Biomeme’s SARS-CoV-2 Assay Detects New United Kingdom, South Africa, Brazil, and California Variants

This variant is classified in clade GR, lineage B.1.1.7. Genome sequences (n=250) of SARS-CoV-2 (filtered for clade GR, lineage B.1.1.7 containing mutation Spike_N501Y) were downloaded from GISAID with collection dates from the 2^nd of November 2020 to the 17^th of December 2020. BLASTn analysis alignments were performed with the oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay against all 250 genomes. 

Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay (Orf1ab and S gene targets) have 100% homology to the 250 genomes analyzed of SARS-CoV-2 variant 20I/501Y.V1.

South Africa New Variant

Biomeme has confirmed, through in silico analysis of the genetic sequences, that our SARS-CoV-2 assay detects the new variant reported by South Africa (20H/501Y.V2) which is a novel mutation combination in the Spike receptor binding site, defined by multiple spike protein mutations. 

This variant is classified in clade GH, lineage B.1.351. Genome sequences (n=267) of SARS-CoV-2 (filtered for clade GH, lineage B.1.351 containing mutation Spike_N501Y) were downloaded from GISAID with collection dates from the 2nd of November 2020 to the 10th of December 2020. BLASTn analysis alignments were performed with the oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay against all 267 genomes. 

Oligonucleotide primer sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology to 99% of the genomes analyzed (n=264 of 267) of SARS-CoV-2 South Africa Clade GH, lineage B.1.351

Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to the 267 genomes analyzed of SARS-CoV-2 South Africa Clade GH, lineage B.1.351.

Brazil New Variant

Biomeme has confirmed, through in silico analysis of the genetic sequences, that our SARS-CoV-2 assay detects the new variant reported by Brazil (20J/501Y.V3).
The SARS-CoV-2 lineage B.1.1.28 has been evolving in Brazil since February 2020, but the recent emergence of sub-lineages with convergent mutations in the spike (S) protein raises concern about the potential impact on viral infectivity and immune escape.

Brazil has reported a strain with multiple spike gene mutations as well as a deletion in Orf1ab gene. This variant is classified as 20J/501Y.V3. Genome sequences (n=178) of SARS-CoV-2 (filtered for clade GR variant 484K.V2) were downloaded from GISAID with collection dates from the 9th of October2020 to the 10th of January 2021. BLASTn analysis alignments were performed with the oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay against all 178 genomes.

Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay (Orf1ab and S gene targets) have 100% homology to the 178 genomes analyzed of SARS-CoV-2 variant 20J/501Y.V3.

California New Variant

Biomeme has confirmed, through in silico analysis of the genetic sequences, that our SARS-CoV-2 assay detects the new variant reported by California (GH/452R.V1, B.1.429, CAL20.C).

California has reported a novel variant with a mutation L452R in the Spike gene. This variant is classified in clade GH, lineage B.1.429. Genome sequences (n=273) of SARS-CoV-2 (filtered for clade GH, lineage B.1.429 containing mutation Spike_L452R) were downloaded from GISAID with collection dates from the 28th of September 2020 to the 18th of January 2021. BLASTn analysis alignments were performed with the oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay against all 273 genomes.

Oligonucleotide primer and probe sequences of the Biomeme SARS-CoV-2 multiplex assay S gene target has 100% homology to 99.6% the 273 genomes analyzed of SARS-CoV-2 Clade GH, lineage B.1.429.

• One sequence were found to have 96% homology containing single mismatch in the S Probe.
  • GISAID Accession # EPI_ISL 911961

Oligonucleotide primer sequences of the Biomeme SARS-CoV-2 multiplex assay Orf1ab gene target has 100% homology the 273 genomes analyzed of SARS-CoV-2 Clade GH, lineage B.1.429.

About Biomeme’s SARS-CoV-2 Assay

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 the SARS-CoV-2 variants of concern from the United Kingdom, South Africa, Brazil, and California. Biomeme is continuously monitoring and analyzing sequence of emerging variants of concern and will update accordingly.