Surveillance & Refinement
Viracor Eurofins' Surveillance and Refinement program enables us to rapidly respond to new clinical and scientific information by developing clinical tools to facilitate the management of patients infected with newly emerging or evolving pathogens.
By utilizing nucleic acid sequences obtained through our Surveillance Program, peer-reviewed published literature and public nucleic acid sequence databases, each qPCR assay is frequently assessed to verify that new pathogen strains or genetic mutations that arise will not lead to a false-negative result.This allows us to:
1) Anticipate the need for new clinical tools
Viracor Eurofins has a long history of anticipating the need to apply new methods to diagnose and manage patients infected with emerging and/or existing pathogens. We were among the first clinical laboratory to apply quantitative, real-time PCR technology for routine detection and monitoring of Adenovirus, BK virus(BKV), JC virus(JCV), HHV-6, HHV-7, HHV-8, Toxoplasma gondii, and Pneumocystis jiroveci. We were among the first clinical reference laboratories to offer the xTAG® Respiratory Viral Panel, and an FDA cleared method of multipathogen screening for routine and emerging respiratory viruses.
2) Rapidly develop assays in response to emerging pathogens
In the event of a newly emerging pathogen, we are able to rapidly develop new assays to enable sensitive and specific high throughput detection. Viracor Eurofins developed one of the first 2009 Influenza A H1N1 real-time PCR assays and obtained Emergency Use Authorization (EUA) for its use. Oseltamivir resistance was soon identified in some isolates, and in response Viracor Eurofins developed the first assay to determine resistance, which became an important consideration in critically ill patients.
Norovirus is an example of a pathogen that has emerged as an important cause of viral gastroenteritis. Due to its highly infectious nature and ability to remain infective in extreme environments, noroviruses have become a significant source for nosocomial infection. Real-time RT-PCR is the method of choice to detect norovirus infection due to its superior sensitivity and specificity4,5. However, designing an assay that accounts for all pathogenic strains in groups I and II is challenging due to a high level of genetic diversity. In response to the growing concern over nosocomial norovirus transmission coupled with the diagnostic challenges of this complex virus, Viracor Eurofins developed an assay that utilizes a multiple primer and probe target design to ensure comprehensive detection of norovirus groups I and II. Furthermore, we continuously monitor both in-house and publically available sequence repositories for new strains and refine our assay when necessary to ensure the most sensitive and accurate detection possible.
3) Identify new variations of pathogens within clinical cases
Viracor Eurofins monitors our clinical results in real-time to evaluate the possible development of pathogen variations that may affect assay performance. Our clinical results surveillance efforts corroborated the CDC’s observation of the spread of 2009 Influenza A H1N1 into the United States, due to a positive Influenza A matrix gene result and negative H1 and H3 subtype result on the FDA-cleared, Luminex xTAG™ Respiratory Viral Panel assay. This result was later declared a presumptive positive for 2009 Influenza A H1N1. Our ability to offer an interim testing solution while we developed and were granted EUA of our 2009 Influenza A H1N1 real-time PCR assay proved to be an invaluable tool for clinicians.
4) Refinement of existing assays in response to new strains or mutations for pathogens of established clinical
Equally important to our surveillance program is the regular monitoring of our assays and subsequent refinement. We believe that continuous monitoring of our current diagnostic offerings in response to new clinical and scientific information is critical to ensure ongoing accuracy of our results.
Under selective pressure, pathogens will often mutate, which may lead to under-quantification or false negative results from outdated assays. To maintain the accuracy of our results, we continuously monitor nucleic acid sequences obtained through our surveillance program, peer-reviewed published literature and public nucleic acid sequence databases, which ensures each real-time PCR assay is able to detect all strains of a particular pathogen (Figure 1).
Our clinical collaborations enable us to frequently refine our drug resistance sequencing assays in response to discovery of new mutations that confer drug resistance, thus assuring the assay’s ongoing clinical relevancy.
Figure 1 1-3
Figure 1. The genetic diversity of BK Virus demonstrates the importance of assay refinement. Without continuous monitoring and refinement, the risk of a false negative result or under-quantification increases significantly.1 A recent study evaluated five different published BKV PCR assays currently in use at major medical centers for primer and probe mismatches with available GenBank® sequences. Coverage of naturally occurring BKV strains varied among different assay methods, and targeted viral sequences showed major mismatch with primer or probe sequence in up to 30.7% of known BKV strains.1
1. Luo C. Bueno M. Kant J, Randhawa P. Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories. J Med Virol. 2008;(80):1850-1857.
2. Chen, Y. P., P. M. Sharp, M. Fowkes, O. Kocher, J. T. Joseph, and I. J. Koralnik. 2004. Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity. J. Gen. Virol. 85:2651–2663
3. Availability of BKV complete genome sequences by year was determined by publish/release date for each sequence as indicated on GenBank.
4. Updated norovirus outbreak management and disease prevention guidelines. MMWR Recomm Rep, 2011; 60(RR-3):1-18.
5. Koo, H.L. and H.L. DuPont, Noroviruses as a potential cause of protracted and lethal disease in immunocompromised patients. Clin Infect Dis. 2009; 49(7):1069-71.