The WHO recently proposed an updated nomenclature for mumps virus (MuV). WHO currently recognizes 12 genotypes of MuV, assigned letters from A to N (excluding E and M), which are based on the nucleotide sequences of small hydrophobic (SH) and haemagglutinin-neuraminidase (HN) genes. A total of 66 MuV genomes are available in GenBank, representing eight of the 12 genotypes. To complete this dataset, whole genomes of seven isolates representing six genotypes (D, H, I, J, K and L) and one unclassified strain were sequenced. SH and HN genes of other representative strains were also sequenced. The degree of genetic divergence, predicted amino acid substitutions in the HN and fusion (F) proteins and geographic distributions of MuV strains were analysed based on the updated dataset. Nucleotide heterogeneity between genotypes reached 20% within the SH gene, with a maximum of 9% within the HN gene. The geographic and chronologic distributions of the 12 genotypes were summarised. This review contributes to our understanding of strain diversity for wild type MuV, and the results support the current WHO nomenclature.

Because of the global spread of Zika virus, accurate and high-throughput diagnostic immunoassays are needed. We compared the sensitivity and specificity of 5 commercially available Zika virus serologic assays to the recommended protocol of Zika virus IgM-capture ELISA and plaque-reduction neutralization tests. Most commercial immunoassays showed low sensitivity, which can be increased.

Varicella-zoster virus (VZV) is considered to be one of the most genetically stable of all the herpesviruses.Yet two VZV strains with a D150N missense mutation within the gE glycoprotein were isolated in North America in 1998 and 2002. The mutant strains have an accelerated cell spread phenotype, which distinguishes them from all wild-type and laboratory viruses. Since the VZV genome contains 70 additional open reading frames (ORFs), the possibility existed that the phenotypic change was actually due to an as-yet-undiscovered mutation or deletion elsewhere in the genome. To exclude this hypothesis, the entire genomes of the two mutant viruses were sequenced and found to contain 124,883 (VZV-MSP) and 125,459 (VZV-BC) nucleotides. Coding single-nucleotide polymorphisms (SNPs) were identified in 14 ORFs. One missense mutation was discovered in gH, but none was found in gB, gI, gL, or gK. There were no coding SNPs in the major regulatory protein ORF 62. One polymorphism was discovered which could never have been anticipated based on current knowledge of herpesvirus genomics, namely, the origins of replication differed from those in the prototype strain but not in a manner expected to affect cell spread. When the two complete mutant VZV sequences were surveyed in their entirety, the most reasonable conclusion was that the increased cell spread phenotype was dependent substantially or solely on the single D150N polymorphism in glycoprotein gE. The genomic results also expanded the evolutionary database by identifying which VZV ORFs were more likely to mutate over time.

During measles outbreaks, it is important to be able to rapidly distinguish between measles cases and vaccine reactions to avoid unnecessary outbreak response measures such as case isolation and contact investigations. We have developed a real-time reverse transcription-PCR (RT-PCR) method specific for genotype A measles virus (MeV) (MeVA RT-quantitative PCR [RT-qPCR]) that can identify measles vaccine strains rapidly, with high throughput, and without the need for sequencing to determine the genotype. We have evaluated the method independently in three measles reference laboratories using two platforms, the Roche LightCycler 480 system and the Applied Biosystems (ABI) 7500 real-time PCR system. In comparison to the standard real-time RT-PCR method, the MeVA RT-qPCR showed 99.5% specificity for genotype A and 94% sensitivity for both platforms. The new assay was able to detect RNA from five currently used vaccine strains, AIK-C, CAM-70, EdmonstonZagreb, Moraten, and Shanghai-191. The MeVA RT-qPCR assay has been used successfully for measles surveillance in reference laboratories, and it could be readily deployed to national and subnational laboratories on a wide scale.

Background: Measles molecular epidemiology was a key component of the verification of elimination of indigenous measles in Canada and is an invaluable tool during public health investigations, both to establish whether connections exist between concurrent measles cases and to indicate possible sources of importations. There are 24 distinct genotypes however the genotype is usually not sufficient to describe the complex molecular epidemiology of measles cases. The exact genetic sequence of the last 450 nucleotides of the nucleoprotein (N) gene (N-450) is used. The measles genome mutates very slowly and so cases within the same chain of transmission usually have identical N-450 sequences. In Canada, the National Microbiology Laboratory (NML) sequences the N-450 and deposits it into the WHO measles sequence database, MeaNS. This database can be used to identify other geographic regions where the measles sequence was detected, supporting or excluding connections. For commonly detected N-450 sequences, MeaNS designates a "sequence variant." Sequence variants are used as the defining characteristic of measles cases with identical sequences and this designation is fundamental to the description of measles molecular epidemiology both locally and globally. As progress is made towards global measles eradication, its genetic diversity decreases and distinct importations of measles from a single reservoir can be difficult to distinguish using current methods. Extending sequencing methods beyond the N-450 is required. While sequencing the entire hemagglutinin (H) gene, which is currently done routinely at the NML, can be helpful, whole genome sequencing will be required for effective molecular surveillance to monitor the sustained elimination of measles in Canada.insert text here.

The province of Ontario continues to experience measles virus transmissions despite the elimination of measles in Canada. We describe an unusual outbreak of measles in Ontario, Canada, in early 2015 that involved cases with a unique strain of virus and no known association among primary case-patients. A total of 18 cases of measles were reported from 4 public health units during the outbreak period (January 25–March 23, 2015); none of these cases occurred in persons who had recently traveled. Despite enhancements to case-patient interview methods and epidemiologic analyses, a source patient was not identified. However, the molecular epidemiologic analysis, which included extended sequencing, strongly suggested that all cases derived from a single importation of measles virus genotype D4. The use of timely genotype sequencing, rigorous epidemiologic investigation, and a better understanding of the gaps in surveillance are needed to maintain Ontario’s measles elimination status.

We describe a case of vaccine-associated measles in a two-year-old patient from British Columbia, Canada, in October 2013, who received her first dose of measles-containing vaccine 37 days prior to onset of prodromal symptoms. Identification of this delayed vaccine-associated case occurred in the context of an outbreak investigation of a measles cluster.

Background. In 1994, Canada committed to eliminate measles by the year 2000. This report presents the epidemiology of measles in Canada between 2002 and 2013 and its implications in sustaining measles elimination.Methods. Cases included individuals reported to the Canadian Measles and Rubella Surveillance System with confirmed measles.Results. In Canada, 1171 cases of measles were reported between 2002 and 2013 (incidence 0.29 cases per 100 000 population). The annual number of cases ranged from 6 to 752. The majority of cases were unvaccinated (63%) or had an unknown vaccination status (19%). The median age of cases was 14.4 years (range, <1 to 63 years) globally and 14 years when excluding the 2011 outbreak in Quebec where 68% of the 678 cases were 10 to 19 years old. With the exclusion of this outbreak, the incidence was highest in infants (1.0 per 100 000), lower but fairly similar between 1 and 19 years of age (0.2 to 0.4 per 100 000), and there was a substantial decline between 20 and 39 years of age (0.1 per 100 000). There was a significant trend towards a greater annual number of importations over the period. Although importations resulted in no transmission sustained for ≥12 months, 5 chains of transmission had >30 cases. The effective reproductive number between 2002 and 2013 was estimated at 0.86 (95% confidence interval, .81–.92).Conclusions. Canada has maintained elimination between 2002 and 2013, but additional efforts are needed to reduce the proportion of unimmunized individuals and respond to importation events.