Rapid genotyping of SARS-CoV-2 variants of concern

Variants of Concern (VOCs) – a growing watch list

A number of concerning lineages classified as VOCs are associated with either higher transmissibility, virulence or ability to evade the immune response gained through prior infection or vaccination. The mutations in the viral genome of these variants are associated with change in 'fitness' or are unique to their lineage and can therefore be used as genetic markers for genotyping. It allows discriminating from the wild-type (WT) strain or other variants. Confronting these new variants demands constant surveillance and accelerated development of innovative early-detection tools.

Table summarizing VOCs and notable mutations¹ (updated periodically)
Although next-generation sequencing (NGS) methods are available for variant surveillance, qRT-PCR and Pyrosequencing present notably quicker options for highly sensitive detection of specific mutations and VOCs, generating same-day genotyping results. 
QIAGEN leverages its expertise in assay design for these two technologies to provide your lab with high-performance genotyping assays.
QIAprep&Amp was developed to simplify and accelerate PCR analysis of SARS-CoV-2 and other RNA viruses for epidemiological research.

LNA-based qPCR genotyping assays

Verified assays to track the current mutations

For labs that need to track currently relevant mutations, wet-lab tested LNA-based qPCR genotyping assays have been designed to detect SARS-CoV-2 variants of concern. Their performances in terms of specificity and sensitivity have been verified using the QIAprep&amp Viral RNA UM Kit.

Note: In some cases, detecting one of the mutations would be sufficient to identify a variant of concern (e.g., Delta/P681R). However, more than one assay is recommended (e.g., Delta/T478K+L452R) to achieve a higher degree of confidence in detection.

Constant surveillance and accelerated development
The SARS-CoV-2 virus keeps constantly evolving through mutations, and these are cause for concern. To keep pace, we continue to develop and verify new genotyping assays. Want to be the first to learn whenever a new assay becomes available?
Start tracking new mutations as quickly as possible

For labs that cannot wait for the availability of validated kits to respond quicker to new mutations, a rapid and straightforward Pyrosequencing workflow allows labs to implement new assays for new variants faster than other techniques.


1. Investigation of SARS-CoV-2 variants of concern: technical briefings. Public Health England. See all updates.

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