Characterisation of single nucleotide polymorphisms in the genome of JC polyomavirus using MALDI TOF mass spectrometry

JC polyomavirus (JCV) infects 80% of the population. In immunosuppressed patients viral replication may be enhanced, resulting in progressive multifocal leukoencephalopathy. There are at least eight distinct strains of JCV of which distribution varies between ethnic groups however there remain issues with identifying viral strains due to the insufficient yield and sensitivity of Sanger sequencing (SS) protocols. In this study matrix assisted laser desorption/ionisation time of flight mass spectrometry (MALDI TOF MS) is presented as an alternative to SS. DNA from 19 urine samples was assessed. Successful amplification and strain identification was possible in all samples with >10 copies of starting material indicating a high sensitivity assay, in contrast to SS (>20 copies). The genotypes defined for each sample via MALDI TOF MS were identical where SS resulted in a readable trace. MALDI TOF MS identified eight novel SNPs in the VP1 gene. This study represents the first application of MALDI TOF MS to viral comparative sequence analysis.