Pathogen‑agnostic diagnostics allow clinicians and public health laboratories to test respiratory samples without needing to know which pathogen to target in advance, unlike conventional testing methods. Metagenomic next‑generation sequencing (mNGS) is one such tool. It has the potential to transform clinical and public health microbiology by detecting infections missed by traditional tests, identifying antimicrobial resistance, enhancing surveillance of seasonal respiratory diseases, and enabling early detection of emerging variants with pandemic potential. However, before mNGS can be widely adopted in Canada, additional validation is needed.

BugSeq, a BC based Canadian company, has developed an industry leading, cloud‑based NGS data analytics platform called RAPID‑mNGS, which performs agnostic pathogen detection. This project will evaluate and validate the RAPID mNGS assay through three components. First, a technical performance study will be conducted at BC Centre for Disease Control (BCCDC) to assess the assay’s limits of detection, reliability and reproducibility. Second, the assay will be tested under real world conditions at three collaborating sites: the BCCDC, the Cadham Provincial Laboratory (CPL), and the Canadian Food Inspection Agency (CFIA). Finally, the project will assess the public health impact and potential cost savings of implementing RAPID‑mNGS and identify barriers to adoption.

The expected benefits of this project include faster diagnoses for patients, reduced healthcare costs, improved tracking of respiratory diseases and earlier detection of emerging variants, key elements that strengthen Canada’s biosecurity and pandemic preparedness. This work will also help align Canada’s biosecurity practices with those of other countries, such as the United Kingdom and the United States, that already incorporate mNGS testing into their national biosecurity strategies.