In its 2026-2027 Departmental Plan, the Canadian Food Inspection Agency announced a significant upgrade to its plant health diagnostic capabilities: the implementation of high-throughput sequencing (HTS) at the Centre for Plant Health in Sidney, British Columbia. This technology represents a generational leap in how Canada detects and identifies plant pests, and its rollout has practical implications for growers, nurseries, importers, and the broader agricultural supply chain.
What Is High-Throughput Sequencing?
High-throughput sequencing, sometimes called next-generation sequencing (NGS), reads millions of DNA or RNA fragments from a sample simultaneously. Unlike conventional diagnostic methods that test for one pathogen at a time, HTS captures the complete genetic content of a sample, including the host plant, any viruses, bacteria, fungi, and even insects present in or on the tissue.
This “catch everything” approach is transformative for plant health diagnostics. Traditional testing requires the diagnostician to have a suspect pathogen in mind and then run a specific test for it. If you suspect Tobacco mosaic virus, you run a TMV test. If you suspect Phytophthora, you run a Phytophthora test. But what if the disease is caused by something unexpected, a novel virus, a new strain, or a pathogen not previously reported in Canada? Traditional methods miss what they are not looking for.
HTS solves this problem by detecting everything in the sample and then using bioinformatics to identify what is present. It has already proven its value in international plant health programs by detecting novel viruses in fruit tree germplasm, identifying mixed infections that traditional tests missed, and confirming the absence of regulated pathogens in imported plant material.
Why the CFIA Is Making This Move
Canada’s plant health system faces several converging pressures that make HTS deployment timely. International trade in plant material continues to grow, bringing with it an increasing diversity of pest risks. Climate change is expanding the geographic range of both pests and their host plants, introducing novel host-pathogen combinations. And the emergence of new pathogens like ToBRFV and hop latent viroid has demonstrated how quickly a previously unknown threat can cause industry-wide damage.
The CFIA’s 2025-2026 priorities already included raising awareness about invasive pests such as spotted lanternfly, oak wilt, emerald ash borer, Japanese beetle, and plum pox virus. HTS gives the agency a more powerful screening tool for detecting these and other threats at ports of entry and in domestic surveillance programs.
At the Centre for Plant Health, HTS will be particularly valuable for screening the facility’s collection of virus-tested fruit tree and grape germplasm. This collection provides clean plant material to the Canadian nursery industry, and ensuring it remains free of viruses and viroids is critical. HTS can detect novel or previously uncharacterized viruses that conventional testing would miss, adding a layer of assurance to the clean stock program.
How HTS Complements Existing Diagnostic Methods
HTS does not replace traditional diagnostic tools. Rather, it fills a gap that existing methods cannot address. Think of plant health diagnostics as a toolkit where different tools serve different purposes.
ImmunoStrip rapid tests remain the fastest and most practical option for field-level screening. A grower who suspects a virus in their greenhouse can test a plant in minutes without any laboratory equipment. This speed and simplicity are irreplaceable for day-to-day crop monitoring.
ELISA testing provides quantitative results for known pathogens and is well-suited to high-volume screening programs where cost per sample matters. Seed companies, nurseries, and certification programs rely on ELISA for routine quality assurance.
Molecular methods like AmplifyRP XRT deliver PCR-level sensitivity without the need for a thermocycler, making them ideal for greenhouse labs that need molecular confirmation of rapid test results. These isothermal amplification platforms bridge the gap between field testing and full laboratory diagnostics.
HTS sits at the top of the diagnostic pyramid. It is the tool you use when you need to identify something unknown, when you want to screen for everything at once, or when you need the highest level of confidence that a sample is pest-free. Its cost and turnaround time are higher than rapid tests or ELISA, but the depth of information it provides is unmatched.
What This Means for Canadian Growers and Nurseries
For most growers, the CFIA’s HTS rollout will be felt indirectly through improved surveillance and faster identification of new pest threats. When a new virus or variant appears in Canadian crops, HTS will enable the CFIA to characterize it quickly and communicate risk information to the industry faster than was previously possible.
Nurseries and importers may see more direct impacts. HTS could become part of the diagnostic toolkit used for phytosanitary certification of imported plant material, particularly high-value propagation material like fruit tree rootstocks, grapevine cuttings, and ornamental liners. Shipments that currently undergo conventional testing might be subject to HTS screening, which could detect issues that traditional tests miss.
For clean stock programs, HTS provides an additional layer of quality assurance. Programs that maintain virus-tested mother plants can use periodic HTS screening to verify that their collections remain clean, catching any new infections before they spread through the propagation pipeline.
Practical Steps for Growers
While HTS is a regulatory and research tool, growers benefit most by maintaining strong diagnostic programs at the farm level. The CFIA’s investment in advanced diagnostics does not reduce the need for on-farm testing. If anything, it increases the importance of growers having their own screening capabilities to catch problems early before they reach the scale where regulatory intervention is triggered.
Building an on-farm testing capability does not require expensive equipment. A basic program might include ImmunoStrip rapid tests for routine screening of the most likely pathogens, an AmplifyRP XRT platform for molecular confirmation when rapid tests are positive or when higher sensitivity is needed, and a relationship with a diagnostic laboratory for sending samples that require advanced testing, including potential HTS analysis.
This tiered approach mirrors the diagnostic hierarchy that the CFIA itself uses, and it ensures that growers can respond quickly to disease threats while having access to deeper diagnostics when needed.
Looking Forward
The CFIA’s deployment of HTS at the Centre for Plant Health positions Canada at the forefront of plant health diagnostics globally. As sequencing costs continue to decline and bioinformatics pipelines become more accessible, HTS may eventually become routine enough for larger greenhouse operations and nurseries to use directly. In the meantime, it strengthens the national surveillance system that protects Canadian agriculture from emerging threats, giving growers greater confidence in the plant material they source and the phytosanitary systems that support the industry.
