Understanding SARS-CoV-2 epidemiology from every angle

Future-proofing SARS-CoV-2 detection

Information on new SARS-CoV-2 variants is constantly arising, with concerns about the effectiveness of current detection methods. The unique assay design offered by the SARS-CoV-2 Neo Assay compensates for emerging mutations. Because the assay addresses 6 targets within 4 genomic regions (ORF1a, ORF1b, ORF3a, ORF7a, N1 and N2), the probability of getting sensitive and specific results is increased to a maximum, providing confidence in detection now and into the future.

The SARS-CoV-2 Neo Assay is optimized to work with the proven QIAprep&amp Viral RNA UM Kit, various transport media, sample types and real-time PCR cyclers, offering a fast and easy detection workflow.


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The next generation of SARS-CoV-2 detection

Learn how an enhanced assay compensates for emerging mutations and increases detection confidence today and in the future

Variants of Concern (VOCs) – a growing watch list

Several concerning lineages classified as VOCs are associated with higher transmissibility, virulence, or the ability to evade the immune response gained through prior infection or vaccination. The mutations in the viral genome of these variants are associated with a change in 'fitness' or are unique to their lineage and can be used as genetic markers for genotyping. It allows discriminating from the wild-type (WT) strain or other variants. Confronting these new variants, including the Omicron/B.1.1.529 variant, demands constant surveillance and the 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.
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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, Omicron/K417N+Del HV 69/70) to achieve a higher degree of confidence in detection.

Variants discrimination assays in overcoming the SARS-CoV-2 research challenges

Find out how these genotyping assays can track the current mutations and variants

One workflow, multiple viruses

Scalable, fast and sensitive PCR-based pathogen detection and mutation verification workflows are critical, but that’s not enough.

The 2021-22 flu season is expected to be strong, and there’s an increasing overlap in symptoms between the co-circulating respiratory viruses. Therefore, the research challenge will be to confidently differentiate between these viruses.

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Multitarget detection assay

Reliable detection of multiple respiratory viruses in one reaction

In a single real-time PCR reaction using your current lab equipment, this highly specific and sensitive multiplex assay can detect and discriminate between Influenza A, Influenza B, RSV A/B and SARS-CoV-2 in under one hour – all while maintaining the workflow simplicity and research costs.

Expand your SARS-CoV-2 research to Flu and RSV

Learn how to confidently differentiate between co-circulating respiratory viruses in a single reaction

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.

Reading list:

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

2. Will Omicron end the pandemic? Here’s what experts say (

3. Mukaigawara, M., Hassan, I., Fernandes, G. et al. An equitable roadmap for ending the COVID-19 pandemic. Nat Med 28, 893–896 (2022)

4. Chen, JM. Novel statistics predict the COVID-19 pandemic could terminate in 2022. J Med Virol. 2022 Jun;94(6):2845-2848

5. SARS-CoV-2 variants of concern as of 18 August 2022 (

6. Boni, M.F., Lemey, P., Jiang, X. et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 5, 1408–1417 (2020)

7. Simon-Loriere, E., Schwartz, O. Towards SARS-CoV-2 serotypes?. Nat Rev Microbiol 20, 187–188 (2022)

8. Singh, D., Yi, S.V. On the origin and evolution of SARS-CoV-2. Exp Mol Med 53, 537–547 (2021)

9. Masters PS. The molecular biology of coronaviruses. Adv Virus Res. 2006;66:193-292

10. Jüni P, Baert S, Corbeil A, et al. Use of Rapid Antigen Tests during the omicron wave. Science Briefs of the Ontario COVID-19 Science Advisory Table. 2022;3(56)

11. Tuekprakhon A. et al., Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum, Cell, Volume 185, Issue 14, 2022, Pages 2422-2433.e13