Our Microbiology Team utilise cutting edge technology and techniques to provide an accurate and efficient laboratory identification of COVID-19 (SARS-CoV-2) in our patients and staff. This information is used by Microbiology Consultants and other Clinicians to diagnose SARS-CoV-2 infection. Our method of choice is magnetic nucleic acid extraction from nose/throat swabs followed by highly specific Real-time PCR to identify the presence of SARS-CoV-2.
We are continuously looking for ways to refine and improve the standards of our service and outlined below is our current system. So far, the team have undertaken over 30,000 tests of SARS-CoV-2.
Sample Type:
- Our sample of choice is a Viral Swab (currently red or green topped) of the Nose and Throat.
- Our Viral swabs contain Viral Transport Media which contains a substance that sustains any viruses present and also antibiotics which will kill of any bacteria present. Both of these additives help to keep the sample as pure as possible during transport before being processed and helps remove the risk of contamination.
- This swab type means our assay is more sensitive or accurate for SARS-CoV-2 than by using dry swabs or those in saline.
Sample Preparation:
- Our main SARS-CoV-2 testing is carried out in our Molecular suite, a room that has limited access via a locked door that is only used by highly trained staff wearing full PPE.
- All staff working in the Molecular suite are fully competent in the process and understand all safety considerations. Any staff member required to work with this level of Pathogen must be a Biomedical Scientist registered with the Health and Care Professions Council.
- Our testing system has been fully assessed by the Health and Safety Executive and approved as COVID secure.
- All sample processing for SARS-CoV-2 testing is initially carried out in a special safety cabinet that protects our Biomedical Scientists from any risk of infection from the samples. These cabinets also protect the sample from being contaminated by our staff.
Nucleic Acid Extraction
- The prepared samples are then loaded into one of our four Extraction instruments.
- These instruments use heat to break down the components of the samples, releasing Nucleic acid (genetic material) in the form of DNA and RNA.
- All viruses can be DNA or RNA based organisms and SARS-CoV-2 is an RNA virus.
- The instruments then use metal beads to bind to any RNA present and are held in place by magnets.
- The unwanted material is then washed away from the sample leaving the purified RNA known as an eluate.
- This eluate is then ready for PCR testing.
- We also add an internal control that must be detected in the final result to guarantee the sample has been extracted correctly.
- This method of magnetic extraction is more sensitive than other methods of extraction relying on heat alone.
Real Time PCR:
- We use Real time PCR (Polymerase Chain Reaction) to detect SARS-CoV-2 in our samples.
- PCR is a highly sensitive and specific method for detecting the DNA or RNA of any Virus or Bacterium.
- PCR kits or assays are uniquely designed to only look for a specific component of the target organism.
- Primers are used which will only bind to the desired target component. This makes the method highly specific as the gene our primers bind to is only found in SARS-CoV-2.
- We have tested the normal strains of Coronavirus and other “common cold” organisms such as Rhinovirus with this assay and not produced any false positives for SARS-CoV-2.
- The PCR method uses cycles of heating and cooling to help the primers bind to the SARS-CoV-2 gene if present. If present, the gene will be amplified and fluorescence will occur.
- This fluorescence is measured throughout the test to give a visual and quantitative result.
- Negative and positive Quality controls are run with every test and all results are checked before authorisation.
- Negative results are sent out by Senior BMS staff and positives telephoned by Consultant Microbiologists.
Our assay has been measured as having a sensitivity (chance of producing true negatives) of 96% and a specificity (chance of producing true positives) of 96%. The LOD (Limit of Detection) of our assay is 30 copies per ul which means our assay can detect very small levels of the virus.
Future Developments:
- We have added a second PCR analyser to our laboratory which will allow us to increase capacity and hopefully reduce turnaround time to result.
- We are taking on a further three fixed-term members of staff to support our testing.
- We are currently verifying a new SARS-CoV-2 assay that is not only faster and even more sensitive but also looks for two separate SARS-CoV-2 This assay is a multiplex assay and will also test for FLU A, FLU B and RSV.