De novo assembly of human herpes virus type 1 HHV-1 genome, mining of non-canonical structures and detection of novel drug-resistance mutations using short- and long-read next generation sequencing technologies.Report as inadecuate




De novo assembly of human herpes virus type 1 HHV-1 genome, mining of non-canonical structures and detection of novel drug-resistance mutations using short- and long-read next generation sequencing technologies. - Download this document for free, or read online. Document in PDF available to download.

Reference: Karamitros, T, Harrison, I, Piorkowska, R et al., Antoniewski, C ed., (2016). De novo assembly of human herpes virus type 1 (HHV-1) genome, mining of non-canonical structures and detection of novel drug-resistance mutations using short- and long-read next generation sequencing technologies. PloS one, 11 (6), e0157600.Citable link to this page:

 

De novo assembly of human herpes virus type 1 (HHV-1) genome, mining of non-canonical structures and detection of novel drug-resistance mutations using short- and long-read next generation sequencing technologies.

Abstract: Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from



Author: Karamitros, T - Oxford, MPLS, Zoology - - - Harrison, I - - - Piorkowska, R - - - Katzourakis, A - Oxford, MPLS, Zoology - - - Ma

Source: https://ora.ox.ac.uk/objects/uuid:20a88f5e-d96c-49e8-b056-5fc049fc1287



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