Details:

Alternative Title:
J Clin Microbiol
Publisher's site:
http://dx.doi.org/10.1128/JCM.02132-16
Personal Author:
Li, Tengguo ; Unger, Elizabeth R. ; Batra, Dhwani ; Sheth, Mili ; Steinau, Martin ; ... More +
Li, Tengguo ; Unger, Elizabeth R. ; Batra, Dhwani ; Sheth, Mili ; Steinau, Martin ; Jasinski, Jean ; Jones, Jennifer ; Rajeevan, Mangalathu S. Less -
Description:
We designed a universal human papillomavirus (HPV) typing assay based on target enrichment and whole-genome sequencing (eWGS). The RNA bait included 23,941 probes targeting 191 HPV types and 12 probes targeting beta-globin as a control. We used the Agilent SureSelect XT2 protocol for library preparation, Illumina HiSeq 2500 for sequencing, and CLC Genomics Workbench for sequence analysis. Mapping stringency for type assignment was determined based on 8 (6 HPV-positive and 2 HPV-negative) control samples. Using the optimal mapping conditions, types were assigned to 24 blinded samples. eWGS results were 100% concordant with Linear Array (LA) genotyping results for 9 plasmid samples and fully or partially concordant for 9 of the 15 cervical-vaginal samples, with 95.83% overall type-specific concordance for LA genotyping. eWGS identified 7 HPV types not included in the LA genotyping. Since this method does not involve degenerate primers targeting HPV genomic regions, PCR bias in genotype detection is minimized. With further refinements aimed at reducing cost and increasing throughput, this first application of eWGS for universal HPV typing could be a useful method to elucidate HPV epidemiology.
Subject:
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Genome, Viral
Genomics
Genotype
Genotyping Techniques
Humans
Papillomaviridae
Papillomavirus Infections
Sequence Analysis, DNA

Source:
J Clin Microbiol. 2017; 55(3):811-823.
Pubmed ID:
27974548
Pubmed Central ID:
PMC5328449
Document Type:
Journal Article
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:567978a63fba06aa1d672505fe17104f6d1578c91d3409a22352d24532b06f78
File Type:

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