New, faster methods to detect and characterize dangerous pathogens developed by researchers at the Public Health Agency of Canada (PHAC) are enhancing the capacity of public health authorities across Canada to respond to COVID-19.
Characterizing samples of any pathogen is essential to tracking its movement, allowing epidemiologists to compare lineages collected from different locations. Tracking the source allows us to respond with measures to limit pathogen spread. Genomics can also monitor the evolution of viruses to see if the vaccine still matches, whether anti-viral drugs are still effective, and determine if mutations associated with greater transmission or new variants of concern arise.
Funded by the Government of Canada's Genomics Research and Development Initiative (GRDI), the research project at PHAC was launched in 2019, aimed at developing protocols to speed characterization of various pathogens using nanopore sequencing technology. With the arrival of the pandemic in the early part of 2020, the researchers quickly narrowed their focus to concentrate exclusively on how the technology could be used to accelerate understanding of SARS-CoV-2—the virus that causes COVID.
Nanopore sequencing: a generational leap
At the PHAC National Microbiology Laboratory in Winnipeg (NML), project leader Dr. Anna Majer says the so-called third-generation genomics technology offers numerous advantages, including delivering faster results at lower cost by eliminating much of the high-skill, hands-on lab work involved in the process.
"With earlier technology, it could take a day or more just to prepare a sample for sequencing, and several more hours to complete the sequencing before you could start analysing the genomic data," says Dr. Majer. "Nanopore technology requires far less sample preparation—you can start sequencing in as little as an hour. On top of that, this technology delivers the genomic data in real time—within minutes of starting the sequencing run, you begin getting the information you need to start understanding what is in the sample."
The COVID challenge
Notwithstanding its advantages, there was a lot of groundwork to be done before nanopore technology could join the battle against COVID.
"Like everyone else in the world, we were pretty much starting from scratch with COVID," says Dr. Majer. "Unlike the known pathogens we'd been working with, there was no validated protocol for sequencing this virus and very little other data to work with—it simply wasn't on anyone's radar. At the same time, what we'd learned in the GRDI project to that point gave us a head start—knowledge we could build on in working with COVID."
Based on their own research and drawing on the work of other researchers in Canada and elsewhere, Dr. Majer's team developed a reliable protocol for extracting COVID genetic material from a specimen and preparing it for nanopore sequencing. To make sense of the genetic data being generated, the bioinformatics team at NML developed the automated analysis pipeline needed to analyze the data and characterize the COVID samples that were coming in from the public health labs in the provinces and territories.
Knowledge transfer, well-timed
By the early summer of 2020 the PHAC team had a fully vetted protocol for sequencing COVID using nanopore technology as well as the bioinformatics pipeline needed to characterize the virus—knowledge and tools passed on to public health labs across the country through the Canadian Public Health Laboratory Network.
From the Saskatchewan Health Authority lab in Regina, Associate Clinical Scientist Dr. Ryan McDonald says that Dr. Majer's work enabled their lab to start working with nanopore technology significantly sooner than would have been otherwise possible.
"In the fall of 2020, Genome Canada provided funding to public health labs across the country specifically for the acquisition of genomic sequencing technology," says Dr. McDonald. "We acquired the nanopore technology in the Spring of 2021 and had it in place by July—and with the nanopore sequencing protocol for SARS-CoV-2 developed by Dr. Majer's team already available, we were able to get our new technology up-and-running almost immediately. It saved us what would have been several weeks searching through the literature and trying to piece together a protocol on our own."
Work to continue
Back at the PHAC, as long as the COVID virus continues to mutate and new variants emerge, Dr. Majer and her team will continue to refine and update their protocols, disseminating new knowledge on an ongoing basis through the public health laboratory network.