PMC

Coverage plots of JC virus genome in brain samples from 5 PML patients. The figure shows the number of times each nucleotide of the JC virus genome was read during the sequencing process (coverage). By using ViroFind we achieved high coverage of the JC virus genome, which is required for the reliable identification of all JC virus variants.

The arrows indicate that more than one syndrome may coexist. PML = progressive multifocal leukoencephalopathy; JCVE = JC Virus Encephalopathy; JCVM = JC Virus Meningitis; JCV GCN = JC Virus Granule Cell Neuronopathy; GCL = Granule Cell Layer; PCL = Purkinje Cell Layer; ML = Molecular layer; WM = white matter; = JC virion

The figure illustrates the genetic divergence between the JC virus sequences found in each PML brain and MAD-1 (red bar), the JC virus prototype sequence associated with PML. Each chord corresponds to a single nucleotide polymorphism. The presence of multiple JCV variants within each PML brain accounts for a remarkable degree of genetic variation and suggests that the genetic complexity of JC virus in the brain compartment has previously been underestimated.

Urine metabolomes of JC virus in A: all samples and B: LUTS samples only. Volcano plots show 3079 and 2658 total m/z features, respectively; enlarged dots indicate significantly modulated features (Student’s t-test p-value < 0.05 and fold-change ≥ 50%); red indicates increase with JC virus, green indicates decrease with JC virus. C: Venn diagram of significantly modulated features shows the urine metabolome of JC virus in LUTS patients is larger and represents more roles, including neurologic, fungal, oxidative stress, and innate immune system (filtered by known compounds with known roles).