Kayla Gaete, Sunnybrook Health Sciences Centre

Kayla Gaete1, Maedeh Naghibosadat1, Patryk Aftanas2, Finlay Maguire1, 2, 4, Henry Wong3,5, Calvin Sjaarda3,5, Kyla Tozer1,3, Xena Li2, Prameet M. Sheth3,5, Robert Kozak1,2 Affiliations: 1. Sunnybrook Health Sciences Centre, Biological Sciences Platform, Toronto, Ontario 2. Shared Hospital Laboratory, Toronto, Ontario 3. Queen's University, Kingston, Ontario 4. Dalhousie University, Faculty of Computer Science, Halifax, Nova Scotia 5. Kingston Health Sciences Center, Kingston, Ontario

Discovering & Evolving

Background Respiratory paramyxoviruses such as human parainfluenza viruses (HPIVs) and human metapneumovirus (HMPV), are often perceived as causing mild disease but contribute substantially to healthcare burden. Data describing their genomic epidemiology and associated clinical outcomes in the post-pandemic period in Canada remains limited. To investigate this, we performed whole-genome sequencing (WGS) and chart review of patients diagnosed with paramyxoviruses at a tertiary care academic hospital in 2023–2024. Methods All patients testing positive for HPIV-1, HPIV-3, or HMPV were included. WGS and viral culture were performed on residual material from nasopharyngeal swabs collected on admission, REB approval was obtained to review clinical data. Results A total of 278 patients were included in the study. While influenza virus peaked in December in both years, by contrast HPIV-3 peaked in March and June 2023, shifting to May–June 2024, while HMPV peaked in March 2023 and April 2024. Antibiotic prescribing frequently exceeded rates of confirmed bacterial pneumonia. In 2023, antibiotic use was highest among HMPV (50%) and HPIV-1 (46.2%) cases; in 2024, HPIV-1 (42.9%) and HPIV-3 (42.1%) had the highest rates. Secondary bacterial pneumonia was most frequent in HPIV-1 (15.4% in 2023; 28.6% in 2024). All-cause mortality was similar for all three viruses (HMPV 2.8%; HPIV-1 5%; HPIV-3 5.5%). Among culturable samples, infectious titers were highest early after symptom onset. Genomic analysis demonstrated limited diversity among circulating HPIV and HMPV strains. Conclusion Respiratory paramyxoviruses cause significant morbidity and mortality. These findings underscore the need for continued surveillance and study of these viruses.