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
https://www.biogx.com/wp-content/uploads/2023/09/img_covid19_scaled1.jpg788940Zeeshan Khanhttps://biogx.com/wp-content/uploads/2021/07/BioGX-New-Logo-final.pngZeeshan Khan2024-05-25 09:47:492024-09-13 05:53:40December 2023 Update: BioGX in silico analysis of SARS-CoV-2 variants of interest and emerging variants
Urinary tract infections (UTIs) are among the most common bacterial infections, affecting millions of individuals worldwide each year. Prompt and accurate diagnosis is essential for guiding appropriate treatment and preventing complications. In recent years, PCR (polymerase chain reaction) reagents have emerged as valuable tools in the diagnosis of UTIs, offering advantages in sensitivity, specificity, and speed compared to traditional microbiology methods. In this article, we’ll explore how PCR reagents are revolutionizing UTI testing and improving patient care.
1. Understanding PCR Reagents in UTI Testing:
PCR reagents are essential components used to amplify and detect specific DNA sequences in clinical samples, such as urine.
– In UTI testing, PCR reagents target genetic markers unique to common uropathogens, such as Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecalis.
– By amplifying and detecting genetic markers specific to these pathogens, PCR assays can rapidly and accurately identify their presence in urine samples, even at low cell counts which are hard to grow and detect by traditional culture methods.
2. Advantages of PCR Reagents in UTI Diagnosis:
Sensitivity: PCR assays using high-fidelity DNA polymerases can detect bacterial DNA with exceptional sensitivity, enabling the diagnosis of UTIs even in cases with low bacterial loads. Specificity: PCR assays can distinguish between different bacterial species and strains, providing clinicians with valuable information for targeted antibiotic therapy. Speed: PCR assays offer rapid turnaround times, with results typically available within a few hours, allowing for prompt initiation of appropriate treatment. Automation: PCR assays can be automated, allowing for high-throughput testing in clinical laboratories, reducing manual labor and increasing efficiency.
3. Applications of PCR Reagents in UTI Testing:
Detection of Uropathogens: PCR assays targeting specific bacterial genes, such as those encoding virulence factors or antibiotic resistance determinants, can identify uropathogens and provide additional information for treatment decisions. Antimicrobial Susceptibility Testing:Antimicrobial Susceptibility Testing: PCR-based methods can detect genetic markers associated with antimicrobial resistance, guiding the selection of appropriate antibiotics and helping to combat the rise of antibiotic resistance in UTIs. Syndromic Panels:Multiplex PCR assays can simultaneously detect multiple uropathogens and differentiate between bacterial and viral causes of UTIs, offering comprehensive diagnostic information in a single test.
4. Challenges and Considerations:
Standardization: Ensuring the accuracy and reliability of PCR assays requires standardization of protocols, quality control measures, and validation studies.
Cost:While PCR assays may offer advantages in sensitivity and speed, they may be more costly than traditional culture-based methods, necessitating careful consideration of cost-effectiveness.
The Challenge of UTI Diagnosis
Traditional methods of UTI diagnosis, such as urine culture and microscopy, have limitations in terms of sensitivity, specificity, and turnaround time. These methods often require prolonged incubation periods and may miss low-level bacterial infections, leading to delayed treatment and potential complications. Moreover, distinguishing between symptomatic infection and asymptomatic bacteriuria can be challenging, particularly in certain patient populations.
In contrast, PCR technology offers a rapid and highly sensitive alternative to traditional UTI diagnostic methods. By targeting specific bacterial DNA sequences present in urine samples, PCR can detect the presence of UTI-causing pathogens with unparalleled accuracy. PCR reagents, which contain all the necessary components for PCR amplification and detection, play a crucial role in facilitating this process.
PCR Reagents: A Cornerstone of Molecular UTI Testing
BioGX custom-manufactured PCR reagents offer a comprehensive solution for the rapid and accurate detection of bacterial pathogens present in urine samples. Packaged in a single tube format, BioGX’s PCR reagents* streamline the testing process, minimize hands-on time and simplify workflow for laboratories. By combining all necessary components for PCR amplification and detection into a single lyophilized mastermix, BioGX ensures laboratories can achieve consistent and reliable performance, during their validation studies and routine testing.
