Alternative names:
SARS-CoV-2 Omicron variant

Specifications for
PepTivator
®
SARS-CoV-2 Prot_S B.1.1.529

Overview

Stimulate T cells reactive to the spike protein of the BA.1 or BA.2 variant of the SARS-CoV-2 B.1.1.529 lineage (Omicron variant) using PepTivator Peptide Pools. PepTivators are pools of lyophilized peptides, consisting mainly of 15-mer sequences with 11 amino acids overlap. PepTivators are available for the BA.1 as well as the BA.2 subvariant of the SARS-CoV-2 B.1.1.529 lineage (Omicron variant). The PepTivator Mutation Pools cover selectively the mutated regions in the surface or spike glycoprotein (“S”) of the respective variant, whereas WT Reference Pools cover the homologous domains of the Wuhan sequence.
In vitro
stimulation of antigen-specific T cells with PepTivator Peptide Pools causes the secretion of effector cytokines and the up-regulation of activation markers, which then allow the detection and isolation of antigen-specific T cells.

Alternative names

SARS-CoV-2 Omicron variant

Detailed product information

Background information

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was first detected in December 2019 in Wuhan, China. Since that time the virus kept mutating, leading to new virus variants. The B.1.1.529 lineage, also known as Omicron variant, is a SARS-CoV-2 variant that was first discovered in South Africa and Botswana in November 2021. The variant has been further classified into the sublineages BA.1, BA.2, and BA.3. The mutations of the BA.1 and the BA.2 variant affect also immune relevant parts of structural SARS-CoV-2 proteins and the respective sequences are available in GISAID, a genome data base. The mutations listed below are either taken from EPI_ISL_6704874 for B.1.1.529/BA.1 or from EPI_ISL_10319603 for B.1.1.529/BA.2. Both lineages, B.1.1.529/BA.1 and B.1.1.529/BA.2, appear to be more infectious than other variants and are classified by the WHO as “variant of concern” in November 2021.
For the B.1.1.529/BA.1 lineage (Omicron variant), there are in total 37 mutations in the surface or spike glycoprotein (“S”) compared to the Wuhan variant (reference genome GenBank MN908947.3): A67V, H69 deletion, V70 deletion, T95I, G142D, V143 deletion, Y144 deletion, Y145 deletion, N211 deletion, L212I, insertion 214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. The PepTivator SARS-CoV-2 Prot_S B.1.1.529/BA.1 Mutation Pool covers selectively the mutated regions. It consists of 83 peptides of 15 aa length. For control purposes, a respective wild-type (WT) reference pool covering the homologous domains of the Wuhan sequence is available. The PepTivator SARS-CoV-2 Prot_S B.1.1.529/BA.1 WT Reference Pool covers the homologous domains of the Wuhan variant: A67, H69, V70, T95, G142, V143, Y144, Y145, N211, L212, (214 w/o insertion), G339, S371, S373, S375, K417, N440, G446, S477, T478, E484, Q493, G496, Q498, N501, Y505, T547, D614, H655, N679, P681, N764, D796, N856, Q954, N969, L981 (reference genome GenBank MN908947.3).
For the B.1.1.529/BA.2 lineage (Omicron variant), there are in total 31 mutations in the surface or spike glycoprotein (“S”) compared to the Wuhan variant (reference genome GenBank MN908947.3): T19I, L24 deletion, P25 deletion, P26 deletion, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K. The PepTivator SARS-CoV-2 Prot_S B.1.1.529/BA.2 Mutation Pool covers selectively the mutated regions. It consists of 68 peptides of 15 aa length. For control purposes, a respective wild-type (WT) reference pool covering the homologous domains of the Wuhan sequence is available. The PepTivator SARS-CoV-2 Prot_S B.1.1.529/BA.2 WT Reference Pool covers the homologous domains of the Wuhan variant: T19, L24, P25, P26, A27, G142, V213, G339, S371, S373, S375, T376, D405, R408, K417, N440, S477, T478, E484, Q493, Q498, N501, Y505, D614, H655, N679, P681, N764, D796, Q954, N969 of the Wuhan variant (reference genome GenBank MN908947.3).
The PepTivator Mutation Pools for the SARS-CoV-2 B.1.1.529 variants can be
  • applied individually to stimulate T cells reactive to the SARS-CoV-2 spike protein of a) the BA.1 subvariant (Prot_S B.1.1.529/BA.1 Mutation Pool) or b) the BA.2 subvariant (Prot_S B.1.1.529/BA.2 Mutation Pool)
  • used together (Prot_S B.1.1.529/BA.1 Mutation Pool plus Prot_S B.1.1.529/BA.2 Mutation Pool) to analyze T cells reactive to both subvariants, BA.1 and BA.2
  • used to supplement PepTivators covering the sequence of the wild-type spike glycoprotein (“S”) in order to detect immune responses towards both variants, Wuhan (wildtype) variant and the respective subvariant of B.1.1.529 lineage (Omicron variant). PepTivator Peptide pools spanning the sequence of the spike glycoprotein (“S”) of the Wuhan (wild-type) variant are, for example, PepTivator SARS-CoV-2 Prot_S1 (N-terminal S1 domain) or Prot_S Complete (all functional domains).
Comparison of the T cell immune response upon stimulation with mutation or wild-type (WT) reference pool can be used to analyze mutation-specific T cell responses. PepTivator SARS-CoV-2 Prot_S B.1.1.529/BA.1 WT Reference Pool serves as a control for the SARS-CoV-2 Prot_S B.1.1.529/BA.1 Mutation Pool, whereas PepTivator SARS-CoV-2 Prot_S B.1.1.529/BA.2 WT Reference Pool serves as a control for the SARS-CoV-2 Prot_S B.1.1.529/BA.2 Mutation Pool.

Applications

The
in vitro
stimulation of SARS-CoV-2–specific CD4
+
and CD8
+
T cells with PepTivators causes secretion of effector cytokines and upregulation of activation markers, which then allow the detection and isolation of SARS-CoV-2–specific T cells:
  • Detection and analysis of antigen-specific CD4+ and CD8+ effector/memory T cells in PBMCs by MACS Cytokine Secretion Assays, intracellular cytokine staining, or other technologies.
  • Isolation of viable antigen-specific CD4+ T cells with the CD154 MicroBead Kit, or of viable CD4+ and CD8+ T cells using MACS Cytokine Secretion Assay – Cell Enrichment and Detection Kits. Subsequently, cells can be expanded for generation of T cell lines.
  • Generation antigen-specific CD4+ and CD8+ effector/ memory T cells from naive T cell populations.
  • Pulsing of antigen-presenting cells, e.g., for research on dendritic cell vaccination.

Technical data

Overview of amino acid mutations in the spike (S) protein in SARS-CoV-2 variants of the B.1.1.529 lineage (Omicron variant).
Overview of amino acid mutations in the spike (S) protein in SARS-CoV-2 variants of the B.1.1.529 lineage (Omicron variant).

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