QUICKLY IDENTIFY KNOWN SARS-COV-2 MUTATIONS WITH RT-PCR INCLUDING THE OMICRON VARIANT

PKamp VariantDetect SARS-CoV-2 RT-PCR Assay

The PKamp VariantDetect SARS-CoV-2 RT-PCR assays utilize real-time RT-PCR multiplexing technology for simultaneous qualitative detection and differentiation of several known SARS-CoV-2 mutations. The assays provide information about SARS-CoV-2 mutations allowing labs to identify known variants from positive samples.

  • Identify mutations in a positive sample within hours
  • Leverage existing RT-PCR workflow used for 1st tier testing
  • Cost-effective 2nd tier mutation typing using extracted sample available from 1st tier testing
  • Different combinations kits can be run on the same PCR run program with as little as 2 µL of RNA/well
  • Compatible with all commonly available real-time PCR instruments
Rapid detection of SARS-CoV-2 mutations
For research use only. Not for use in diagnostic procedures.

Detectable SARS-CoV-2 Mutations

The PKamp VariantDetect SARS-CoV-2 RT-PCR assay allows labs to promptly perform secondary testing on positive COVD-19 samples to identify mutations in the SARS-CoV-2 virus in the samples.

Omicron VOC (B.1.1.529) : Contains at least 32 mutations in the spike protein gene including some seen in the Alpha, Beta, Gamma, and Delta variants*. These mutations have been previously known to increase transmissibility of SARS-CoV-2 as well as potentially evade vaccine and naturally gained immunity.

Delta VOC (B.1.617):  There are eight mutations in the Delta virus’s spike protein including the common signature mutations D111D, G142D, L452R, E484Q, D614G and P681R in the spike protein coding region, including within the receptor binding domain (RBD).

Alpha VOC (B.1.1.7) : Amongst other mutations, a 69/70 deletion in the spike protein gene has been reported in the Alpha variant*. This variant is of concern because it is associated with increased transmissibility.

Beta VOC (B.1.351): Multiple mutations have been reported in the spike protein for the Beta variant, including E484K and N501Y.* B.1.351 does not have the residue 69-70 deletion observed in B.1.1.7, but a deletion at residues 242-244 has been reported***.

Gamma VOC (P.1): Three mutations in the spike protein receptor binding domain: K417T, E484K, and N501Y have been reported in the Gamma variant. This variant also does not contain the deletion at 69/70 in the spike protein gene.* The P.1 variant may increase transmissibility or propensity for SARS-CoV-2 to re-infect individuals.

PKamp™ VariantDetect™ SARS-CoV-2 RT-PCR Assay Workflow

KIT INFORMATION

KIT PART NUMBER MUTATIONS OF INTEREST
COMBINATION 4 SDX-56618 N501Y, E484K, E484Q
COMBINATION 5 SDX-56619 K417N, K417T, 69-70 Deletion
COMBINATION 6 SDX-56620 L452R, P681H, P681R
COMBINATION 7
Combination F (CE-IVD)
SDX-56621
SDX-56617 (Combination 7 plus control set)
L452R, E484K, E484Q
COMBINATION 8 SDX-56622 K417T, K417N, P681R
COMBINATION 9 Inquire L452Q, P681H, P681R
COMBINATION 10 Inquire L452Q, E484K, E484Q
COMBINATION 11 SDX-56627 Q493R
COMBINATION 12 Inquire L452R, E484K, 69-70 Deletion
COMBINATION 13 Inquire L452R, E484K, Q493R
COMBINATION 14 Inquire E484A, E484K, E484Q
COMBINATION 15 Inquire Q493R, R408S, P681R
COMBINATION 16 Inquire Q493R, R408S, V213G
CONTROL SET TO SUPPORT COMBINATION 3-8 SDX-56626
CONTROL SET TO SUPPORT COMBINATION 9-10 Inquire
CONTROL SET TO SUPPORT COMBINATION 11 SDX-56628
CONTROL SET TO SUPPORT COMBINATION 12-16 Inquire
Example surveillance panel to identify Omicron mutations utilizing Combination 5 & 15. Note: In addition to identifying Omicron mutations, this surveillance panel can also identify and distinguish Delta and Delta Plus mutations.

Additional mutations that may of interest: D614G, A222V, Y453F, N439K , A570D, T716I, S982A, A1708D, A701V, Q27stop, delY144, D80A, L18F, R246I, D215G, N856K, H655Y, Q498R, S373P, del 143/145, D796Y,G496S, G446S, S371L, G142D, L981F, N764K, T547K, Q493K, N440K, G339D, T95I, N969K, Y505H, E484A, ins214EPE, Q954H, N679K, T478K, S375F, del211/212, A67V . Please contact us about assays for targeting these mutations. Our team is closely tracking literature and trends in partner labs across the globe to identify and design assays for detecting emerging mutations related to increased penetration, vaccine efficacy, immune response, and therapy.

PerkinElmer’s Complete SARS-CoV-2 RT-PCR Workflow

PerkinElmer enables labs to simplify secondary SARS-CoV-2 variant detection while maintaining sample integrity and avoid cross contamination of SARS-CoV-2 PCR samples by providing modular and scalable automated workflow solutions. PerkinElmer’s RT-PCR-based SARS-CoV-2 variant identification workflow provides automation with flexible throughput, and full traceability.

The assays are designed for real-time RT-PCR instruments with FAM, ROX, Cy®5 and/or HEX/VIC channels.

PKamp VariantDetect Workflow
  1. Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Boudet et al., Diagnostics 2021, 11(7), 1241; https://doi.org/10.3390/diagnostics11071241.
  2. Spread of SARS-CoV-2 Delta variant infections bearing the S:E484Q and S:T95I mutations in July and August 2021 in France. Verdurme, et al. https://www.medrxiv.org/content/10.1101/2021.09.13.21263371v1.full.pdf

Figure 1. Combo 7 RT-PCR Amplification Sensitivity Test on Applied Biosystems™ QuantStudio™ Dx Real-Time PCR System. Combo 7 specifically amplified target mutations in synthetic SARS-CoV-2 variant RNA from Twist Bioscience at 200 copies/reaction. WT: wild type, NTC: negative control.

Figure 1. Combo 7 RT-PCR Amplification Sensitivity Test on Applied Biosystems™ QuantStudio™ Dx Real-Time PCR System. Combo 7 specifically amplified target mutations in synthetic SARS-CoV-2 variant RNA from Twist Bioscience at 200 copies/reaction. WT: wild type, NTC: negative control.


Figure 3. Combo 8 RT-PCR Amplification Sensitivity Test on Applied Biosystems™ QuantStudio™ Dx Real-Time PCR System. Combo 8 specifically amplified target mutations in synthetic SARS-CoV-2 variant RNA from Twist Bioscience at 40 copies/reaction. WT: wild type, NTC: negative control.

Figure 2. Combo 8 RT-PCR Amplification Sensitivity Test on Applied Biosystems™ QuantStudio™ Dx Real-Time PCR System. Combo 8 specifically amplified target mutations in synthetic SARS-CoV-2 variant RNA from Twist Bioscience at 40 copies/reaction. WT: wild type, NTC: negative control.

* ECDC SARS-CoV-2 variants of concern as of 26 November 2021.

** CDC Emerging SARS-CoV-2 Variants. March 2, 2021.

*** ECDC Risk related to the spread of new SARS-CoV-2 variants of concern in the EU/EEA – first update, January 21, 2010.

Contact us to Quickly identify known SARS-CoV-2 mutations
For research use only. Not for use in diagnostic procedures.