Investigating Local Patterns of Mumps Virus Circulation, Using a Combination of Molecular Tools

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.

Keywords: MF-NCR sequence; SH sequence; genotyping; laboratory surveillance; molecular epidemiology; mumps; mumps virus.

Figure 1

Temporal distribution of mumps virus SH variants and haplotypes in the Community of Madrid from 2015 to 2020. The Y-axis shows the number of confirmed cases (PCR-positive) and the annual incidence rate of mumps per 100.000 inhabitants in the CM. The X-axis represents the epidemiological weeks, grouped into years. The percentages represent positive cases detected in the CNM-ISCIII out of the total number of cases reported in the same year. Cases belong to the variants and haplotypes are coloured according to the legend assignation.

Figure 2

Geographical distribution of mumps virus SH variants and haplotypes from 2015 to 2020 in the Community of Madrid. Each case is represented by a coloured spot, according to the associated SH variant, as indicated in the legend. Derived haplotypes of SH variants are represented by triangles following the same coloured code. Other haplotypes are represented by a yellow spot. Clusters are marked with a black circle.

Figure 3

Phylogenetic analysis of the sequences obtained from cases geographically clustered. (A) Phylogenetic tree of MF-NCR sequences (452 nt). (B) Phylogenetic tree of SH sequences (316 nt). (C) Phylogenetic tree of MF-NCR-SH concatenated sequences (768 nt). Phylogenetic trees were made using the maximum likelihood method in W-IQ-TREE, using GTR + I, TN93 and GTR as substitution models, respectively. MuVi/Sheffield.GBR/1.05/ (ON148331) and MuVi/Gloucester/32.96/[G] (AF280799) were used as outgroup. Each name sequence is coloured according to the SH variant assignation.