Herpesvirus_whole_genome_sequencing
Very little is known about genome diversity of herpesviruses and there are currently very few genome sequences in Genbank. Whole genome sequencing of large DNA viruses is complicated by the difficulty in separating virus DNA from human DNA. In this project we will address this issue by using Agilent SureSelect technology and Illumina deep sequencing to sequence several members of the herpesvirus family, including Epstein Barr virus (EBV, HHV4), Kaposi’s sarcoma associated herpesvirus (KSHV, HHV8) and varicella zoster virus (VZV, HHV3). We have designed custom baits to the available reference sequences and will use these to pull out virus sequence from host DNA and then Illumina sequence the captured virus DNA. The short read data will be assembled into a genome consensus sequence for each virus and importantly, allow analysis of virus minority species, which may be important for pathogenesis.  We will use a range of samples including DNA from cell lines latently infected with either EBV or KSHV or both viruses. These data will enable an initial estimation of genome diversity and highlight differences at the genetic level between EBV and KSHV from different cell lines. Further studies will generate herpesvirus genome sequences from clinical samples, including varicella, Kaposi’s sarcoma and nasopharyngeal carcinoma to investigate virus genetic diversity and pathogenic determinants.  http://www.sanger.ac.uk/resources/downloads/viruses/herpesviridae-lymphocryptovirus  http://www.sanger.ac.uk/resources/downloads/viruses/herpesviridae-rhadinovirus  http://www.sanger.ac.uk/resources/downloads/viruses/herpesviridae-simplexvirus