Microbiologists: the unsung heroes of the pandemic

Nov 19, 2020

In March 2020, the lives of millions of Canadians changed due to the COVID-19 pandemic.

For scientists working in laboratories across the University of Toronto network, this has been a time of dramatic change and action.

The challenges surrounding testing soon came to light: lack of availability, the limited reagent supply chain, and the shortage of trained laboratory staff and scientists.

Our scientists, based in the Department of Laboratory Medicine & Pathobiology (LMP), who have the necessary testing equipment in their laboratories, immediately offered up their labs to help resolve the testing dilemma.

Diagnostic testing must be done in accredited labs by certified medical lab technologists - individuals who have specialized training.

So, test ramp-up fell to a subgroup of our LMP community, microbiologists and microbiologists-in-training. Some anatomical pathology residents were redeployed to help.

Two microbiologists who are part of LMP explain more about COVID-19 testing and what it has been like to be part of the frontline in the battle against the pandemic.

Dr Tony Mazzulli, Microbiologist in Chief at Mount Sinai Hospital and University Health Network

Dr Kevin Katz, Medical Director of Shared Hospital Laboratory, and Head of Microbiology, Sunnybrook Health Sciences Centre

How we are testing for COVID-19

The main way to test for COVID-19 is based on the detection of the RNA (essentially the genetic material) of the SARS CoV-2 virus in a nasopharyngeal swab using molecular-based assays known as PCR (Polymerase Chain Reaction) tests.

Recently, Health Canada approved both molecular and antigen-based point of care tests for COVID-19, although the exact role these tests will play has not yet been determined.

The molecular point of care tests detect the RNA of the SARS CoV-2 virus, while the antigen-based ones detect protein of the virus.

These tests can be performed on patients who physically go to clinics and can provide a result within 15 minutes. However, the tests' overall sensitivity and specificity appear to be less accurate than standard laboratory-based PCR tests.

Serology tests (also known as antibody tests) have also become available during the course of the pandemic, but their use has been limited. These tests require testing of a blood sample and determine whether someone has had COVID-19. We will cover this topic in more detail at a later date. 

Responding to the testing need

“Shortly after the diagnosis of the first laboratory-confirmed COVID-19 case in Toronto by the Public Health Ontario Laboratory (PHOL) in January, the number of requests for COVID-19 testing began to increase tremendously” says Dr Tony Mazzulli, Professor in the Department of Laboratory Medicine & Pathobiology at the Temerty Faculty of Medicine. 

“By late February, the capacity for testing by PHOL was being exceeded and hospital-based Microbiology Laboratories were asked to implement testing to meet the ever-increasing demand.”

Within a few short weeks, hospital laboratories responded to the testing need. On March 11th, the Mount Sinai Hospital/University Health Network Microbiology Department went live with COVID-19 testing, quickly followed by Shared Labs/Sunnybrook, Unity Health, Sick Kids, and others.

Ontario Health and KPMG formed an Ontario Network Operations Committee. This included all labs testing for COVID-19 across the province. The aim was to coordinate testing, build capacity, and respond to changes in testing guidelines.

The plan was to increase testing capacity, which stood at 3,900 tests per day, to 18,900 tests per day by mid-April. Most of this capacity increase was to be built by the hospital laboratories.

By the end of October, the provincial testing capacity was at 60,000 tests per day.

“The University of Toronto affiliated laboratories (excluding the PHOL) have been contributing to around a third of the provincial testing to date – at around 20,000 tests a day. For us to meet the requested provincial capacity of over 100,000 tests a day by early January 2021, our laboratories have an important role to play” says Dr Kevin Katz, Associate Professor in the Department of Laboratory Medicine & Pathobiology at the Temerty Faculty of Medicine.

Challenges in meeting testing demands

Although testing laboratories across the province have developed in-house PCR tests, the majority are using commercially sourced tests and supplies.

“Unfortunately, our laboratories have been competing with the rest of the world for supplies and reagents which has made testing challenging at times as some vendors have capped the supplies we can order” says Mazzulli.

As time has moved on, some labs have expanded to accept saliva samples for testing. Others have tried to conserve resources by ‘pooling’ samples before testing.

“In addition to struggling with limited reagents and supplies, COVID-19 testing labs have struggled with hiring well trained lab personnel to perform the testing, space for equipment and technologists (particularly while trying to maintain social distancing), as well as space for supplies, and IT connectivity for logging receipt of specimens, tracking results, and reporting. All of this has been in the face of trying to maintain all other microbiology services.“ says Katz.

By the end of September 2020, testing for COVID-19 had surpassed all other testing activities performed in the many hospital-based microbiology laboratories, accounting for 60-80% of all tests processed.

“What makes this all work is our people - we have incredibly talented and dedicated scientists and staff in our laboratories who have sacrificed much on a personal level, as have many others during this pandemic, to keep these testing machines going. For all of us, our primary motivation is to play our part in protecting the health of the people of Ontario" says Mazzulli.

When the pandemic will end is unknown.

However, COVID-19 testing will likely remain for the foreseeable future and laboratories will have to continue to meet the demand.

“I will never forget when our lives changed immeasurably because of the COVID-19 pandemic. Our world has become smaller and constrained in many ways" says Dr. Rita Kandel, Professor and Chair of the Department of Laboratory Medicine & Pathobiology at the Temerty Faculty of Medicine.

"Our microbiologists, keeping the testing engine running, are the unsung heroes of our fight against COVID-19. Please thank microbiologists for their work. Your life, as well as the lives of those close to you, may have depended on them and what they have accomplished.”

Find out more about how LMP is helping us understand, treat and live with COVID-19