December 2023 Update: BioGX in silico analysis of SARS-CoV-2 variants of interest and emerging variants

BioGX continuously monitors the evolution of SARS-CoV-2 variants to ensure our market leading SARS-CoV-2 RT-PCR tests will continue to detect emerging variants.

BioGX has completed in silico analysis of over 290,000 complete high coverage Omicron genomes of sublineages belonging to the JN.1, EG.5, BA.2.86, XBB.1.5, XBB.1.16, HV.1, HK.3, JD.1.1, and JG.3 clades present in the Global Initiative on Sharing Avian Influenza Data (GISAID) EpiCoV™ database as of 31 December, 2023 (Table 1). Sequence analysis of the variant genomes was compared against the SARS-CoV-2 reference genome to identify any mutations within the regions of the nucleocapsid (N-gene), membrane (M-gene), and the coding region of the ORF1a gene (RdRp) targeted by BioGX products.

Based on in silico analysis and empirical testing, the nucleotide mutations present in the JN.1, EG.5, BA.2.86, XBB.1.5, XBB.1.16, HV.1, HK.3, JD.1.1, and JG.3 clades at the time of this analysis will not affect the detection capability of the BioGX portfolio of SARS-CoV-2 products and all variants analyzed will be detected.

BioGX continues to monitor emerging SARS-CoV-2 lineage variants and any mutations with the potential to impact performance.

Table 1. Number of sequences analyzed for each Omicron sublineage available from GISAID as of 31 December 2023.

Omicron Sublineages Analyzed by BioGX

Omicron sublineage Nextstrain clade Emergence Location (Date) No. Sequences Present and Analyzed

(as of 31DEC2023)

JN.1 23I Luxembourg / Iceland (AUG 2023) 15,548
EG.5 23D Denmark
(JUL 2023)
1795
BA.2.86 21L Denmark
(JUL 2023)
416
XBB.1.5 23A USA (OCT 2022) 172,673
XBB.1.16 23B USA (JAN 2023) 33,318
HV.1 23F China (JAN 2023) 30,422
HK.3 23H USA (OCT 2022) 22,572
JD.1.1 23A USA (JUL 2023) 7,601
JG.3 23F France (JUL2023) 8,370

Advancements in Multiplex PCR for Comprehensive STI Testing

Sexually Transmitted Infections (STIs) continue to be a global health concern, impacting millions of individuals every year. In many parts of the world, including the United States, there has been a concerning increase in reported cases of STIs, such as chlamydia, gonorrhea, and syphilis.

 

Prompt and accurate detection of STIs is crucial not only for individual health but also for public health efforts to control the spread of these infections. In recent years, advancements in diagnostic technology, particularly Multiplex Polymerase Chain Reaction (PCR) testing, have streamlined STI testing. This blog explores the significance of Multiplex PCR in comprehensive STI testing, highlighting its advantages, applications, and the impact it has on women’s health.

 

Understanding Multiplex PCR

 

Multiplex PCR allows for simultaneous detection and identification of several pathogens within a single test. This technology has revolutionized the field of STI testing by offering the following advantages:

 

  1. Comprehensive Screening

 

One of the most significant advantages of Multiplex PCR is its ability to screen for multiple STIs in a single test. Traditionally, patients had to undergo separate tests for different pathogens, making the screening process time-consuming and potentially costly. With Multiplex PCR, healthcare providers can screen for a wide range of STIs simultaneously, including chlamydia, gonorrhea, syphilis, herpes simplex virus (HSV), and more. This comprehensive approach enables early detection and treatment of multiple infections, reducing the risk of complications. 

 

  1. Increased Sensitivity and Specificity

 

Multiplex PCR assays are highly sensitive and specific, meaning they can detect even low levels of pathogens while minimizing false-positive or false-negative results. This accuracy is crucial in STI testing, where early diagnosis is key to preventing complications and transmission.

 

  1. Faster Results

 

Traditional culture-based methods for STI testing often require several days to yield results. Multiplex PCR delivers rapid results, typically within a few hours to a day. This quick turnaround time allows for prompt treatment initiation and partner notification, reducing the spread of infections.

 

  1. Streamlined Testing Process

 

Multiplex PCR simplifies the testing process for both patients and healthcare providers. Patients can provide a single sample for comprehensive testing, reducing discomfort and inconvenience. Healthcare providers can efficiently assess a patient’s STI status and develop personalized treatment plans.

 

Applications in Women’s Health

 

Multiplex PCR’s impact on women’s health is substantial:

 

  1. Early Detection of Asymptomatic Infections

STIs, such as chlamydia can be asymptomatic and reinforce the need for rapid, simplified testing. Multiplex PCR identification of these infections allow for early intervention and reduce the risk  for long-term  complications.

