AS part of the larger microbiology community, public-health laboratories play a unique role in supporting the work of public-health programs and services at the local, national and international level, through detection, screening, outbreak response and surveillance activities.
Cadham Provincial Laboratory plays a key role in undertaking, co-ordinating and managing a range of specialized work to help address this pandemic.
Cadham started testing for COVID-19 in January 2020, just a few weeks after the news of the novel coronavirus was announced. One year later, staff have performed more than 225,000 diagnostic tests, evaluated more than a dozen diagnostic platforms and have helped other labs implement COVID-19 testing.
Other work at Cadham is the screening for and sequencing of different bacteria and viruses, and experts at Cadham have been involved in this work since the H1N1 pandemic. This work is needed because every virus changes over time, resulting in new variants. While most COVID-19 variants are not that different, some have the potential to spread more easily. These are known as variants of concern.
Currently, there are three main variants of concern, including B.1.1.7 (first identified in the United Kingdom), B.1.351 (first identified in South Africa) and P.1 (first identified in Brazil).
While diagnostic testing shows if someone tests positive for COVID-19, additional work is needed to identify variants. Identifying variants is a two-step process — screening and sequencing.
Screening for variants is a second test, done only if a person’s COVID-19 diagnostic test comes back positive. Positive samples must be sent to Cadham for screening to determine if a key mutation of a particular variant of concern is present. This takes additional time to complete.
Sequencing is far more complex. If a screening test is like looking for a typo on one page of a book, then sequencing is like looking for all typos in the entire book. Sequencing maps out the entire genetic fingerprint of the virus (the genome) and compares it to other viral genomes in the community, the province and the country.
This process tells lab experts if there are any variations and mutations, including variants of concern. Many different variants are discovered and tracked this way, including some that might be unique to Manitoba. However, not all positive samples will be able to be screened or sequenced, for technical reasons. These could include not enough volume of the sample, or enough virus in the sample, for the processes.
However, viral screening and sequencing cannot prevent the spread of illness. We must continue to stick to public-health fundamentals, such as practising physical distancing and isolating cases and contacts.
As announced last fall, Cadham joined the Canadian COVID-19 Genomics Network (CanCOGeN). This national network, funded by Genome Canada and, in Manitoba, Genome Prairie, has led the development of protocols for sequencing, data analysis and data sharing.
This has ensured a consistent, co-ordinated and reliable response to the pandemic right across the country. In addition, the network has been paying close attention to public-health privacy concerns of the provinces, territories and Indigenous groups.
Samples are selected for sequencing by following the CanCOGeN’s framework. This prioritizes samples related to outbreaks and other areas of particular concern, such as travel. Experts agree only a small number of samples need to be sequenced to understand what is occurring in the population. Like Manitoba, most jurisdictions aim to sequence five per cent of screened samples.
Manitoba has COVID-19 sequence data going back to March 2020. This means there is an excellent understanding of the changes in the virus from the beginning of the Manitoba pandemic. Cadham has sequenced more than 1,200 viral genomes from more than 140 COVID-19 outbreaks in personal care homes, hospitals, jails and northern communities.
Manitoba, in partnership with the National Microbiology Laboratory and provincial partners, continues to ramp up screening and sequencing efforts. We are fortunate to have well-established protocols, federal supports and data-sharing agreements in place. Data "pipelines" with our federal partners have taken years to build, allow better and more efficient data analysis from infectious disease outbreaks, and are now well positioned to assist with the COVID-19 pandemic.
Cadham’s evidence-based approach to surveillance and the tireless efforts and expertise of staff on this highly specialized work means Manitoba’s public-health officials have been able to make informed, co-ordinated decisions on how to address COVID-19 in Manitoba. As COVID-19 continues to evolve, so will the work and the technologies used to protect Manitobans.
Paul Van Caeseele is the medical director at the Cadham Provincial Laboratory.