May 2022 Update: BioGX in silico analysis of SARS-CoV-2 Variants of Concern

BioGX continuously monitors the evolution of COVID-19 variants to ensure our market leading SARS-CoV-2 RT-PCR tests will continue to detect emerging variants without impacting performance.

 

BioGX has completed in-silico analysis of over 2.5 million SARS-CoV-2 genome sequences available as of May 31, 2022. Sequence analysis compared the available Omicron genomes against the SARS-CoV-2 nucleocapsid (N-gene) and envelope (E-gene) , targeted by BioGX products. In-silico analysis and empirical testing of the Omicron variant confirmed the gene mutations will not affect the performance of the BioGX portfolio of SARS-CoV-2 products.

 

BioGX portfolio of SARS-CoV-2 products

  1. BioGX Xfree™ COVID-19 Direct RT-PCR – FDA EUA
  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™
  5. BioGX SARS-CoV-2 N1, N2, E-gene (RUO)
  6. BioGX SARS-CoV-2 N1, Flu A, Flu B, RSV A/B (RUO)

 

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 E
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) 430,915

(31MAY2022)

>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) 26,248

(31MAY2022)

>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)

82,494

(31MAY2022)

>99%
Delta B.1.617.2

AY.x

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

(OCT 2020)

1,690,105

(31MAY2022)

>99%
Omicron B.1.529

BA.x☨

GR/484A 21K, 21L, 21M +R346K Multiple Countries

(NOV 2021)

457,058

(31MAY2022)

>99%

 

*Variants of concern being monitored by US CDC and WHO

**Present in a subset of sequences

BA.1, BA.2, BA.3, BA.4, BA.5, and XE are sub-lineages of Omicron variant

April 2022 Update: BioGX in silico analysis of SARS-CoV-2 Variants of Concern

BioGX continuously monitors the evolution of COVID-19 variants to ensure our market leading SARS-CoV-2 RT-PCR tests will continue to detect emerging variants without impacting performance.

 

BioGX has completed in-silico analysis of over 2.5 million SARS-CoV-2 genome sequences available as of March 31, 2022. Sequence analysis compared the available Omicron genomes against the SARS-CoV-2 nucleocapsid (N-gene) and envelope (E-gene) , targeted by BioGX products. In-silico analysis and empirical testing of the Omicron variant confirmed the gene mutations will not affect the performance of the BioGX portfolio of SARS-CoV-2 products.

 

BioGX portfolio of SARS-CoV-2 products

  1. BioGX Xfree™ COVID-19 Direct RT-PCR – FDA EUA
  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™
  5. BioGX SARS-CoV-2 N1, N2, E-gene (RUO)
  6. BioGX SARS-CoV-2 N1, Flu A, Flu B, RSV A/B (RUO)

 

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 E
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) 428,332

(31MAR2022)

>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) 26,051

(31MAR2022)

>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)

80,477

(31MAR2022)

>99%
Delta B.1.617.2

AY.x

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

(OCT 2020)

1,664,949

(31MAR2022))

>99%
Omicron B.1.529

BA.x☨

GR/484A 21K, 21L, 21M +R346K Multiple Countries

(NOV 2021)

314,442

(31MAR2022)

>99%

*Variants of concern being monitored by US CDC and WHO. 

**Present in a subset of sequences.

BA.2 is a sub- lineage of Omicron variant

BioGX Omicron Variant Update

On November 26, 2021 and November 30, 2021, the WHO and the United States government SARS-CoV-2 Interagency Group (SIG), respectively, designated Omicron (SARS-CoV-2 variant B.1.1.529) as the newest variant of concern. On December 1, 2021 the first confirmed US case of Omicron coronavirus variant was detected in California. 

 

BioGX continuously monitors the evolution of COVID-19 variants to ensure our market leading SARS-CoV-2 RT-PCR tests will continue to detect emerging variants without impacting performance. 

 

BioGX has completed in-silico analysis of the 219 Omicron genome sequences available as of November 30, 2021. Sequence analysis compared the available Omicron genomes against the SARS-CoV-2 nucleocapsid (N-gene) and envelope (E-gene) , targeted by BioGX products. In-silico analysis and empirical testing of the Omicron variant confirmed the gene mutations will not affect the performance of the BioGX portfolio of SARS-CoV-2 products.

 

BioGX portfolio of SARS-CoV-2 products

  1. BioGX Xfree™ COVID-19 Direct RT-PCR – FDA EUA
  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™
  5. BioGX SARS-CoV-2 N1, N2, E-gene (RUO)
  6. BioGX SARS-CoV-2 N1, Flu A, Flu B, RSV A/B (RUO)

 

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 E
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) 417,046

(31DEC2021)

>99% >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) 25,299

(31DEC2021)

>99% >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)

78,303

(31DEC2021)

>99% >99% >99%
Delta B.1.617.2

AY.x

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

(OCT 2020)

1,417,558

(31DEC2021)

>99% >99% >99%
Omicron B.1.529 GR/484A 21K, 21L, 21M +R346K Multiple Countries

(NOV 2021)

76,835

(31DEC2021)

>99% >99% >99%

 

*Variants of concern being monitored by US CDC and WHO. 

**Present in a subset of sequences.

BioGX Lambda and Mu Variant Update

Lambda and Mu Variant Update – 13 September 2021

On June 14th and August 30th the WHO recognized two SARS-CoV-2 strains (“Lambda” and “Mu”) as variants of interest (VoI). Lambda and Mu were both first identified in South America and to date there have been over 6,344 and 5,752, respectively, sequences deposited in GISAID and NCBI genome sequence repositories. As of Sept. 13, 2020, BioGX COVID-19 diagnostic products targeting unique regions of the Nucleocapsid gene and Envelope genes are unaffected by the mutations distinguishing Lambda and Mu.

BioGX COVID-19 Portfolio

  1. BioGX Xfree™ COVID-19 Direct RT-PCR – FDA EUA
  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™
  5. BioGX SARS-CoV-2 N1, N2, E-gene (RUO)
  6. BioGX SARS-CoV-2 N1, N2, E-gene / Flu A, Flu B, RSV A/B (RUO)

 

U.S. CDC and WHO Variants of Concern*

% Clades detected by targets
WHO designation
Pango lineage
GISAID
clade
Next strain clade
Spike Protein
(a.a. changes)
Region Initially Documented (Date)
No. Sequences Analyzed
(Date)
N1
N2
E
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) 390,372

(30SEPT2021)

>99% >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) 22,571

(30SEPT2021)

>99% >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)

58,234

(30SEPT2021)

>99% >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)

571,492 (30SEPT2021) >99% >99% >99%

*Variants of concern being monitored by US CDC and WHO. 

**Present in some sequences but not all

 

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.

 

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.