The emergence, impact, and evolution of human metapneumovirus variants from 2014 to 2021 in Spain

• DOI: 10.1016/j.jinf.2023.05.004
• Publication Date: 2023-05-11T20:51:43Z
• Authors: Maria Piñana; Alejandra Gonzále...; Cristina Andrés; Michel Abanto; Jorgina Vila; Juliana Esperalba; Noelia Moral; Elena Espartosa; Narcís Saubi; Anna Creus; Maria Gema Codina; Dolores Folgueira; Jaime Martinez-Ur...; Tomàs Pumarola; Andrés Antón
• Keywords: Paramyxoviridae Infections; Genotype; SARS-CoV-2; Infant; COVID-19; :fenómenos genéticos::genotipo [FENÓMENOS Y PROCESOS]; :virus::virus ARN::Mononegavirales::Paramyxoviridae::Pneumovirinae::Metapneumovirus [ORGANISMOS]; 3. Good health; :Genetic Phenomena::Genotype [PHENOMENA AND PROCESSES]; :enfermedades respiratorias::infecciones del tracto respiratorio [ENFERMEDADES]; Virosis - Epidemiologia; :Viruses::RNA Viruses::Mononegavirales::Paramyxoviridae::Pneumovirinae::Metapneumovirus [ORGANISMS]; Spain; Infeccions respiratòries - Epidemiologia; Humans; Metapneumovirus; Genotip; Respiratory Tract Infections; Phylogeny; :Respiratory Tract Diseases::Respiratory Tract Infections [DISEASES]

Human metapneumovirus (HMPV) is an important aetiologic agent of respiratory tract infection (RTI). This study aimed to describe the prevalence, genetic diversity, and evolutionary dynamics of HMPV.Laboratory-confirmed HMPV were characterised based on partial-coding G gene sequences with MEGA.v6.0. WGS was performed with Illumina, and evolutionary analyses with Datamonkey and Nextstrain.HMPV prevalence was 2.5%, peaking in February-April and with an alternation in the predominance of HMPV-A and -B until the emergence of SARS-CoV-2, not circulating until summer and autumn-winter 2021, with a higher prevalence and with the almost only circulation of A2c111dup. G and SH proteins were the most variable, and 70% of F protein was under negative selection. Mutation rate of HMPV genome was 6.95 × 10-4 substitutions/site/year.HMPV showed a significant morbidity until the emergence of SARS-CoV-2 pandemic in 2020, not circulating again until summer and autumn 2021, with a higher prevalence and with almost the only circulation of A2c111dup, probably due to a more efficient immune evasion mechanism. The F protein showed a very conserved nature, supporting the need for steric shielding. The tMRCA showed a recent emergence of the A2c variants carrying duplications, supporting the importance of virological surveillance.