Epidemiology of Human Metapneumovirus Infection in a Community-Based Setting, Seattle, WA, USA

To better quantify human metapneumovirus (hMPV) prevalence, associated risk factors, and genomic epidemiology in a community setting. Methods: This is a secondary analysis using data from the Seattle Flu Study (SFS). SFS was a community-based observational surveillance study for respiratory infections among clinical and community populations across the greater Seattle area from 2018-2022. SFS utilized prospective cross-sectional sampling, prospective cohort sampling, and retrospective cross-sectional sampling to obtain clinical and community samples representative of the greater Seattle area. Whole genome sequencing of samples was performed for a select number of samples meeting viral load cutoff criteria (Relative cycle threshold < 20). Clinical samples were matched to community samples based on respiratory season to allow for comparison of subtypes across sampling methods. Results: Of the 52,036 community samples collected, 247 (0.47%) tested positive for hMPV. 74% of hMPV positive samples were collected prior to the COVID-19 pandemic and 47% were among those under the age of 18. The most commonly reported symptoms were cough and rhinorrhea. The presence of additional symptoms varied by age group, with fever more commonly reported among those under 5 and headaches more commonly reported among those over 65. In our multivariable model, lower income (aOR: 2.05 95% CI: 1.12 – 3.74), larger household size (aOR: 2.94 95% CI: 1.44 – 6.00), and international travel (aOR: 2.71 95% CI: 1.23 – 5.97) were found to be significant risk factors for testing positive. Testing from January 2019 through February 2020 was associated with an increased odds of testing positive for hMPV compared to testing from March 2020 through July 2022 (aOR 3.02 95% CI: 1.90 – 4.81). There was co-circulation of multiple hMPV subtypes across community and clinical samples. Community sampling captured subtypes A2b, A2c, B1 and B2 whereas clinical sampling captured A2b, B1, and B2. There was variation of subtype prevalence by age, with those under 18 having a larger proportion of A2b subtypes in community settings compared to clinical settings. Subtype prevalence changed after the start of the COVID-19 pandemic, with the proportion of B1 subtype increasing after the start of the pandemic. This change was observed in both clinical and community settings. Percent positivity for hMPV was highest prior to the start of the COVID-19 pandemic. Clinical samples had higher percent positivity compared to community samples (1.74% vs 0.47%). The highest percent positivity across community and clinical samples was among clinical samples who resided in the Southwest Seattle Public Use Microdata Area (PUMA) (5.3%). This PUMA is an area with a large proportion of low socioeconomic status (SES) census tracts. Conclusion: In a study of individuals with respiratory illness in community settings, risk factors for testing positive included lower income, larger household size, and international travel. Testing prior to the start of the COVID-19 pandemic was also associated with an increased odds of testing positive. The COVID-19 pandemic had an impact on both frequency and diversity of hMPV subtypes in clinical and community settings. Percent positivity among clinical and community samples were highest prior to the start of the COVID-19 pandemic, and the highest percent positivity was in a PUMA with a large proportion of low SES census tracts.