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Transcriptomal analysis of varicella-zoster virus infection using long oligonucleotide-based microarrays

¹ Glasgow University Department of Neurology, Southern General Hospital, Institute of Neurological Sciences, Glasgow G51 4TF, UK
² Scottish Centre for Genomic Technology and Informatics, Medical School, University of Edinburgh, Edinburgh EH16 4SB, UK

Correspondence
Peter G. E. Kennedy
P.G.Kennedy{at}clinmed.gla.ac.uk

Varicella-zoster virus (VZV) is a human herpes virus that causes varicella as a primary infection and herpes zoster following reactivation of the virus from a latent state in trigeminal and spinal ganglia. In order to study the global pattern of VZV gene transcription, VZV microarrays using 75-base oligomers to 71 VZV open reading frames (ORFs) were designed and validated. The long-oligonucleotide approach maximizes the stringency of detection and polarity of gene expression. To optimize sensitivity, microarrays were hybridized to target RNA and the extent of hybridization measured using resonance light scattering. Microarray data were normalized to a subset of invariant ranked host-encoded positive-control genes and the data subjected to robust formal statistical analysis. The programme of viral gene expression was determined for VZV (Dumas strain)-infected MeWo cells and SVG cells (an immortalized human astrocyte cell line) 72 h post-infection. Marked quantitative and qualitative differences in the viral transcriptome were observed between the two different cell types using the Dumas laboratory-adapted strain. Oligonucleotide-based VZV arrays have considerable promise as a valuable tool in the analysis of viral gene transcription during both lytic and latent infections, and the observed heterogeneity in the global pattern of viral gene transcription may also have diagnostic potential.

A list of VZV PCR primers is shown in Supplementary Table S1, a summary of RT-PCR results in MeWo and SVG cells in Supplementary Table S2, in situ hybridization using DIG-labelled probes to VZV gene 63 in VZV-infected MeWo and SVG cells at 72 h post-infection in Supplementary Fig. S1, and gels of RT-PCR experiments for VZV genes 31 and 61 in Supplementary Figs S2 and S3, available as supplementary material in JGV Online.

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