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Gavilán AM, Perán-Ramos P, Sanz JC, García-Comas L, Pérez-Abeledo M, Castellanos AM, Berciano JM, López-Perea N, Masa-Calles J, Echevarría JE, Fernández-García A. Investigating Local Patterns of Mumps Virus Circulation, Using a Combination of Molecular Tools. Viruses 2023; 15:2420. [PMID: 38140661 PMCID: PMC10747990 DOI: 10.3390/v15122420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Mumps is a vaccine-preventable disease caused by the mumps virus (MuV). However, MuV has re-emerged in many countries with high vaccine coverage. The World Health Organization (WHO) recommends molecular surveillance based on sequencing of the small hydrophobic (SH) gene. Additionally, the combined use of SH and non-coding regions (NCR) has been described in different studies, proving to be a useful complement marker to discriminate general patterns of circulation at national and international levels. The aim of this work is to test local-level usefulness of the combination of SH and MF-NCR sequencing in tracing hidden transmission clusters and chains during the last epidemic wave (2015-2020) in Spain. A database with 903 cases from the Autonomous Community of Madrid was generated by the integration of microbiological and epidemiological data. Of these, 453 representative cases were genotyped. Eight different SH variants and thirty-four SH haplotypes were detected. Local MuV circulation showed the same temporal pattern previously described at a national level. Only two of the thirteen previously identified outbreaks were caused by more than one variant/haplotype. Geographical representation of SH variants allowed the identification of several previously undetected clusters, which were analysed phylogenetically by the combination of SH and MF-NCR, in a total of 90 cases. MF-NCR was not able to improve the discrimination of geographical clusters based on SH sequencing, showing limited resolution for outbreak investigations.
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Affiliation(s)
- Ana M. Gavilán
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
| | - Paula Perán-Ramos
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
| | - Juan Carlos Sanz
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
- Laboratorio Regional de Salud Pública de la Comunidad de Madrid, 28055 Madrid, Spain;
| | - Luis García-Comas
- Servicio de Epidemiología, Consejería de Sanidad de la Comunidad de Madrid, 28009 Madrid, Spain;
| | - Marta Pérez-Abeledo
- Laboratorio Regional de Salud Pública de la Comunidad de Madrid, 28055 Madrid, Spain;
| | - Ana M. Castellanos
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
| | - José M. Berciano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
| | - Noemí López-Perea
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Medicina Preventiva y Salud Pública, Universidad Autónoma de Madrid/IdiPAZ, 28049 Madrid, Spain
| | - Josefa Masa-Calles
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Juan E. Echevarría
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
| | - Aurora Fernández-García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
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Gavilán AM, van de Nes-Reijnen L, Castellanos A, Woudenberg T, López-Perea N, Masa-Calles J, Echevarría JE, Fernández-García A, Bodewes R. Comparison of circulation patterns of mumps virus in the Netherlands and Spain (2015-2020). Front Microbiol 2023; 14:1207500. [PMID: 37396375 PMCID: PMC10311905 DOI: 10.3389/fmicb.2023.1207500] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Background Mumps is a viral infection mainly characterized by inflammation of the parotid glands. Despite of vaccination programs, infections among fully vaccinated populations were reported. The World Health Organization (WHO) recommends molecular surveillance of mumps based on sequencing of the small hydrophobic (SH) gene. The use of hypervariable non-coding regions (NCR) as additional molecular markers was proposed in multiple studies. Circulation of mumps virus (MuV) genotypes and variants in different European countries were described in the literature. From 2010 to 2020, mumps outbreaks caused by genotype G were described. However, this issue has not been analyzed from a wider geographical perspective. In the present study, sequence data from MuV detected in Spain and in The Netherlands during a period of 5 years (2015- March 2020) were analyzed to gain insights in the spatiotemporal spread of MuV at a larger geographical scale than in previous local studies. Methods A total of 1,121 SH and 262 NCR between the Matrix and Fusion protein genes (MF-NCR) sequences from both countries were included in this study. Analysis of SH revealed 106 different haplotypes (set of identical sequences). Results Of them, seven showing extensive circulation were considered variants. All seven were detected in both countries in coincident temporal periods. A single MF-NCR haplotype was detected in 156 sequences (59.3% of total), and was shared by five of the seven SH variants, as well as three minor MF-NCR haplotypes. All SH variants and MF-NCR haplotypes shared by both countries were detected first in Spain. Discussion Our results suggest a transmission way from south to north Europe. The higher incidence rate of mumps in Spain in spite of similar immunization coverage in both countries, could be associated with higher risk of MuV exportation. In conclusion, the present study provided novel insights into the circulation of MuV variants and haplotypes beyond the borders of single countries. In fact, the use of MF-NCR molecular tool allowed to reveal MuV transmission flows between The Netherlands and Spain. Similar studies including other (European) countries are needed to provide a broader view of the data presented in this study.
