Dec 30, 2020 4:23:51 PM
Written By: Biomeme Staff
Biomeme continuously monitors and analyzes sequences of emerging variants of concern and updates this table accordingly.
||CDC Variant Classification||Biomeme Assay Detection|
|B.1.1.529, BA.1, BA.1.1, BA.2, BA.3, BA.4 and BA.5 lineages||Omicron||Concern|
Variant of Concern (VOC)
A SARS-CoV-2 variant that meets the definition of a VOI (see below) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance:
Variant of Interest (VOI)
A SARS-CoV-2 variant with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; and:
Variant Under Monitoring (VUM)
A SARS-CoV-2 variant with genetic changes that are suspected to affect virus characteristics with some indication that it may pose a future risk, but evidence of phenotypic or epidemiological impact is currently unclear, requiring enhanced monitoring and further assessment pending new evidence.
(Source: WHO - Tracking SARS-CoV-2 variants)
Biomeme performed in-silico analysis of genetic sequences of variants of concern. Sequences were downloaded from GISAID filtered for each variant by pango lineage and local BLAST alignments were performed. Results are as follows:
B.1.1.529, BA.1, BA.1.1, BA.2, BA.3, BA.4 and BA.5 lineages (Pango lineageexternal icon)a
Name (Nextstrainexternal icon)b: 21K
Spike Protein Substitutions: A67V, del69-70, T95I, del142-144, Y145D, del211, L212I, ins214EPE, 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
WHO Label: Omicron
First Identified: Multiple Countries
A total of 166 genomes of SARS-CoV-2 lineage B.1.1.529 were downloaded from GISAID.
BLASTn analysis alignments were performed with the oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay.
Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 100% of the genomes analyzed (n=166).
Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 100% of the genomes analyzed (n=166).
Update (1/6/2023): The Biomeme SARS-CoV-2 assay detects Omicron subvariant XBB.1.5, projected to make up 40.5% of COVID-19 cases nationally by the CDC the week of 12/25/22, and all other currently known Omicron subvariants.
B.1.617.2 (Pango lineageexternal icon)
Spike Protein Substitutions: T19R, (G142D*), 156del, 157del, R158G, L452R, T478K, D614G, P681R, D950N
Name (Nextstrainexternal icon): 20A/S:478K
WHO Label: Delta
First Identified: India
B.1.525 (Pango lineageexternal icon)
Spike Protein Substitutions: A67V, 69del, 70del, 144del, E484K, D614G, Q677H, F888L
Name (Nextstrainexternal icon): 20A/S:484K
WHO Label: Eta
First Identified: United Kingdom/Nigeria – December 2020
B.1.621 (Pango lineageexternal icon)
Name (Nextstrainexternal icon): 21H
First Identified: Colombia, Jan 2021
B.1.1.7 (Pango lineageexternal icon)
Spike Protein Substitutions: 69del, 70del, 144del, (E484K*), (S494P*), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H (K1191N*)
Name (Nextstrainexternal icon): 20I/501Y.V1
WHO Label: Alpha
First Identified: United Kingdom
B.1.351 (Pango lineageexternal icon)
Spike Protein Substitutions: D80A, D215G, 241del, 242del, 243del, K417N, E484K, N501Y, D614G, A701V
Name (Nextstrainexternal icon): 20H/501.V2
WHO Label: Beta
First Identified: South Africa
P.1 (Pango lineageexternal icon)
Spike Protein Substitutions: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I
Name (Nextstrainexternal icon): 20J/501Y.V3
WHO Label: Gamma
First Identified: Japan/Brazil
B.1.526 (Pango lineageexternal icon)
Spike Protein Substitutions: L5F, (D80G*), T95I, (Y144-*), (F157S*), D253G, (L452R*), (S477N*), E484K, D614G, A701V, (T859N*), (D950H*), (Q957R*)
Name (Nextstrainexternal icon): 20C/S:484K
WHO Label: Iota
First Identified: United States (New York) – November 2020
B.1.617.1 (Pango lineageexternal icon)
Spike Protein Substitutions: (T95I), G142D, E154K, L452R, E484Q, D614G, P681R, Q1071H
Name (Nextstrainexternal icon): 20A/S:154K
WHO Label: Kappa
First Identified: India – December 2020
C.37 (Pango lineageexternal icon)
Name (Nextstrainexternal icon): 21G
First Identified: Peru, Dec 2020
The Biomeme test detects two different SARS-CoV-2 genes and it is conveniently multiplexed together with our RNA Process Control (RPC) for RNA extraction and RT-PCR. Each reaction well of our test already contains lyophilized master mix, enzymes, and multiplexed primer/probes for the following triplex reaction:
In summary, the Biomeme SARS-CoV-2 Real-Time PCR Test will detect all the SARS-CoV-2 variants of concern and interest. Biomeme is continuously monitoring and analyzing sequence of emerging variants of concern and will update accordingly.
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