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. 2025 Jul 16;232(Supplement_1):S78-S92.
doi: 10.1093/infdis/jiaf142.

Epidemiology of Human Metapneumovirus Infection in a Community Setting, Seattle, Washington, USA

Annalyse Elias-Warren  1   2 , Julia C Bennett  1   2 , Chidozie D Iwu  1   2 , Lea M Starita  3   4 , Jeremy Stone  3 , Ben Capodanno  3 , Robin Prentice  3 , Peter D Han  3   4 , Zack Acker  3 , Sally B Grindstaff  3 , David Reinhart  3 , Jennifer K Logue  1 , Caitlin R Wolf  1 , Michael Boeckh  1   3   5 , Kevin Kong  6 , Hong Xie  6 , Geon Kim  6 , Alexander L Greninger  6 , Amanda C Perofsky  3   7 , Cécile Viboud  7 , Timothy M Uyeki  8 , Janet A Englund  9 , Pavitra Roychoudhury  5   6 , Helen Y Chu  1
Affiliations

Epidemiology of Human Metapneumovirus Infection in a Community Setting, Seattle, Washington, USA

Annalyse Elias-Warren et al. J Infect Dis. .

Abstract

Background: The clinical and genomic epidemiology of human metapneumovirus (hMPV) infections in community settings is not well understood.

Methods: From 2018 to 2022, individuals with respiratory symptoms were recruited and enrolled from the greater Seattle, Washington community in the United States. Residual clinical specimens from individuals presenting with respiratory symptoms were additionally collected. Specimens were tested for hMPV by reverse-transcription polymerase chain reaction, with whole genome sequencing performed on a subset (209/1002).

Results: hMPV positivity was higher among clinical specimens (835/21 539 [3.9%]) compared to community specimens (167/28 348 [0.6%]). Children aged 0-4 years had the highest percent positivity across both clinical and community settings (497/10 213 [4.9%] and 28/1640 [1.7%], respectively). In multivariate analysis, a household income of ≤US$100 000 (adjusted odds ratio [aOR], 1.72 [95% confidence interval {CI}, 1.07-2.85]), and recent international travel (aOR, 6.51 [95% CI, 3.11-12.22]) were associated with hMPV positivity. A subset of 209 of 1002 samples (21%) was sequenced; the distribution of subtypes A2b, A2c, B1, and B2 were similar across both community and clinical settings, with an increase in the proportion of subtype B1 after the start of the pandemic.

Conclusions: Risk factors of testing positive for hMPV in a community setting included lower household income and recent international travel. Co-circulation of hMPV subtypes was observed across community and clinical settings.

Keywords: clinical epidemiology; community setting; genomic epidemiology; geospatial percent positivity; human metapneumovirus.

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Conflict of interest statement

Potential conflicts of interest. H. Y. C. has served on advisory boards for Roche, Vir, Merck, and AbbVie; has conducted continuing medical education teaching with Medscape, Vindico, and Clinical Care Options; has received research funding from the Gates Foundation, the National Institutes of Health, and the Defense Advanced Research Projects Agency; and currently serves on the CDC’s Advisory Committee on Immunization Practices board. J. A. E. has served as a consultant with AbbVie, AstraZeneca, GlaxoSmithKline, Merck, Meissa, Pfizer, Shionogi, and Cidarra, outside of the submitted work; and has received research funding from AstraZeneca, Moderna, GlaxoSmithKline, and Pfizer. M. B. has served as a consultant with AstraZeneca, outside of the submitted work, and has received research funding from AstraZeneca and Pulmotect. A. L. G. reports central laboratory contract testing from Abbott, Cepheid, Novavax, Pfizer, Janssen, and Hologic, and research support from Gilead, outside of the described work. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

Figures

Figure 1.
Figure 1.
Seattle Flu Study enrollment strategies and nasal swab collection methods. aKiosk swabs were collected by research/clinical staff between 2018 and 2019, and self-collected by the participants in 2020 under supervision due to coronavirus disease 2019 precautions. bSwab & Send swabs were self-collected at home unsupervised and mailed to the laboratory. cSeattle Coronavirus Assessment Network (SCAN) swabs were self-collected unsupervised and mailed to the laboratory. dThese individuals are in clinical wait rooms for a multitude of reasons other than seeking care for influenza-like illness.
Figure 2.
Figure 2.
Percent positivity by collection site and age group (A), collection site and sex (B), and collection site and season (C).
Figure 3.
Figure 3.
Percentage of reported symptoms by age for human metapneumovirus community positive cases for all positives (n = 156; 11 excluded due to missing age profiles) (A) and positives within 4 days of symptom onset (n = 85; 11 excluded due to missing age profiles, 71 excluded for being outside 4 days of symptom onset) (B).
Figure 4.
Figure 4.
Maximum likelihood phylogenetic trees of sequenced samples (colored tips) compared to contextual human metapneumovirus (hMPV) sequences from GenBank (gray) identifying the 3 main circulating hMPV subtypes (A2b, B1, and B2, zoomed in view in the 3 lower panels).
Figure 5.
Figure 5.
Sequence logo plot illustrating amino acid variation within the F1 subunit of the RSV F gene overall across all sequences (n = 237), and within each subtype (n = 82, 75, and 80 sequences for subtype A2, B1, and B2 respectively). At each position, the total height of the stack is measured in bits and reflects the information content—i.e., how conserved that position is across sequences as measured by Shannon entropy. Taller stacks indicate higher conservation. The height of each individual letter within a stack represents the relative frequency of that amino acid at that site. Only positions with observed variation are shown (see Supplemental Tables 4 and 5).
Figure 6.
Figure 6.
Human metapneumovirus subtypes observed from November 2018 to July 2022 in the Seattle Flu Study overall (A), by community vs clinical settings (B), and by age (C). Total number of sequences is the sum of counts in a year above and below zero on the y-axis and data are smoothed over time. In C, 204 sequences were included as 5 sequences were missing age data.
Figure 7.
Figure 7.
Human metapneumovirus percent positivity by public use microdata area in Seattle, Washington, across respiratory season and sampling method.
Figure 8.
Figure 8.
Human metapneumovirus percent positivity by Public Use Microdata Area (PUMA) in Seattle, Washington, across respiratory season, sampling method, and age group (<18 years old and ≥18 years old). Gray areas represent a percent positivity that is >10%. See Supplementary Tables 7 and 8 for PUMA-specific counts.
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