title: Specific capture and whole-genome sequencing of viruses from clinical samples.
abstract: 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.
authors: Division of Infection and Immunity, University College London, London, United Kingdom. d.depledge@ucl.ac.uk
authors: Daniel P
authors: DP
authors: Depledge
authors: Anne L
authors: AL
authors: Palser
authors: Simon J
authors: SJ
authors: Watson
authors: Imogen Yi-Chun
authors: IY
authors: Lai
authors: Eleanor R
authors: ER
authors: Gray
authors: Paul
authors: P
authors: Grant
authors: Ravinder K
authors: RK
authors: Kanda
authors: Emily
authors: E
authors: Leproust
authors: Paul
authors: P
authors: Kellam
authors: Judith
authors: J
authors: Breuer
mesh_terms: D045744:Cell Line, Tumor; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics*; D006564:Herpesviridae / Q000145:classification / Q000235:genetics*; D006566:Herpesviridae Infections / Q000097:blood / Q000134:cerebrospinal fluid / Q000821:virology; D014645:Herpesvirus 3, Human / Q000235:genetics; D004854:Herpesvirus 4, Human / Q000235:genetics; D019288:Herpesvirus 8, Human / Q000235:genetics; D006801:Humans; D009154:Mutation; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D012463:Saliva / Q000821:virology; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D004279:DNA, Viral