Biomeme’s SARS-CoV-2 Assay Detects All Current Variants of Concern and Interest

What do the Variant Classifications Mean?

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:

• Increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
  
• Increase in virulence or change in clinical disease presentation; OR
  
• Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.

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:

• Identified to cause significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside an increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health.

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)

How Does Each Variant Impact Biomeme's SARS-CoV-2 Test?

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:

VARIANTS OF CONCERN

  Omicron Variant  

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.

VARIANTS OF INTEREST (VOI)

• No current Variants of Interest
  
  

VARIANTS UNDER MONITORING (VUM)

  Delta Variant  

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

• A total of 1,983 genomes of SARS-CoV-2 lineage B.1.617.2 were analyzed.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 61.17% of the genomes analyzed (n=1,983).
• There is a single mismatch in the middle of the Orf1ab forward primer sequence in 38.78% of the sequences analyzed. Given the type of mismatch and its position in the primer sequence we predicted no impact to the assay's performance.
• However, given the large percentage of sequence that contain the mismatch we empirically tested the impact to the assay by creating an invitro-transcribed RNA template which contains the mutation.
• The RNA template was tested across 6 orders of magnitude down to 50 copies of RNA per reaction, resulting in 95% efficiency and detection at all template concentrations. 
• No impact to performance due to this mutation.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 99.80% of the genomes analyzed (n=1,983).
  
  

  Eta Variant  

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

• A total of 1,313 genomes of SARS-CoV-2 lineage B.1.525 were analyzed.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 99.54% of the genomes analyzed (n=1,313).
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 99.77% of the genomes analyzed (n=1,313).
  
  

  Mu Variant 

B.1.621 (Pango lineageexternal icon)

Name (Nextstrainexternal icon): 21H

First Identified: Colombia, Jan 2021

• A total of 2,384 genomes of SARS-CoV-2 lineage B.1.621 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 99.54% of the genomes analyzed (n=2,384).
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 99.83% of the genomes analyzed (n=2,384).
  
  

  Alpha Variant  

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

• A total of 7,185 genomes of SARS-CoV-2 lineage B.1.1.7 were analyzed.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 99.67% of the genomes analyzed (n=7,185).
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 99.30% of the genomes analyzed (n=7,185).

  Beta Variant  

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

• A total of 5,605 genomes of SARS-CoV-2 lineage B.1.351 were analyzed.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 99.82% of the genomes analyzed (n=5,605).
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 98.95% of the genomes analyzed (n=5,605).

  Gamma Variant  

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

• A total of 9,562 genomes of SARS-CoV-2 lineage P.1 were analyzed.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 88.52% of the genomes analyzed (n=9,562).
• There is a single mismatch in the middle of the Orf1ab probe sequence in 11.32% of the sequences analyzed.
• Given the type of mismatch and its position in the probe sequence we predict 99.7% of the probe to bind at the anneal temperature of the assay. Therefore we anticipate no impact to the overall performance of the assay.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 99.69% of the genomes analyzed (n=9,562).

   Iota Variant   

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

• A total of 10,561 genomes of SARS-CoV-2 lineage B.1.526 were analyzed.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 99.73% of the genomes analyzed (n=10,561).
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 99.75% of the genomes analyzed (n=10,561).

  Kappa Variant  

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

• A total of 1,436 genomes of SARS-CoV-2 lineage B.1.617.1 were analyzed.
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 98.96% of the genomes analyzed (n=1,436).
• 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=1,436).

  Lambda Variant  

C.37 (Pango lineageexternal icon)

Name (Nextstrainexternal icon): 21G

First Identified: Peru, Dec 2020

• A total of 213 genomes of SARS-CoV-2 lineage C.37 were analyzed. 
• 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=213).
• Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 99.53% of the genomes analyzed (n=213).
  
  

More About Biomeme’s SARS-CoV-2 Test

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:

• Orf1ab - Open reading frame 1ab gene
• S - Spike gene
• RPC - RNA Process Control
  

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.