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HSV-1 Strain H129

Identifiers: SRA: SRP002156
Princeton University: HSV1 Strain H129
Study Type: 
Whole Genome Sequencing
Submission: SRA010966 on 2010-02-06 13:09:00
Abstract: Herpes simplex virus 1 (HSV-1) is a well-adapted human pathogen that can invade the peripheral nervous system and persist there as a lifelong latent infection. Despite their ubiquity, only one natural isolate of HSV-1 (strain 17) has been sequenced. Using Illumina high-throughput sequencing of viral DNA, we obtained the genome sequence of both a laboratory strain (F) and a low-passage clinical isolate (H129). These data demonstrate the extent of inter-strain variation across the entire genome of HSV-1 in both coding and non-coding regions. We find many amino acid differences distributed across the proteome of the new strain F sequence and the previously known strain 17, demonstrating the spectrum of variability among wild-type HSV-1 proteins. The clinical isolate, strain H129, displays a unique anterograde spread phenotype for which the causal mutations were completely unknown. We define the sequence differences in H129 and propose a number of potentially causal genes, including the neurovirulence protein ICP34.5 (RL1). Further studies will be required to demonstrate which change(s) are sufficient to recapitulate the spread defect of strain H129. Unexpectedly, these data also revealed a frameshift mutation in the UL13 kinase in our strain F isolate, demonstrating how deep genome sequencing can reveal the full complement of background mutations in any given strain, particularly those passaged or plaque-purified in a laboratory setting. These data increase our knowledge of sequence variation in large DNA viruses and demonstrate the potential of deep sequencing to yield insight into DNA genome evolution and the variation among different pathogen isolates. (From JVI 2010 paper by Szpara, Parsons, & Enquist)
Description: Illumina data for Strain H129, one run of 36 bp, and one run of 75 bp. Same preparation of viral nucleocapsid DNA, then used to generate two separate libraries for sequencing. Libraries were run ~2 months apart, with different sequence-read lengths (36 bp & 75 bp).
Center Project: HSV1 Strain H129 genome sequencing and assembly

Related SRA data

2 (948.8 Mbp; 675.9 Mb)