BioGX Delta Variant (B.1.617.2) Update

Delta Variant (B.1.617.2) Update – 14 July 2021

BioGX has been closely surveilling the emergence of new coronavirus variants ensuring its products performance in detecting SARS-CoV-2. The emerging variant known as “delta variant” or B.1.617.2 has been documented globally.  Variant B.1.617.2  is considered to be more transmissible than variants  B.1.1.7 and B.1.351.  BioGX has utilized the GISAID database to analyze over 110,000 sequences of the B.1.617.2 variant (available as of July 12, 2021) to assess any potential impact the mutations may have on the performance of all BioGX SARS-CoV-2 tests. The in silico analysis demonstrated >99% of the B.1.617.2 sequences did not possess mutations that would affect the performance of any BioGX SARS-CoV-2 tests.

 

U.S. CDC and WHO Variants of Concern*

% Clades detected by targets

WHO designation

Pango lineage

GISAID

clade

Nextstrain clade

Spike Protein

(a.a. changes)

Region Initially Documented (Date)

No. Sequences Analyzed

(Date)

N1

N2

Alpha

B.1.1.7

Q.x

GRY 20I (V1) 69del, 70del, 144del, (E484K**),(S494P**),N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, (K1191N**) United Kingdom (SEP 2020) 371,793 (31AUG2021) >99% >99%

Beta

B.1.351

B.1.351.2

B.1.351.3

GH/501Y.V2 20H (V2) L18F, D80A, D215G, 241del, 242del, 243del, K417N, E484K, N501Y, D614G, A701V South Africa (MAY 2020) 22,029

(31AUG2021)

>99% >99%

Gamma

P.1

P.1.x

GR/501Y.V3 20J (V3) 681H,L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I Brazil

(NOV 2020)

53,644

(31AUG2021)

>99% >99%

Delta

B.1.617.2

AY.x

G/478K.V1 21A 417N, T19R, (V70F**), T95I, G142D, E156-, F157-, R158G, (A222V**), (W258L**), (K417N**), L452R, T478K, D614G, P681R, D950N India

(OCT 2020)

305,740 (31AUG2021) >99% >99%

 

COVID-19 New Variant Update – 08 January 2021 

During the course of the SARS-CoV-2 pandemic the virus has accumulated a number of mutations in its genome, causing concern not only for whether the mutations might affect vaccine effectiveness, but also for diagnostic test detection of emerging strain variants.  Most recently, a number of reports have hypothesized that strains from the B.1.1.7 lineage of SARS-CoV-2 possess a higher infectivity rate compared to the other SARS-CoV-2 lineages. The strains from this lineage are the predominant strains currently circulating in the United Kingdom and have been recently identified in other countries. In addition to this lineage, a strain variant designated 501Y.V2 (within B.1.351 lineage) has been associated with increased infectivity and is currently circulating in South Africa.  

There are 17 non-synonymous mutations and deletions identified to date within the B.1.1.7 lineage, with 15 of those being located in the ORF1ab, ORF8, and Spike Protein genes.  None of these mutations affect viral detection ability by any of the BioGX assays which target the N gene.   Moreover, out of the 17 identified mutations only 2 are located in the N gene region, but are located outside of the region targeted by BioGX assays.  The BioGX assays target a unique region of the N gene which is unaffected by the N gene mutations in the B.1.1.7 lineage or the 501Y.V2 variants. 

BioGX utilizes primers and probes for detection of SARS-CoV-2, targeting the viral nucleocapsid gene (N gene region), human RNaseP gene as an endogenous control, and a non-naturally occurring internal amplification control (IAC).  Both the SARS-CoV-2 N1/N2, and RNase P primer/probe sets are based upon those designed and recommended by the US Centers for Disease Control and Prevention. The following four BioGX SARS-CoV-2 testing products utilize the US Centers for Disease Control and Prevention primer/probe set designs for N-gene region(s):

  1. BioGX Xfree™ COVID-19 Direct RT-PCR
  2. BD BioGX SARS-CoV-2 Reagents for BD MAX™ System 
  3. BioGX SARS-CoV-2 HMP – N1, N2 & RNase P Multiplex 
  4. BioGX COVID-19, Flu A, Flu B, RSV RT-PCR for BD MAX™

