious Diseases. Griffiths E, Tanner J, Knox N, Hsiao W, Van Domselaar G on behalf of the CPHLN and CanCOGeN. CanCOGeN Interim Recommendations for Naming, Identifying, and Reporting SARS-CoV-2 Variants of Concern, Version 1.0. [Revised 2021-01-15; cited 2021-03-04]. Available from: https://nccid.ca/wp-content/uploads/sites/2/2021/02/CanCOGeN-Interim-Recommendations-for-Naming-Identifying-and-Reporting-SARS-CoV-2-Variants.pdf.


2. U.S. Food & Drug Administration. Genetic Variants of SARS-CoV-2 May Lead to False Negative Results with Molecular Tests for Detection of SARS-CoV-2 - Letter to Clinical Laboratory Staff and Health Care Providers. [Dated 2021-01-08; cited 2021-03-04]. Available from: https://www.fda.gov/medical-devices/letters-health-care-providers/genetic-variants-sars-cov-2-may-lead-false-negative-results-molecular-tests-detection-sars-cov-2.


3. Hasan MR, Sundararaju S, Manickam C, Mirza F, Al-Hail H, Lorenz S, et al. A novel point mutation in the N gene of SARS-CoV-2 may affect the detection of the virus by RT-qPCR. J Clin Microbiol. 2021:JCM.03278-20. 


4. Ziegler K, Steininger P, Ziegler R, Steinmann J, Korn K, Ensser A. SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene. Euro Surveill. 2020;25:2001650.