Advantages of BioGX’s PCR Reagents for UTI Testing:
1. High Sensitivity:
BioGX’s PCR reagents* are optimized to detect low levels of bacterial DNA, even in cases of low bacterial load, ensuring reliable detection of UTI pathogens from urine samples.
2. Specificity: With carefully designed primer sets targeting conserved regions of bacterial genomes, BioGX’s PCR reagents* offer exceptional specificity, minimizing the risk of false-positive results and ensuring accurate detection.
3. Rapid Turnaround Time: By leveraging the speed and efficiency of PCR technology, BioGX’s PCR reagents* provide results within hours, enabling timely initiation of targeted antibiotic therapy and improving patient outcomes.
4. User-Friendly FormatPackaged in a single lyophilized tube format, BioGX’s PCR reagents* are easy to use, requiring minimal hands-on manipulation and reducing the risk of contamination, thereby enhancing laboratory efficiency and productivity.
Conclusion:
PCR reagents have transformed the landscape of UTI testing, offering unparalleled sensitivity, specificity, and speed compared to traditional methods. By harnessing the power of PCR technology, clinicians can diagnose UTIs with greater precision, guide targeted antibiotic therapy, and improve patient outcomes. As PCR assays continue to evolve and become more accessible, they hold tremendous promise for enhancing the diagnosis and management of UTIs, ultimately benefiting patients and healthcare systems alike.
*Custom manufactured as per customer specified requirements
Disclaimer: Information in the blog is provided to educate and propagate general awareness and not intended to make any recommendations for diagnosis or treatment of a disease. The reader is encouraged to independently verify the accuracy of information presented in the blog.
https://www.biogx.com/wp-content/uploads/2024/05/uti_blog2_img.jpg449556Zeeshan Khanhttps://biogx.com/wp-content/uploads/2021/07/BioGX-New-Logo-final.pngZeeshan Khan2024-05-23 03:54:382024-05-24 14:00:10Enhancing UTI Detection with PCR Reagents
Robert Martinez, Ph.D, VP, Business Development & Scientific Affairs
Dr. Martinez joined BioGX in 2015. Dr. Martinez is responsible for Business Development and Scientific Affairs, expanding our portfolio of IVD products, managing the global technical support efforts of all molecular diagnostic products, and manages a team of scientists responsible for product and technology innovation in conjunction with existing corporate partnerships. Dr. Martinez has over 20 years of experience in molecular biology. Prior to joining BioGX, Dr. Martinez held research positions focusing on cancer cell biology at Albany Medical College, microbial community dynamics at The Georgia Institute of Technology and microbial physiology at The University of Alabama. Dr. Martinez holds a BA in Biology from Boston University and a Ph.D. in Microbiology from The Georgia Institute of Technology.
Hardy Green, Controller
Mr. Green joined BioGX as a Controller in 2020. He has 30+ years of leadership experience in accounting across diverse industries, including healthcare, water utility management, waste management, mineral extraction, and cash handling. At BioGX, Mr. Green is responsible for managing finance and purchasing departments. He has a BS degree in Accounting from The University of Alabama, and he is a Certified Public Accountant (inactive).
Shazi Iqbal, Ph.D, Venture Partner
Dr. Shazi Iqbal is a Co-Founder of BioGX and served as its CEO from 2011 to June 2024. Now, as a Venture Partner, he leads M&A and strategic investment opportunities to enable innovation partnerships. Dr. Iqbal has over 25+ years of experience in building healthcare startups into profitable growth companies. He holds a Ph.D. in Biology (Neuroscience), two M.S. degrees in Biochemistry & Biotechnology, and several patents and publications.
