The emergence, impact, and evolution of human metapneumovirus variants from 2014 to 2021 in Spain - 10/07/23

Doi : 10.1016/j.jinf.2023.05.004

Maria Piñana ^a,^{^{1
These first authors contributed equally to this article.},}^{^{2
ORCID: 0000-0002-4766-2613.}}, Alejandra González-Sánchez ^a,^{^{1
These first authors contributed equally to this article.},}^{^{3
ORCID: 0000-0002-1809-3415.}}, Cristina Andrés ^a,^{^{4
ORCID: 0000-0002-3200-0895.}}, Michel Abanto ^b,^{^{5
ORCID: 0000-0001-9136-0041.}}, Jorgina Vila ^c,^{^{6
ORCID: 0000-0001-9715-0627.}}, Juliana Esperalba ^a,^{^{7
ORCID: 0000-0003-1326-1341.}}, Noelia Moral ^d, Elena Espartosa ^d, Narcís Saubi ^a,^{^{8
ORCID: 0000-0001-5493-1044.}}, Anna Creus ^c, Maria Gema Codina ^a,^{^{9
ORCID: 0000-0002-5313-5086.}}, Dolores Folgueira ^d, Jaime Martinez-Urtaza ^e,^{^{10
ORCID: 0000-0001-6219-0418.}}, Tomàs Pumarola ^a,^⁎,^{^{11
These two authors are co-principal investigators.},}^{^{12
ORCID: 0000-0002-5171-7461.}} , Andrés Antón ^a,^{^{11
These two authors are co-principal investigators.},}^{^{13
ORCID: 0000-0002-1476-0815.}}
^a Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
^b Genomics and Bioinformatics Unit, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
^c Paediatric Hospitalization Unit, Paediatrics Department, Hospital Universitari Maternoinfantil Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
^d Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Universidad Complutense de Madrid, Madrid, Spain
^e Department of Genetics and Microbiology, School of Biosciences, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain

^⁎Correspondence to: Respiratory Viruses Unit – Microbiology Department, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, Barcelona, Spain.Respiratory Viruses Unit – Microbiology Department, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute, Universitat Autònoma de BarcelonaPasseig Vall d’Hebron 119-129BarcelonaSpain

Summary

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 A2c_111dup. 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.

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 A2c_111dup, 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.

Le texte complet de cet article est disponible en PDF.

Keywords : Human metapneumovirus, Duplication, Epidemiology, Evolution, Whole-genome sequencing

Plan

Introduction

Materials and methods

Sample collection

Respiratory viruses’ laboratory-confirmation

HMPV phylogenetic analysis

Whole genome sequencing

Evolutionary analysis

Results

HMPV epidemiology

Phylogenetic analyses of viral strains

Evolutionary analyses of whole-genome sequences

Discussion

Funding

Export

Vol 87 - N° 2

P. 103-110 - août 2023 Retour au numéro

Article précédent

4CMenB sustained vaccine effectiveness against invasive meningococcal B disease and gonorrhoea at three years post programme implementation
Bing Wang, Lynne Giles, Prabha Andraweera, Mark McMillan, Sara Almond, Rebecca Beazley, Janine Mitchell, Michele Ahoure, Emma Denehy, Louise Flood, Helen Marshall

| Article suivant

Intradermal skin test with mRNA vaccines as a surrogate marker of T cell immunity in immunocompromised patients
Benedict Fallet, Mathilde Foglierini, Raphael Porret, Ana Alcaraz-Serna, Christophe Sauvage, Raphael Jenelten, Teofila Caplanusi, Michel Gilliet, Laurent Perez, Craig Fenwick, Raphael Genolet, Alexandre Harari, Sara Bobisse, Raphael Gottardo, Giuseppe Pantaleo, Yannick D. Muller

Bienvenue sur EM-consulte, la référence des professionnels de santé.
L’accès au texte intégral de cet article nécessite un abonnement.

Déjà abonné à cette revue ?

connectez-vous ou créez un compte

The emergence, impact, and evolution of human metapneumovirus variants from 2014 to 2021 in Spain - 10/07/23

Summary

Background

Methods

Results

Conclusion

Plan

Export citations

Fichier

Contenu

Accès rapides

Mon compte

Aide & support

Plateformes Elsevier Masson

Déclaration CNIL