10th February 2020 Editorial by: Paul Carton
Insight into GPS™ 2019-nCoV Ready-to-Use qPCR Kit - Interview with CEO Prof. Martinez-Murcia
To date, there have been up to sixty full genomes of 2019-nCoV published into the public domain. This coronavirus has similarity to the SARS and MERS coronaviruses and is found in very low concentrations in a patient's sample. Real-time PCR (qPCR) is at present the most appropriate solution to detect the virus, that WHO now announce as a global health emergency. Prof. Dr Antonio Martinez-Murcia, Director & CEO of Genetic PCR Solutions (GPS™) and Professor of Microbiology at The Universidad Miguel Hernández talks to rapidmicrobiology.com about the primer/probe design of the GPS qPCR 2019-nCoV test kit, the response from laboratories both nationally and internationally and how a ready-to-use format in these situations is the best practice to avoid any cross-contamination.
Q: What type of sample from the patient is used in the GPS™ qPCR 2019-nCoV test?
A: The material usually used for 2019-nCoV detection are upper and lower respiratory samples, including nasopharyngeal and oropharyngeal swabs, sputum, endotracheal aspirate and/or bronchoalveolar lavage. The GPS™ assay is compatible with all kind of samples, including serum, ensuring an effective method of testing.
Q: How can your primers account for all the mutations?
A: Primers and probes designed by GPS™ are located in highly conserved regions of genomic sequences in the full genomes published to date. And so they are fully inclusive to all isolates described to date, since the first full genome obtained on 7th January.
Q: If the virus keeps mutating, how long could it be before these primers are obsolete?
A: From the 2019-nCoV genomes so far retrieved, we have found they are extremely similar. They only showed variation ranging from 0 to ca.15 nucleotides, and spread, in a total of ca. 30.000 bp of its genome. Consequently, the possibility that some mutations occur together in the primers/probe location is extremely low. More studies are needed to understand the mode of evolution of this concrete virus. If new data shows any significant mutations, GPS™ will update the primers/probes.
Q: Have there been many requests for the product since the release of the product?
A: GPS™ 2019-nCoV qPCR kit has already been supplied to several laboratories of private and public institutions since it was made commercially available. The assay will be tested with human and environmental samples, and these results will, in turn, improve validation for diagnostic purposes.
Q: What is the international/national policy on validating this kit?
A: Typically, to register a kit for diagnostic validation with the national/international agencies, real samples must be tested by reference laboratories. Of course, samples are not easily available except in laboratories dealing with virus control and clinical testing. GPS™ is currently undertaking these activities in collaboration with stakeholders and will support registration in countries where the kit is exported.
Q: How were the primers designed?
A: The primers/probes by GPS™ are designed by following strict phylogenetic and thermodynamic criteria to ensure full specificity with 100% inclusivity and exclusivity, but also providing the best robustness in PCR to avoid inhibition effects of samples.
Q: How is contamination dealt with in the lab?
A: Cross-contamination risks should be minimized by using the best-known practices in molecular biology. Our MONODOSE format, which is a ready-to-use PCR tube helps with this aspect by reducing pipetting to a minimum. Technicians only need to add the sample to each single PCR tube and run the PCR.
Q: How can latent infections be detected?
A: Right now, very little is known about the life cycle of the virus. Chinese Officials report that sustained person-to-person transmission is occurring in China, with similar reports coming from outside China. During the early stages of the incubation period, the virus seems to be at low concentrations. Consequently, the detection limit of the assay plays a critical role during these steps, and genetic testing by PCR is the most sensible technology to use.
Date Published: 10th February 2020
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