Genomic Surveillance of Human Metapneumovirus in the United States, 2010-2025.
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Bendall Emily E, Fitzsimmons William J, Valvano Weronika Damek, Truscon Rachel, Self Wesley H, Halasa Natasha, Chappell James D, Zhu Yuwei, Safdar Basmah, Ginde Adit A, Peltan Ithan D, Gaglani Manjusha, Columbus Cristie, Shapiro Nathan I, Gibbs Kevin W, Hager David N, Prekker Matthew E, Mohamed Amira, Johnson Nicholas J, Steingrub Jay S, Khan Akram, Duggal Abhijit, Wilson Jennifer G, Qadir Nida, Busse Laurence W, Kwon Jennie H, Exline Matthew C, Vaughn Ivana A, Mosier Jarrod M, Harris Estelle S, Dawood Fatimah S, Ma Kevin C, Surie Diya, Monto Arnold S, Martin Emily T, Lauring Adam S, Investigating Respiratory Viruses in the Acutely Ill (IVY) Network
Аннотация
METHODS: Hybrid capture and whole-genome sequencing were performed on 616 HMPV-positive specimens from 2 cohorts: the household-based HIVE study (2010-2022) in Michigan and the multicenter IVY network (2022-2025) of hospitalized adults. Consensus sequences were generated using IRMA, clades were annotated using Nextclade, and phylogenetic trees were constructed separately for HMPV-A and HMPV-B using IQ-TREE and TreeTime. Analysis of selection by dN/dS was performed using SLAC.
RESULTS: We obtained complete genomes from 325 specimens. Our analyses revealed the continued predominance of the A2.2.2 clade and little geographic structure in the United States. Genomic diversity was highest in the glycoprotein (G); we identified a shift from variants bearing the 180nt duplication to ones with a 111nt duplication. Phylogenetic analyses supported the duplication-deletion model for the origin of the duplications. The conserved fusion (F) protein showed limited antigenic variation and low rates of nonsynonymous substitutions.
CONCLUSIONS: These findings underscore the utility of enhanced genomic surveillance for understanding HMPV evolution and informing vaccine development. There was little genomic diversity in vaccine-targeted epitopes.