An enrichment method for capturing mumps virus whole genome sequences directly from clinical specimens

Recently there has been a significant increase in the number of mumps outbreaks occurring in highly vaccinated populations. These outbreaks are often due to a mumps genotype G virus, where sequencing of the SH gene does not reveal enough genetic diversity to sufficient to resolve outbreaks. This has elevated the need to be able to sequence complete mumps viruses from clinical samples without laborious methods. Here we describe a probe enrichment method that allows for whole genome sequencing of the mumps virus directly from clinical specimens. Using 136 clinical samples, we show this method allows for a significant increase in the percentage of viral sequencing reads, resulting in the capture of mumps genomes. This method will be an asset in investigating future mumps outbreaks.