Staphylococcus epidermidis group (S. hominis ,S. simulans, S.warneri, S. epidermidis, S. haemolyticus)
Staphylococcus haemolyticus
Staphylococcus lugdunensis
Staphylococcus saprophyticus
Streptococcus agalactiae
Streptococcus pyogenes
Treponema pallidum
Ureaplasma parvum
Ureaplasma urealyticum
HSV-1
HSV-2
Fungi
Candida albicans
Candida auris
Candida glabrata
Candida krusei
Candida parapsilosis
Candida spp. (C.albicans, C. auris, C. dubliniensis, C. glabrata, C. krusei, C.lusitaniae, C. parapsilosis, C. tropicalis)
Candida tropicalis
Protozoan
Trichomonas vaginalis
Antimicrobial Resistance
GES
KPC
mcr-1
mecA
mecC
NDM
OXA-48
van B
vanA
vanC1/C2/C3
VIM
SAMPLE-TO-ANSWER IN 3 EASY STEPS!
Shahin Iqbal, Ph.D, President and COO
Dr. Shahin Iqbal is the President and Chief Operating Officer at BioGX. He has over 25 years of experience in clinical molecular diagnostics. Before joining BioGX, Dr. Iqbal led the Abbott Diagnostics Global Service & Support specifically for informatics, core lab automation, immunoassay and clinical chemistry systems. He was also responsible for design and development of FISH automation systems at Abbott Molecular. He is the recipient of the President awards and multiple service & innovation awards at Abbott. Dr. Iqbal holds multiple patents on optical sensors, automation systems development, RFID applications and robotics for system dispensing. Prior to joining Abbott, Dr. Iqbal was Head of operations, quality & regulatory, systems development and manufacturing of IHC systems at BioGenex in California. Dr. Iqbal has an MBA and Ph.D as well as a Masters in Electrical Engineering degree from the University of Texas in San Antonio.
George Blackstone, VP, Research & Development
Mr. Blackstone joined BioGX in 2007. He has served at BioGX in various senior R&D and quality management roles prior to his current position as VP of Research & Development. Mr. Blackstone has designed and directed the development of over 100 multiplex real time PCR products in the fields of food safety, water quality, pharma QC, and clinical diagnostics. Mr. Blackstone previously served for eight years at the US Food and Drug Administration and as a Commissioned Research Officer in the US Public Health Service Commissioned Corps where he achieved the rank of Lieutenant Commander. George Blackstone received his Master of Science degree from Louisiana State University.
Christopher Hughes, VP, Operations & QRA
Mr. Hughes joined BioGX in 2015. Prior to joining BioGX, Mr. Hughes led efforts for a diverse range of companies with the development and implementation of certified quality management systems ranging from data storage devices with SONY Corporation, security & detention devices with Norment Security Group, textile manufacturing with Twitchell Corporation, combat vehicle manufacturing with General Dynamics, and therapeutic medical devices with Steris Corporation. Christopher has a BSE from Auburn University and an MBA from Troy State University.
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We, BioGX, Inc., (registered trademark “BioGX”) with offices in Birmingham, AL, Dallas, TX, and Amsterdam, The Netherlands, are a diagnostic test manufacturer and not a testing laboratory, and we are not in any way affiliated with such callers. We do not know who is making these calls.
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The BioGX Xfree™ COVID-19 Direct RT-PCR is validated for use with respiratory specimens collected from individuals suspected of COVID-19 by their healthcare provider.
Michael Vickery, PhD, EVP, Chief Scientific Officer
Dr. Vickery founded BioGX in 2007 and served as President and CEO until 2011. Prior to founding BioGX, Dr. Vickery worked in sales and as a technical consultant at Cepheid. Prior to Cepheid, Dr. Vickery worked at the FDA as a University of Maryland JIFSAN postdoctoral fellow at the University of Maryland, and later served as the Lead for Molecular Methods Development at the U.S. FDA Gulf Coast Seafood Laboratory. He holds multiple patents in biotechnology, has authored or co-authored many publications, and has extensive experience in gene expression analysis, and in the design and development of rapid multiplex molecular tests for microbial and viral detection. Dr. Vickery holds a B.S. degree in Physics and both M.S. and Ph.D. degrees in Biology (molecular biology and molecular genetics focus – both prokaryotic and eukaryotic). Prior to entering graduate school, Dr. Vickery worked as an executive in the lowbed trailer industry for almost 10 years, pioneering the sale of American made heavy equipment transport trailers into China (ROC) and Japan during his tenure in the industry, and resupplying the oilfields of Kuwait with specialized trailers after the Gulf War.