High Viral Diversity and Mixed Infections in Cerebral Spinal Fluid From Cases of Varicella Zoster Virus Encephalitis.

Abstract

Background: Varicella zoster virus (VZV) causes encephalitis both in association with chickenpox (varicella) and shingles (herpes zoster) and without rash. Here we investigate whether viruses recovered from cases of encephalitis differ genetically from those causing non-central nervous system disease. Methods: A highly sensitive enrichment-based sequencing methodology enabled the recovery and deep sequencing of 54 VZV genomes from Cerebral Spinal Fluid (CSF), plasma, bronchoalveolar lavage (BAL) and vesicle fluid collected from 34 patients with and without VZV encephalitis. Results: Viruses recovered from more than one site in the same patient were identical. There was no evidence for any viral single nucleotide polymorphisms (SNPs) associated with encephalitis. The low numbers of variant alleles and diversity of virus from vesicle fluid was in keeping with previous data suggesting individual vesicles arise from single VZV virions. By contrast plasma, BAL and CSF samples generally had higher variant numbers. Three samples with most genetic diversity had variant frequency patterns typical of mixed infections. In two of these, both CSF samples, infection with more than one clade had occurred, while the highly diverse plasma sample showed evidence both of mixed infection with viruses from the same clade and of substitutions mutations in genomic regions known to be mutagenic. Conclusions: Deep sequencing of CSF from twelve cases of encephalitis revealed mixed infections with VZV strains from different clades in two cases, with higher variant numbers than seen for vesicular fluid in nine of the remaining ten. We hypothesise that reactivation from multiple neurons may contribute to the pathogenesis of VZV encephalitis.