Evidence map›Paper›PMID 29898986›Full record

ArticlemSphere2018

Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture.

Alexander L Greninger, Pavitra Roychoudhury, Hong Xie, Amanda Casto, Anne Cent, Gregory Pepper, David M Koelle, Meei-Li Huang, Anna Wald, Christine Johnston and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in mSphere, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed
6.6field-weighted citation impact, top 3% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

37 citing papers in PubMed, 60 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 3 institutions in 1 country.

Alexander L GreningerDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA agrening@uw.edu.
Pavitra RoychoudhuryDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Hong XieDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Amanda CastoDepartment of Medicine, University of Washington, Seattle, Washington, USA.
Anne CentDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Gregory PepperDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
David M KoelleDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Meei-Li HuangDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Anna WaldDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Christine JohnstonFred Hutchinson Cancer Research Institute, Seattle, Washington, USA.
Keith R JeromeDepartment of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
University of Washington · USFred Hutch Cancer Center · USBenaroya Research Institute

Funding

VENEREAL DISEASET32AI007140 · NIAID · UNIVERSITY OF WASHINGTON · PI Julia Cook Dombrowski · 1985 to 2026
$19.4M
NIAID NIH HHS T32 AI007140
6 · The paper itself

Abstract

Herpes simplex viruses (HSVs) are difficult to sequence due to their large DNA genome, high GC content, and the presence of repeats. To date, most HSV genomes have been recovered from culture isolates, raising concern that these genomes may not accurately represent circulating clinical strains. We report the development and validation of a DNA oligonucleotide hybridization panel to recover nearly complete HSV genomes at abundances up to 50,000-fold lower than previously reported. Using copy number information on herpesvirus and host DNA background via quantitative PCR, we developed a protocol for pooling for cost-effective recovery of more than 50 HSV-1 or HSV-2 genomes per MiSeq run. We demonstrate the ability to recover >99% of the HSV genome at >100× coverage in 72 h at viral loads that allow whole-genome recovery from latently infected ganglia. We also report a new computational pipeline for rapid HSV genome assembly and annotation. Using the above tools and a series of 17 HSV-1-positive clinical swabs sent to our laboratory for viral isolation, we show limited evolution of HSV-1 during viral isolation in human fibroblast cells compared to the original clinical samples. Our data indicate that previous studies using low-passage-number clinical isolates of herpes simplex viruses are reflective of the viral sequences present in the lesion and thus can be used in phylogenetic analyses. We also detect superinfection within a single sample with unrelated HSV-1 strains recovered from separate oral lesions in an immunosuppressed patient during a 2.5-week period, illustrating the power of direct-from-specimen sequencing of HSV.

Indexed as

Genomic InstabilityVirus CultivationCells, CulturedEvolution, MolecularFibroblastsGenome, ViralHerpes SimplexHerpesvirus 1, HumanHumansNucleic Acid HybridizationWhole Genome Sequencingcapture sequencingculturedual-strain infectiongenomicsherpesvirusHSV-1HSV-2superinfection

Identifiers

PMID29898986
PMCPMC6001610
OpenAlexW2804481833

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.