 

  1. Improved Pregnancy Outcomes

Comprehensive STI testing through Multiplex PCR is essential for pregnant women. Untreated STIs during pregnancy can lead to  preterm birth and neonatal infections. Multiplex PCR ensures thorough screening and timely treatment to protect both the mother and the baby.

 

  1. Enhanced Preventive Strategies

Multiplex PCR not only aids in diagnosis but also supports sexual health programs that control STI rates and can mitigate spread of multidrug resistant infections. 

 

Conclusion

 

Advancements in Multiplex PCR have transformed the landscape of STI testing, offering a comprehensive, accurate, and efficient approach to sexual health. This technology plays a pivotal role in early detection, prevention, and management of STIs.. With Multiplex PCR, we are taking significant strides toward a healthier and safer future for all individuals at risk of STIs.

 

BioGX real-time PCR reagents for STI and Women’s Health are offered lyophilized in a variety of multiplex configurations to afford flexible workflow adoption by laboratories as per their testing needs. BioGX reagents have compatibility with open platforms including BD MAX™, ABI QuantStudio™, ABI 7500 Fast Dx, BioRAD CFX Touch™ and the BioGX pixl™. The multiplexes* are ready to be validated to run together with universal cycling conditions on a platform of choice.

BioGX in silico analysis of recent update on a surge of SARS-CoV-2 Omicron variant strains

BioGX continuously monitors the evolution of SARS-CoV-2 variants to ensure our market leading SARS-CoV-2 RT-PCR tests will continue to detect emerging variants.

BioGX has completed in silico analysis of over 44,000 complete high coverage Omicron genomes of sublineages belonging to the EG.5, EG.5.1, BA.2.86, and XBB.1.9.1 (including FL.1.5.1) present in the Global Initiative on Sharing Avian Influenza Data (GISAID) EpiCoV™ database as of 31 August, 2023 (Table 1). Sequence analysis of the variant genomes was compared against the SARS-CoV-2 reference genome to identify any mutations within the regions of the nucleocapsid (N-gene), membrane (M-gene), and the coding region of the ORF1a gene (RdRp) targeted by BioGX products. In silico analysis and empirical testing confirmed any nucleotide mutations present at the time of this analysis will not affect the detection capability of the BioGX portfolio of SARS-CoV-2 products.

Table 1. Number of sequences analyzed for each Omicron sublineage available from GISAID as of 31 August 2023.

Omicron Sublineages Analyzed by BioGX

Omicron sublineage Nextstrain clade Emergence Location (Date) No. Sequences Present and Analyzed

(as of 31AUG2023)

BA.2.86 21L Denmark (JUL 2023) 26
EG.5 23D Denmark (MAR 2023) 1,227
EG.5.1 23F Indonesia (MAR 2023) 15,953
XBB.1.9.1* 23D Singapore (DEC 2022) 26,816

* Including FL.1.5.1

The Future of UTI Diagnosis: Advances in PCR Technology

Urinary tract infections (UTIs) are a widespread health concern affecting millions of individuals globally. Timely and accurate diagnosis is crucial for effective treatment and prevention of complications. As technology continues to advance, Polymerase Chain Reaction (PCR) testing is shaping the future of UTI diagnosis. In this blog post, we will explore the exciting advances in PCR technology that hold immense potential for revolutionizing UTI diagnostics, offering improved sensitivity, specificity, and efficiency.

 

The Evolution of UTI Diagnosis: A Need for Precision

UTIs have long been diagnosed using urine cultures, a process that requires time and often delays treatment. Moreover, the overuse of antibiotics has contributed to the growing concern of antibiotic resistance. The need for a rapid and accurate diagnostic solution has spurred advancements in PCR technology.

 

Unveiling the Power of PCR: Revolutionizing UTI Diagnosis

Polymerase Chain Reaction (PCR) technology offers a breakthrough in diagnosing UTIs. By targeting and amplifying specific DNA sequences of pathogens, PCR provides unparalleled accuracy and sensitivity. This innovation not only identifies the presence of pathogens but also distinguishes between different strains and detects antibiotic resistance genes.

 

The Promise of Multiplex PCR: Detecting More, Faster

Multiplex PCR assays are evolving to detect multiple pathogens simultaneously in a single test. These assays utilize panels that target various UTI-causing bacteria, viruses, and fungi, providing a comprehensive assessment of the infecting pathogens. Multiplex assays not only save time and resources but also aid in tailoring specific treatment regimens based on the identified pathogens. As multiplex technology advances, the range of detectable pathogens is expanding, enabling a more accurate diagnosis and personalized treatment approach.