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Affiliation(s)
- Ana M. Gavilán
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
| | - Linda van de Nes-Reijnen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Ana Castellanos
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
| | - Tom Woudenberg
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Noemí López-Perea
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Josefa Masa-Calles
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Juan E. Echevarría
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
| | - Aurora Fernández-García
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain
| | - Rogier Bodewes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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Hiebert J, Saboui M, Frost JR, Zubach V, Laverty M, Severini A. Mumps resurgence in a highly vaccinated population: Insights gained from surveillance in Canada, 2002-2020. Vaccine 2023:S0264-410X(23)00513-3. [PMID: 37169652 DOI: 10.1016/j.vaccine.2023.04.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
Although mumps vaccination has been routine in Canada for decades, mumps cases and outbreaks continue to occur periodically. Mumps surveillance, including monitoring of the mumps virus genotype associated with disease activity, is important to document baseline activity and to advance further research into vaccine effectiveness. Here we describe a detailed analysis of mumps cases that have been detected in Canada from 2002 to 2020, with a focus on the mumps molecular epidemiology. In total, 7395 cases of mumps were reported to the surveillance system, with outbreaks occurring in the years 2007, 2010 and 2016 to 2018. Adolescents and young adults aged 15 to 29 years had the highest risk of being a case (rate ratios ranging from 1.50 to 2.29), compared to adults aged 30 to 39. Genotypes of mumps viruses were determined in 3225 specimens. Genotype G was predominantly detected (96% of genotyped specimens) and was first reported in 2005. Other genotypes were more likely to be detected in cases that also reported travel (or were linked to imported cases) than the cases with genotype G detected (p < 0.0001). The genotype G viruses had little sequence diversity in the 316 nucleotide window used for genotyping (the small hydrophobic protein gene) and mainly belonged to a single phylogenetic lineage that included the MuVi/Sheffield.GBR/1.05 reference sequence. The analysis of over ten years of data has demonstrated that mumps genotype G, specifically belonging to a single lineage, the Sheffield lineage, is the endemically circulating virus in Canada. This lineage is seen also in other countries using the genotype A vaccine. Mumps remains endemic despite high MMR vaccination coverage which has been sufficient to eliminate circulation of measles and rubella in Canada, raising the hypothesis of the evolution towards a vaccine escape mumps virus.
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Affiliation(s)
- Joanne Hiebert
- Viral Exanthemata and STD section, National Microbiology Laboratory Branch, Public Health Agency of Canada, JC Wilt Infectious Diseases Research Centre, 745 Logan Avenue, Winnipeg R3E 3L5, Canada.
| | - Myriam Saboui
- Centre for Immunization and Respiratory Infectious Diseases, Public Health Agency of Canada, Ottawa, Canada
| | - Jasmine Rae Frost
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Vanessa Zubach
- Viral Exanthemata and STD section, National Microbiology Laboratory Branch, Public Health Agency of Canada, JC Wilt Infectious Diseases Research Centre, 745 Logan Avenue, Winnipeg R3E 3L5, Canada
| | - Meghan Laverty
- Viral Exanthemata and STD section, National Microbiology Laboratory Branch, Public Health Agency of Canada, JC Wilt Infectious Diseases Research Centre, 745 Logan Avenue, Winnipeg R3E 3L5, Canada
| | - Alberto Severini
- Viral Exanthemata and STD section, National Microbiology Laboratory Branch, Public Health Agency of Canada, JC Wilt Infectious Diseases Research Centre, 745 Logan Avenue, Winnipeg R3E 3L5, Canada; Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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Muñoz-Chimeno M, Rodriguez-Paredes V, García-Lugo MA, Avellon A. Hepatitis E genotype 3 genome: A comprehensive analysis of entropy, motif conservation, relevant mutations, and clade-associated polymorphisms. Front Microbiol 2022; 13:1011662. [PMID: 36274715 PMCID: PMC9582770 DOI: 10.3389/fmicb.2022.1011662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Hepatitis E virus genotype 3 (HEV-3) is an EU/EEA emergent zoonosis. HEV-3 clades/subtypes have been described. Its genome contains ORF1, which encodes nonstructural proteins for virus replication, ORF2, the capsid protein, and ORF3, a multifunctional protein involved in virion pathogenesis. The study aims with respect to HEV-3 are to: (1) calculate genome entropy (excluding hypervariable region); (2) analyze the described motifs/mutations; (3) characterize clade/subtype genome polymorphisms. Seven hundred and five sequences from the GenBank database were used. The highest entropies were identified in zoonotic genotypes (HEV-3 and HEV-4) with respect to HEV-1 in X domain, RdRp, ORF2, and ORF3. There were statistically significant differences in the entropy between proteins, protease and ORF3 being the most variable and Y domain being the most conserved. Methyltransferase and Y domain motifs were completely conserved. By contrast, essential protease H581 residue and catalytic dyad exhibited amino acid changes in 1.8% and 0.4% of sequences, respectively. Several X domain amino acids were associated with clades. We found sequences with mutations in all helicase motifs except number IV. Helicase mutations related to increased virulence and/or fulminant hepatitis were frequent, the 1,110 residue being a typical HEV-3e and HEV-3f-A2 polymorphism. RdRp motifs III, V, VII also had high mutation rates. Motif III included residues that are polymorphisms of HEV-3e (F1449) and HEV-3 m (D1451). RdRp ribavirin resistance mutations were frequent, mainly 1479I (67.4, 100% in HEV-3efglmk) and 1634R/K (10.0%, almost 100% in HEV-3e). With respect to ORF2, 19/27 neutralization epitopes had mutations. The S80 residue in ORF3 presented mutations in 3.5% of cases. Amino acids in the ORF3-PSAP motif had high substitution rates, being more frequent in the first PSAP (44.8%) than in the second (1.5%). This is the first comprehensive analysis of the HEV-3 genome, aimed at improving our knowledge of the genome, and establishing the basis for future genotype-to-phenotype analysis, given that viral features associated with severity have not been explored in depth. Our results demonstrate there are important genetic differences in the studied genomes that sometimes affect significant viral structures, and constitute clade/subtype polymorphisms that may affect the clinical course or treatment efficacy.
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Affiliation(s)
- Milagros Muñoz-Chimeno
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, Madrid, Spain
- Alcalá de Henares University, Madrid, Spain
| | | | | | - Ana Avellon
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, Madrid, Spain
- CIBERESP Epidemiology and Public Health, Madrid, Spain
- *Correspondence: Ana Avellon,
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