Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada

Abstract

In 2017 Ontario experienced the largest mumps outbreak in the province in 8 years, at a time when multiple outbreaks were occurring across North America. Of 259 reported cases, 143 occurred in Toronto, primarily among young adults. Routine genotyping of the small hydrophobic gene indicated that the outbreak was due to mumps virus genotype G. We performed a retrospective study of whole genome sequencing of 26 mumps virus isolates from early in the outbreak, using a tiling amplicon method. Results indicated that two of the cases were genetically divergent, with the remaining 24 cases belonging to two major clades and one minor clade. Phylogeographic analysis confirmed circulation of virus from each clade between Toronto and other regions in Ontario. Comparison with other genotype G strains from North America suggested that the presence of co-circulating major clades may have been due to separate importation events from outbreaks in the United States. A transmission network analysis performed with the software program TransPhylo was compared with previously collected epidemiological data. The transmission tree correlated with known epidemiological links between nine patients and identified new potential clusters with no known epidemiological links.

Molecular epidemiology of mumps viruses detected in the Netherlands, 2017-2019

“…The presence of two lineages with multiple closely related mumps viruses in recent years, suggests that there was endemic transmission of mumps in the Netherlands and surrounding countries. This is supported by the fact that complete genomes of both lineages are distinct from mumps viruses detected recently in mainly the United States of America and Canada [10, 18]. Of interest, viruses of the first lineage were not detected before the second part of 2018, suggesting that this lineage emerged recently in the Netherlands.…”

“…Main mumps clusters in recent years in the Netherlands could be identified by analysis of SH+NCRs data. However, NCR+SH sequence data cannot be used to study exact transmission trees, which is possible for mumps virus if complete genomes are analyzed [10, 18].…”

“…In this context, sequencing of the hemagglutinin-neuraminidase protein gene (HN) and fusion protein gene (F) provides similar sequence resolution compared to sequencing of the sum of three the non-coding regions (NCRs), present between the nucleocapsid protein and phosphoprotein (N-P), between phosphoprotein and matrix protein (P-M) and between matrix protein gene and F gene (M-F). While both contributes to the molecular resolution, sequencing of the complete genome might provide the more complete resolution that is necessary to compare mumps viruses on a larger geographic scale and identify exact transmission chains [10-14].…”

Parotiditis: Una enfermedad inmunoprevenible que requiere atención

“…En la región de las Américas se ha descrito la circulación del genotipo G, en E.U.A. y Canadá 5 . En Chile, Le Corre N y cols.…”

Molecular epidemiology of mumps viruses in the Netherlands, 2017-2019

“…In this context, sequencing of the hemagglutinin-neuraminidase protein gene (HN) and fusion protein gene (F) provides similar sequence resolution compared to sequencing of the sum of three non-coding regions (NCRs), present between the nucleocapsid protein and phosphoprotein (N-P), between phosphoprotein and matrix protein (P-M) and between matrix protein gene and F gene (M-F). However, sequencing of the complete genome might provide the more complete resolution that is necessary to identify exact transmission chains and it has the advantage of easy comparison with other mumps viruses on a global scale [ 11 – 15 ].…”