CHOOSING A REAL TIME PCR PLATFORMS FOR COVID-19 TESTING
As the scourge of the coronavirus outbreak intensifies, Nigeria is responding through the rapid setting up of Covid-19 testing centers across the country. Questions about the suitable equipment, kits and consumables have also come to the fore.
As a trailblazer in molecular diagnostics, DemyHealth proffers a set of solutions from sample collection, preservation to nucleic acid extraction and detection. This is aimed at a more accurate, faster and safer detection of the novel coronavirus.
The primary question that has been coming from stakeholders is “what type of real time PCR should we buy”. The hat of many brands names has been thrown into the ring and newcomers in the world of molecular diagnostics are having a hard time on which to choose. To this end, we will attempt to make explicit what it takes to choose the right qPCR platform.
Choosing a qPCR platform requires the consideration of a number of factors:
Number of wells:
How may samples do you want to run at once?
Number of detection channels:
How many targets do you want to be able to detect in one reaction? A typical SARS-CoV-2 detection experiment will normally require a minimum two to three targets to be detected. One for the internal control (which monitors the integrity of a PCR reaction by detecting a specific gene that is normally found in everyone or introduced at the point of extraction). The other targets can be a set of “coronavirus genes”.
Number of pre-calibrated dyes:
For a qPCR experiment to be feasible, the dyes used to design the primer/probes of the SARS-CoV-2 amplification kits must be pre-calibrated on your qPCR machine. The more the fatory-calibrated dyes, the more compatible your qPCR machine is with kits from most manufacturers around the world.
Because Covid-19 testing has to be precisely detected in human, extraction and amplification kits as well as qPCR equipment must either be CE marked or validated for in vitro diagnostics (IVD)
Comparative studies involving the qPCR platform of interest
To be confident that your qPCR platform is the best in its class, its properties such as efficiency and sensitivity should have been compared to industry standards in journal publications.
After sales support
Real time PCR machine need to be serviced from time to time. It is therefore crucial that the manufacturer have licensed engineers readily available in your country when the need arises.
Other technical factors that are key to a qPCR sensitivity are: ramp rate (the time it takes for a qPCR to change temperature from one PCR step to another over time) and temperature variation between wells of a qPCR platform.
FEW FACTS ABOUT OUR PCR PLATFORMS
A publication proposing a field deployable Real-time PCR (mobile laboratory) workflow for COVID-19 detection recommended the use MyGO Pro PCR (IT-IS Life Science, UK). It was observed that the total work flow of MyGo Pro PCR was considerable shorter compared to the Bio-Rad PCR work flow (Nyaruaba et. al 2020).
Figure 1: Comparing MyGO PCR mobile laboratory work flow and traditional Biorad workflow (Nyaruaba et. al 2020)
The superior efficiency and sensitivity of MyGo PCR’s have been compared to Rotor-gene PCR platform during an assay validation experiment investigating mutations in codon 12 and 13 of KRAS (Kirsten rat sarcoma viral oncogene homolog) (Fig 2, Riva et al ., 2017).
DemyHealth closed the country’s Hep C genotype testing gap. We were the first molecular lab in Nigeria to identify mixed Hepatitis C virus infections involving three serogroups in the Nigerian population—an uncommon feat. This earned us double space to present our findings at the Nigerian Gastroenterology and Hepatology Conference, in August, 2018. The experiment was carried out on LineGene K Plus (Bioer, Japan/China).
Below is a list of real time that DemyHealth exclusively distributes in Nigeria and their specifications.
Fig 3: Real time PCR platforms exclusively distributed by DemyHealth
Nyaruaba, R., Zhang, B., Muema, C., Muturi, E., Oyejobi, G., Xiong, J., Li, B., Shi, Z., Mwaliko, C., Yu, J. and Li, X., 2020. Development of a field-deployable RT-qPCR workflow for COVID-19 detection.
Riva, A., BØrgesen, M., Guldmann-Christensen, M., Kyneb, M.H., Voogd, K., Andersen, C., Epistolio, S., Merlo, E., Wolff, T.Y., Hamilton-Dutoit, S. and Lorenzen, J., 2017. SensiScreen® KRAS exon 2-sensitive simplex and multiplex real-time PCR-based assays for detection of KRAS exon 2 mutations. PloS one, 12(6).