Rapid, Highly Sensitive Mumps Genotyping with NGS

Despite widespread vaccination, the mumps virus is making a comeback—and that’s only half the problem. The mumps genome has continued to evolve, acquiring new mutations that make it harder to detect and virtually impossible to trace with conventional genotyping tools. Recognizing the limits of these methods, researchers have now turned to NGS for rapid, highly sensitive sequencing of the entire mumps genome.

How has the mumps genome evolved?

In 2006, there was a large mumps outbreak among midwestern college students, totaling 6500 cases, and caseloads have only increased since then. What is striking about these events is that they are concentrated among the more than 90% of young adults who received the measles-mumps-rubella (MMR) combined vaccine as children, which has historically prevented mumps infection and transmission. One factor that may be contributing to these breakthrough cases is a mismatch between the target strain of the vaccine, termed genotype A, and the new circulating strain, genotype G. According to Bryant et al¹ from the Laboratory of Viral Diseases at the New York State Department of Health, 98% of mumps samples collected in New York state between 2013 and 2019 were mumps genotype G (743 of 758 samples), indicating a sea change in viral genotype composition in recent years that may portend future outbreaks.

What are the limits of conventional genotyping methods?

Conventional genotyping analysis for mumps relies on sequencing three specific genes: F, SH, and HN. This approach is laborious, time-consuming, and not sensitive enough to properly track transmission. The SH gene in particular is nearly identical across genotype G, making contact tracing more difficult. Genomic sequencing with would greatly increase the information used to track and study the mumps virus population, making it ideal for ongoing epidemiological surveillance.

What are the advantages of NGS for mumps genotyping?

Bryant et al. describe a new rapid, highly sensitive NGS assay for mumps genotype G based on a custom Ion AmpliSeq panel, which uses the whole mumps genome to comprehensively study each sample. The AmpliSeq genotype G assay can make direct use of samples rather than requiring a preliminary isolation or amplification step to increase RNA yield. It achieves 99% coverage, a minimum depth of 20X, a maximum depth of 10,000X, an average of 1,014X, and a Ct detection limit of 34, vastly exceeding the performance of conventional three-gene mumps genotyping assays. Integrated with the Ion Torrent platform, including the Ion Chef System and Ion GeneStudio S5 System, AmpliSeq panels provide an easy, highly automated platform for genomic sequencing, minimizing hands-on time and freeing key laboratory personnel for other tasks. AmpliSeq and Ion Torrent have already proven their worth for SARS-CoV-2 genomic surveillance, and other viruses like mumps involve similar workflows.

With genomic sequencing using AmpliSeq and Ion Torrent, mutations can be identified across the entire mumps genome instead of specifically the F, SH, and HN genes, making it possible to understand transmission patterns and distinguish between samples with closely related mutations. This enhanced sequence resolution is likely critical for tracing in mumps genotype G cases. For example, Bryan et al. found that genomic sequencing was the only method capable of accurately tracing all genotype G samples that were collected in New York state from 2016-2019.

Conclusion

Genomic surveillance is a powerful tool for epidemiological research. By identifying genetic mutations across the whole genome, instead of only a subset of genes, we can better understand how viruses like mumps evolve and spread and inform potential interventions to limit future outbreaks. Ion Torrent provides a fast, easy, and highly sensitive approach for genomic sequencing of viruses like mumps, SARS-CoV-2, Ebola, and more and can be directly applied to individual samples for epidemiological research. In turn, AmpliSeq technology gives you the flexibility to design custom NGS panels for infectious pathogens and can be tailored to specific genotypes of interest, which is vital for rapidly evolving pathogens that are evading the protection provided by vaccines.

For Research Use Only. Not for use in diagnostic procedures

1. Bryant P, H Caldwell, DM Lamson, et al. (2021) Streamlined Whole-Genome Sequencing of Mumps Virus for High-Resolution Outbreak Analysis. J. Clin. Microbiol.