Since mid-March, BIOS scientist Rachel Parsons has been sharing her skills and expertise with Helix Bermuda, a clinical testing laboratory that is conducting COVID-19 testing on the island. Until late April, Helix Bermuda had the only COVID-19 authorized PCR instrument used for these tests. Parsons uses PCR instruments in her work at BIOS, where she runs the Microbial Ecology Laboratory, and was keen to assist in Bermuda's response to the growing pandemic. Here, she is seen working with the real-time PCR machine for part of the COVID-19 testing process known as amplification, in which small samples of DNA are multiplied to allow for more accurate testing and analysis.
As the COVID-19 disease reached the people of Bermuda this spring, BIOS was one of many local organizations that stepped up to provide the equipment and expertise required by healthcare workers, the Bermuda Government, and private companies to facilitate accurate testing and treatment.
Since mid-March, BIOS microbiologist Rachel Parsons, manager of the Microbial Ecology Laboratory, has been on assignment at Helix Bermuda, an accredited local forensic and clinical testing laboratory owned and managed by Dr. Desiree Spriggs, where one of two COVID-19 authorized PCR (polymerase chain reaction) instruments is operated on the island. The PCR instrument is widely used in medicine and molecular biology to create many copies of a single segment of DNA through a process called amplification. This allows for very small samples of genetic material to be studied in greater detail, allowing for more accurate testing and reporting of cases of the virus on island, and helping to ensure that infected Bermudians receive treatment.
In the early days of the outbreak, the Helix team was testing between three and 30 samples a day from Bermuda residents. However, with more testing kits, resources, and manpower available, they now run 30 to 80 samples a day, depending on how many are collected from the hospital each morning.
Parsons, who now spends her days in the Helix Bermuda lab, shared more about her current work via email interviews.
How did you come to work at Helix?
Desiree knows that I am a microbiologist and that I work on PCR protocols at BIOS, as she used to run the Lab Ops Department here years ago. We have stayed in touch and from time to time I help her source supplies and reagents. When I asked what help was needed during the COVID-19 crisis, she suggested that I come work for Helix Bermuda to help with the COVID-19 testing as she could use another set of trained hands with the PCR protocols. She felt that my experience with trouble-shooting molecular methods would be beneficial to setting up the COVID-19 testing on island.
What were your first few days like?
I trained over Skype with Dr. Lionel Gresh, an international virologist for the region with the Pan American Health Organization (PAHO), which is a division of the World Health Organization (WHO). I was also fitted with protective gear and advised on the safety precautions required for this type of work. Finally, we completed training and completed practice runs and validations on the testing procedure until we were confident that our protocol met WHO criteria and our data analyses were accurate. Dr. Gresh remains available to us virtually and via email should we need assistance.
How does the testing process work?
First, let me provide you with some background information so the process makes sense. DNA is the molecule within cells that carries genetic instructions for living organisms. Viruses need to insert their DNA into other cells in order to replicate, or amplify. DNA is converted to RNA during a process called transcription that occurs when a gene is needed or active. We are looking at the viral RNA, or genetic code, that is active within a patient’s cells. Since RNA is single stranded, we need to convert the RNA back to DNA using a process called reverse-transcription. Once it is back in DNA form, it is known as cDNA, and can be amplified since DNA is double stranded and more stable.
To start with, we make a master mix of buffers, enzymes, and primers that bind to the gene specific for SARS-COVID-2, the virus that causes COVID-19. The process first converts the viral RNA to cDNA and then the cDNA is amplified if the SARS-COVID-2 gene is present.
The original method uses three different master mixes, or reactions: one to look for a gene specific to the SARS-COVID-2 virus; a second that confirms the presence of SARS-COVID-2 using another gene specific to this virus; and a third to ensure the extracted RNA meets protocol standards. With each reaction performed, there are several controls needed to ensure the reaction works. That way we are not reporting false positives or negatives.
Then, the master mix is added to the samples and run on the RT-PCR (real-time PCR) instrument. If the sample has the SARS-COVID-19 gene, it will amplify and you will see a fluorescent signal; if it does not, there will be no signal. Any positive samples are then confirmed using another reaction and verified with Dr. Gresh. We report our findings to the Department of Health, which then disseminates the information to doctors, patients, and the Bermuda Government, who then inform the public through daily press conferences.
Can you describe your typical day working in tandem with the medical testing community?
Dr. Spriggs and medical technologists from the Bermuda Health Board process viral samples at the hospital using their safety hood—an enclosed, ventilated workspace that is used for working with hazardous chemicals and infectious diseases. Viral RNA is extracted from the nasal swab, which involves adding reagents to make the RNA stick to a column and then performing several washes and rinses by centrifugation. Once the sample has been converted to clean RNA through this process, it is no longer infectious.
Meanwhile, I’m in the lab at Helix Bermuda working in conjunction with Marshalita Tota, the Senior Medical Technologist and Laboratory Manager. Once we know the number of samples, we can start setting up a template for the real-time PCR run.
Is there anything else you’d like to share about this experience so far?
Clinical testing is very different from marine research. It is more stressful given the importance of the testing to the COVID-19 policies in Bermuda. Every day, new information is available on SARS-COVID-2 and the testing protocol changes. With every change, we need to verify and confirm the results. We have had amazing support from PAHO and Dr. Spriggs’ contacts in Cayman, Public Health UK, the Caribbean Public Health Authority and even some past BIOS faculty and staff who are familiar with real-time PCR. It has been an honor to work with PAHO, Helix Bermuda and Dr. Spriggs. I appreciate the chance to assist with Bermuda’s response to this global pandemic.
Helix Bermuda is owned and managed by Dr. Desiree Spriggs (right), shown here with microbiologist Helen Haigh, also part of the Helix team working on COVID-19 testing.