BioGX performed exhaustive genomic sequence database (GISAID & NIH) analysis in order to determine if any of the genomic sequences from the potentially more infectious B.1.1.7 lineage or 501Y.V2 variant possess any mutations in the N region targeted by the BioGX test might affect detection of the virus. Our in silico analysis utilized over 4,200 SARS-CoV-2  B.1.1.7 lineage genomes available from the GISAID and NIH databases (as of January 4, 2021).The predicted detection of 99.9% of the SARS-CoV-2 B.1.1.7 lineage remains unchanged with the BioGX tests. In silico analysis of the 320 sequences available in the GISAID database (as of January 4, 2021) belonging to the 501Y.V2 variant (within B.1.351 lineage) predicted no change in PCR detection with the BioGX tests.

In summary, as of January 4, 2021, in silico analysis of the N gene regions targeted by the BioGX tests predicts strains within the potentially more infectious B.1.1.7 lineage and 501Y.V2 variants (within B.1.351 lineage) of SARS-CoV-2 circulating in the United Kingdom, South Africa, and other countries will be detected. 

BioGX Receives FDA EUA for a Novel, High-Throughput, Direct Sample RT-PCR Test for COVID-19

Xfree™ COVID-19 Direct RT-PCR TestBirmingham, Alabama, July 01, 2021 – BioGX, a global provider of molecular diagnostic solutions, announced that the United States Food and Drug Administration has issued Emergency Use Authorization (EUA) for their breakthrough direct sample addition, Xfree COVID-19 test. Xfree COVID-19 is a complete test lyophilized in a single tube, for extraction-free, direct sample addition real-time RT-PCR testing.  The Xfree COVID-19 test eliminates all upfront sample processing steps and enables clinical laboratories to generate high-throughput Sample-to-Answer results using widely available real-time PCR platforms. 

 

Matthew Beckman, Ph.D., Director of Laboratory Services at GENETWORx said, “The staff at GENETWORx has been very pleased with the performance of the BioGX Xfree COVID-19 test. In our studies, the test performed superior to other SARS-CoV-2 tests we evaluated in head-to-head comparisons. BioGX test is very simple to use while providing increased quality assurance of well-by-well monitoring of the PCR reaction. The product also offers the consistency and platform flexibility to rapidly increase throughput without needing to invest in additional resources and new systems.”

 

Our test not only enables laboratories of all sizes to perform high-performance cost-effective testing, but also provides robust strain coverage for all prevalent strains, including the rapidly spreading Delta variant”, said Shazi Iqbal, Ph.D., CEO of BioGX. “The FDA authorization of our Xfree chemistry paves the way for us to leverage our expansive menu of tests to create an Xfree line of point-of-care (POC) tests for respiratory and urinary tract infections”, he added.     

 

The FDA has authorized the Xfree COVID-19 test with broad specimen coverage to include nasopharyngeal, anterior nasal, mid-turbinate, and oropharyngeal swab specimens, nasopharyngeal wash/aspirate and nasal aspirates. Additionally, the test is authorized to run with extracted samples offering options for the laboratory to adapt the test in any laboratory workflow. The test is already in use in several laboratories and costs $7-12 per sample depending on its use as direct sample addition or with extracted sample.    

 

Xfree is a complete test in a single vial, lyophilized in the trusted BioGX Sample-Ready format. To perform the RT-PCR test, the user simply rehydrates the lyophilized test with molecular grade water, adds a patient sample, and runs the test on a validated real-time PCR instrument. The test can be shipped anywhere in the world without refrigeration.  

Customers can request information on Xfree COVID-19 by contacting BioGX at Ph: +1.205.250.8055 or sales@biogx.com

About BioGX

BioGX is a leading global provider of lyophilized real-time PCR reagents for molecular diagnostics.  BioGX, Inc., headquartered in Birmingham, Alabama and Dallas, TX, and its wholly owned subsidiary BioGX B.V., based in Amsterdam, The Netherlands, (collectively “BioGX”), operates in a cGMP compliant environment certified to ISO 13485 medical device development and manufacturing standards. The proprietary Sample-Ready technology is at the core of all product offerings for Clinical, Food Safety, Pharma QC and Water Quality molecular testing. BioGX’s 60+ multiplex real-time PCR products are marketed and sold in several countries through its Global Distribution Network.  

For more information on BioGX, please visit BioGX.com.

Sample-Ready, Just Add Water and Xfree are trademarks of BioGX, Inc.