The Omicron Variant
On November 26th, the World Health Organization (WHO) designated B.1.1.529 (Omicron) a variant of concern (VOC), the fifth variant to receive this designation 1. While information is still pouring in, researchers suspect that this variant might have:
- Higher transmissibility than the Delta variant 1
- The ability to evade vaccine/immunity effectiveness 1
- Been the cause for a recent surge in SARS-CoV-2 cases in South Africa 1
There have been more than 30 mutations identified in the B.1.1.529 variant’s spike protein. Several of these mutations are present in other variants that have shown to be associated with increased transmissibility of the virus and impairing effectiveness of vaccines and/or immunity. Currently, it is unknown if the Omicron variant causes more severe disease than other variants. The WHO asked countries to enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants 1.
Diagnosing Samples Containing the Omicron Variant
PerkinElmer constantly monitors SARS-CoV-2 variants databases on NCBI, GISAID and SARS-CoV-2 publications (PubMed). The information is used to perform thorough bioinformatics analysis routinely. Based on the analysis performed as of November 28, 2021, the performance of PerkinElmer SARS-CoV-2 RT-PCR Detection Kits is not impacted by mutations associated with the Omicron variant. These include:
- PerkinElmer® New Coronavirus Nucleic Acid Detection Kit (2019-nCOV-PCR-AUS)*** – FDA EUA
- SARS-CoV-2 RT-qPCR Reagent kit (3501-0010)** – CE-IVD
- PerkinElmer® SARS-CoV-2 Plus RT-qPCR Reagent kit (3515-0010)** – CE-IVD
- PerkinElmer® SARS-CoV-2 Real-time RT-PCR assay (COVID-19-PCR-AUS-C)** – CE-IVD
- PKamp™ Respiratory SARS-CoV-2 RT-PCR Panel 1 (SDX-56390, SDX-56391)*** – FDA EUA
- PKamp™ Respiratory SARS-CoV-2 RT-PCR Panel kit (3504-0010, 3504-001B)** – CE-IVD
- PKamp™ Respiratory SARS-CoV-2 RT-PCR Panel (SDX-56392, SDX-56393)** – CE-IVD
- EURORealTime® SARS-CoV-2 assay – MP 2606-0100, MP 2606-0200, MP 2606-1000** – CE-IVD
- EURORealTime® SARS-CoV-2 assay – MP 2606-0100, MP 2606-0200, MP 2606-1000*** – FDA EUA
- EURORealTime® SARS-CoV-2 Influenza A/B assay – MP 2606-0100-20, MP 2606-0200-20, MP 2606-1000-20** CE-IVD
Most of the Omicron mutations are in the S gene (coding for the Spike protein), which PerkinElmer prudently avoided or specifically targeted given that the S gene is prone to mutations.2
Detecting Mutations Associated with the Omicron Variant
The PKamp™ VariantDetect™ SARS-CoV-2 RT-PCR Assay* enables fast identification of mutations associated with variants such as Omicron in a positive SARS-COV-2 sample, delivering results within hours. It is a cost-effective solutions for 2nd tier mutation typing using extracted sample available from 1st tier testing. The PKamp™ VariantDetect™ SARS-CoV-2 RT-PCR Assay has combinations available to support the identification of mutations associated with both the omicron and the silent omicron variant.
The PerkinElmer® SARS-CoV-2 Plus RT-qPCR Reagent kit** explicitly picks up SARS-CoV-2 signatures in ORF1ab, Envelope (E), and Nucleocapsid (N) genes – this enables detection of the Omicron variant, alongside detection of SARS-CoV-2 in the 1st tier RT-PCR assay.
Detecting Omicron with NGS
Two of the primary advantages NGS offers over alternative methods of SARS-CoV-2 mutation detection, are identifying new variants and tracking variants rapidly after they are characterized. The NEXTFLEX® Variant-Seq™ SARS-CoV-2 Kit v2* detects all mutations associated with variants in a SARS-CoV-2 positive sample. With the incorporation of normalization beads, this kit reduces turn-around time by three hours primarily due to elimination of individual library quantification prior to the pooling step. Additionally, 1,536 UDIs incorporated in the NEXTFLEX® Variant-Seq™ SARS-CoV-2 Kit v2* enable the sequencing of 6,000 SARS-CoV-2 libraries in one flow cell, providing extremely high throughput. The kit has detected and reported the Omircon VOC. The image below is taken from the analysis report of a sample containing the Omicron VOC detected using the NEXTFLEX® Variant-Seq™ SARS-CoV-2 kit.