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Variant-specific PCR is a quicker, cheaper way to identify specific mutations that are considered variant-defining. In seventeen SARS-Cov-2 samples from Galicia, Spain, a discrepant difference between vsPCR and NGS was discovered. a cluster of BA. 1 Omicron SARS-CoV-2 variants displayed a BA. 2-like melting temperature pattern due to a point mutation downstream the deletion of the spike aminoacids 69/70. C21772T can cause BA. 1 samples to be misinterpreted as BA. 2. As the 69/70 deletion is commonly used for differentiation between BA. 1 and BA. 2 by vsPCR, C21772T can cause BA. 1 samples to be misinterpreted as BA. 2. BA. 2. This is the first case of a point mutation that caused a vsPCR algorithm to misclassify BA. 1 samples as BA. 2. This is an example of how mutations in the target of vsPCR tests based on melting curve analysis may lead to variant misclassification. The results of the epidemiological surveillance should be relying on NGS results.
Source link: https://europepmc.org/article/PPR/PPR506278
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