Keeping up with SARS-CoV-2 variants

Constant re-evaluation of primers/probes of SARS-CoV-2 nucleic acid amplification tests

Each time a virus replicates, errors (mutations) occur naturally in the process of copying its genetic material. This is how variants arise.

In the medical world, scientists and epidemiologists are always one step behind in determining whether these changes in the genome allow the virus to spread more easily or affect pathogenicity and disease severity.

The rapid emergence of novel variants and mutant strains of SARS-CoV-2 might inevitably give rise to “escape variants” that are capable of limiting the efficacy of vaccines, pharmaceutical interventions, and diagnostic detection.

For the area of diagnostics, a recent report by Nayar et al. (2021) estimates that there is a 2% increase/month in the number of mismatches between SARS-CoV-2 RT-PCR primers in use today, and in the genome targets reported over time and spatially.

This highlights the importance of constant re-evaluation of all primers and probes used in commercial SARS-CoV-2 assays and lab-developed tests (LDT) to prevent false-negative results. Assay developers may then update or redesign the primer and probe sequences to ensure "catching" of the latest variants.

Regulatory bodies should also be agile enough to allow for these quick changes in assay modifications by assay manufacturers to be rolled out for in vitro diagnostics use in a safe and timely manner.


Nayar, G., Seabolt, E. E., Kunitomi, M., Agarwal, A., Beck, K. L., Mukherjee, V., & Kaufman, J. H. (2021). Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2. Scientific reports, 11(1), 8988.