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Review article: Biomedical intelligence

Vol. 151 No. 4950 (2021)

PCR performance in the SARS-CoV-2 Omicron variant of concern?

  • César M. J. A. Metzger
  • Reto Lienhard
  • Helena M. B. Seth-Smith
  • Tim Roloff
  • Fanny Wegner
  • Jonas Sieber
  • Michael Bel
  • Gilbert Greub
  • Adrian Egli
Cite this as:
Swiss Med Wkly. 2021;151:w30120



The new SARS-CoV-2 Omicron variant (B.1.1.529) has been recently declared a Variant of Concern due to a series of important mutations in the viral spike protein and especially in the receptor-binding domain. While investigations into the spread of this new variant are ongoing, the first cases have been detected in Switzerland. Important questions have been raised: (1) Will the PCR assays commonly used to detect SARS-CoV-2 still work for the Omicron variant? (2) Can specific PCR features, e.g. S-gene dropout, be used to identify potential Omicron samples?

In this minireview we provide current knowledge on the Omicron variant and guidance on its PCR validation.


  1. Hodcroft E. CoVariants. 2021. (accessed 06.12.2021).
  2. Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. 2020 May;581(7807):215–20.
  3. Lazarevic I, Pravica V, Miljanovic D, Cupic M. Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Viruses. 2021 Jun;13(7):1192.
  4. Zhang J, Xiao T, Cai Y, Lavine CL, Peng H, Zhu H, et al. Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science. 2021 Oct;374(6573):eabl9463.
  5. Filkins L, SoRelle JA, Schoggins J, Park JY. Laboratory Action Plan for Emerging SARS-CoV-2 Variants. Clin Chem. 2021 Apr;67(5):720–3.
  6. Babb de Villiers C, Blackburn L, Cook S, et al. SARS-CoV-2 variants. In: Diagnostics FfIN, editor.; 2021. p. 1.
  7. Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KH, Althaus CL, et al.; SeqCOVID-SPAIN consortium. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature. 2021 Jul;595(7869):707–12.
  8. Liu Y, Liu J, Plante KS, Plante JA, Xie X, Zhang X, et al. The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature. 2021 Nov.
  9. Washington NL, White S, Barrett KM, Cirulli ET, Bolze A, Lu JT. S gene dropout patterns in SARS-CoV-2 tests suggest spread of the H69del/V70del mutation in the US. medRxiv 2020: 2020.12.24.20248814.
  10. Goncalves Cabecinhas AR, Roloff T, Stange M, Bertelli C, Huber M, Ramette A, et al. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms. 2021 Mar;9(4):677.
  11. Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B, Ferreira IA, et al.; Indian SARS-CoV-2 Genomics Consortium (INSACOG); Genotype to Phenotype Japan (G2P-Japan) Consortium; CITIID-NIHR BioResource COVID-19 Collaboration. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature. 2021 Nov;599(7883):114–9.
  12. Campbell F, Archer B, Laurenson-Schafer H, Jinnai Y, Konings F, Batra N, et al. Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. Euro Surveill. 2021 Jun;26(24).
  13. Organization WH. Update on Omicron. 2021. (accessed 02.12.2021 2021).
  14. Control ECfDPa. European Centre for Disease Prevention and Control. Implications of the further emergence and spread of the SARS CoV 2 B.1.1.529 variant of concern (Omicron) for the EU/EEA first update. 2021. (accessed 03.12.2021 2021).
  15. Gu H, Krishnan P, Ng DY, Chang LD, Liu GY, Cheng SS, et al. Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021. Emerg Infect Dis. 2021 Dec;28(2).
  16. Cele S, Jackson L, Khan K, et al. SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. MedRxiv 2021; 267417v1.
  17. Mullen JL, Tsueng G, Abdel Latif A, et al. 2020. (accessed 03.12.2021 2021).
  18. Vogels CB, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, et al.; Brazil-UK CADDE Genomic Network; Network for Genomic Surveillance in South Africa. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biol. 2021 May;19(5):e3001236.
  19. Lienhard R, Metzger CM, Sieber J, et al. What does the UK variant tell the clinical microbiologists? Pipette. 2021;(2):3.
  20. ERSTER O. Beth Din A, Asraf H, et al. SPECIFIC DETECTION OF SARS-COV-2 B.1.1.529 (OMICRON) VARIANT BY FOUR RT-qPCR DIFFERENTIAL ASSAYS. medRxiv 2021: 2021.12.07.21267293.
  21. SARS-CoV-2 V4.1 update for Omicron variant. 01.12.2021. (accessed 05.12.2021 2021).
  22. Health FOoP. COVID-19 Switzerland. 2021. (accessed 05.12.2021 2021).

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