 

Benefits Beyond Accuracy: Speed and Antibiotic Stewardship

PCR technology offers rapid results, enabling healthcare providers to make timely treatment choices. This speed is crucial in cases where infections can escalate rapidly. Additionally, PCR’s accuracy aids in antibiotic stewardship, ensuring that appropriate antibiotics are prescribed, thereby curbing the risk of antibiotic resistance.

 

The Accessibility Factor: Convenience and Patient Empowerment

PCR-based UTI tests have the potential to utilize various sample types, including urine, swabs, and even self-collected samples. This accessibility extends beyond the healthcare setting, allowing patients to take an active role in their own health. The rise of telemedicine further enables remote UTI diagnosis and monitoring.

 

A Transformative Impact on Healthcare Practice

The integration of PCR-based UTI testing into clinical practice is poised to transform patient care. Timely and accurate diagnoses can lead to faster recovery times, reduced hospitalizations, and enhanced patient satisfaction. Healthcare providers can optimize treatment plans based on precise information.

 

Challenges and Considerations: The Path Forward

While PCR technology presents immense potential, challenges such as cost, access, and healthcare provider training need to be addressed. Ensuring that healthcare professionals are well-versed in utilizing PCR technology effectively is crucial for maximizing its benefits.

 

Embracing the Future: Shaping UTI Diagnosis

As we look ahead, the future of UTI diagnosis is undeniably intertwined with the advancements in PCR technology. With its accuracy, speed, and potential for multiplex testing, PCR is poised to revolutionize how UTIs are diagnosed and managed, ushering in an era of more precise and patient-centric care.

 

Conclusion:

The future of UTI diagnosis holds great promise, thanks to the leaps and bounds made in PCR technology. This innovation not only accelerates diagnosis but also elevates the quality of patient care. As healthcare continues to evolve, PCR stands as a beacon of hope, heralding a new era where UTIs are swiftly and accurately diagnosed, and patients receive the treatment they deserve.

 

BioGX real-time PCR reagents for UTI are offered lyophilized in a variety of multiplex configurations to afford flexible workflow adoption by laboratories as per their testing needs. BioGX reagents have compatibility with open platforms including BD MAX™, ABI QuantStudio™, ABI 7500 Fast Dx, BioRAD CFX Touch™ and the BioGX pixl™. The multiplexes* are ready to be validated to run together with universal cycling conditions on a platform of choice.

Jan 2023 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 930,000 SARS-CoV-2 genome sequences available as of December, 2022. Sequence analysis compared the available Omicron genomes against the SARS-CoV-2 nucleocapsid (N-gene), membrane (M-gene), and RdRp coding region of the ORF1a gene (RdRp) targeted by BioGX products. In-silico analysis and empirical testing of the Omicron variants confirmed gene mutations present as of this analysis, 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. BioGX SARS-CoV-2 HMP – N1, N2 & RNase P Multiplex
  3. BioGX COVID-19, Flu A, Flu B, RSV RT-PCR for BD MAX™
  4. BioGX SARS-CoV-2 N1, Flu A, Flu B, RSV A/B (RUO)

 

U.S. CDC and WHO Variants of Concern Omicron Lineages* 

WHO designation Pango lineage GISAID
clade 
Nextstrain clade Emergence Location (Date) No. Sequences Analyzed 

(DEC 2022)

% Clades Detected for

N1 Target

Omicron B.1.1.529 GR/484A 21K, 21L, 21M, 22A, 22B, 22C, 22D Multiple Countries (NOV 2021) 61,891 > 99%

Omicron Sublineages Analyzed by BioGX

Omicron sublineage Nextstrain clade Emergence Location (Date) No. Sequences Analyzed 

(DEC 2022)

BA.1* 21K Southern Africa (NOV 2021) 1,716
BA.1.1* 21K Southern Africa (NOV 2021) 3,812
BA.2* 21L Southern Africa (NOV 2021) 5,853
BA.3* 21K Southern Africa (NOV 2021) 0
BA.4* 22A Southern Africa (JAN 2022) 457
BA.5* 22B Southern Africa (JAN 2022) 1,888
XE* N/A UK (FEB 2022) 0
BQ.1** 22E Nigeria (JUL 2022) 11,841
BQ.1.1** 22B  Nigeria (JUL 2022) 35,142
XBB** 22F Multiple Countries (SEP 2022) 1,120

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

**Variants not included in CDC or WHO variant of concern list

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.