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

Background: 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. Methods: 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. Results: 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 x 10-4 substitutions/site/year. Conclusion: 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. & COPY; 2023 The Author(s). Published by Elsevier Ltd on behalf of The British Infection Association. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Automated summary

This study aimed to describe the prevalence, genetic diversity, and evolutionary dynamics of HMPV. The findings showed that HMPV had a prevalence of 2.5% and peaked in February-April, circulating alternately between HMPV-A and -B until the emergence of SARS-CoV-2. HMPV re-emerged in summer and autumn 2021 with a higher prevalence and the almost exclusive circulation of A2c111dup. The F protein exhibited a highly conserved nature, supporting the need for steric shielding. The mutation rate of the HMPV genome was 6.95 x 10-4 substitutions/site/year. The study highlights the importance of effective viral surveillance and maintenance of viral epidemiological characteristics.