Specific capture and whole-genome sequencing of viruses from clinical samples

PLoS One. 2011;6(11):e27805. doi: 10.1371/journal.pone.0027805. Epub 2011 Nov 18.


Whole genome sequencing of viruses directly from clinical samples is integral for understanding the genetics of host-virus interactions. Here, we report the use of sample sparing target enrichment (by hybridisation) for viral nucleic acid separation and deep-sequencing of herpesvirus genomes directly from a range of clinical samples including saliva, blood, virus vesicles, cerebrospinal fluid, and tumour cell lines. We demonstrate the effectiveness of the method by deep-sequencing 13 highly cell-associated human herpesvirus genomes and generating full length genome alignments at high read depth. Moreover, we show the specificity of the method enables the study of viral population structures and their diversity within a range of clinical samples types.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • DNA, Viral / chemistry
  • DNA, Viral / genetics*
  • Genome, Viral / genetics*
  • Herpesviridae / classification
  • Herpesviridae / genetics*
  • Herpesviridae Infections / blood
  • Herpesviridae Infections / cerebrospinal fluid
  • Herpesviridae Infections / virology
  • Herpesvirus 3, Human / genetics
  • Herpesvirus 4, Human / genetics
  • Herpesvirus 8, Human / genetics
  • Humans
  • Mutation
  • Polymerase Chain Reaction
  • Reproducibility of Results
  • Saliva / virology
  • Sequence Analysis, DNA / methods*
  • Species Specificity


  • DNA, Viral