Evidence map›Paper›PMID 28711653›Full record

ArticleVirology2017

Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U

Christine Johnston, Amalia Magaret, Pavitra Roychoudhury, Alexander L Greninger, Anqi Cheng, Kurt Diem, Matthew P Fitzgibbon, Meei-Li Huang, Stacy Selke, Jairam R Lingappa and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Virology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
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

14 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Alphaherpesvirus Genomics: Past, Present and Future.Current issues in molecular biology · 2021
    Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Article
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

14 authors.

Christine JohnstonDepartment of Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA. Electronic address: cjohnsto@uw.edu.
Amalia MagaretDepartment of Laboratory Medicine, University of Washington, USA; Department of Biostatistics, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
Pavitra RoychoudhuryDepartment of Laboratory Medicine, University of Washington, USA.
Alexander L GreningerDepartment of Laboratory Medicine, University of Washington, USA.
Anqi ChengDepartment of Biostatistics, University of Washington, USA.
Kurt DiemDepartment of Laboratory Medicine, University of Washington, USA.
Matthew P FitzgibbonGenomics and Bioinformatics Resource, Fred Hutchinson Cancer Research Center, USA.
Meei-Li HuangDepartment of Laboratory Medicine, University of Washington, USA.
Stacy SelkeDepartment of Laboratory Medicine, University of Washington, USA.
Jairam R LingappaDepartment of Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Department of Pediatrics, University of Washington, USA.
Connie CelumDepartment of Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Department of Global Health, University of Washington, USA.
Keith R JeromeDepartment of Laboratory Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
Anna WaldDepartment of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
David M KoelleDepartment of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA; Benaroya Research Institute, Seattle, WA, USA.

Funding

THE PERINATAL COMPLICATIONS OF ASYMPTOMATIC GENITAL HERPES SIMPLEX VIRUSP01AI030731 · NIAID · UNIVERSITY OF WASHINGTON · PI ZHU, JIA · 1991 to 2017
$34.3M
Genomic systems approach to measure HSV-1-specific T-cell dominance in humansR01AI094019 · NIAID · UNIVERSITY OF WASHINGTON · PI KOELLE, DAVID M · 2012 to 2016
$1.9M
The gender specific prevalence of multiple strain genital HSV-2 infectionR21AI096058 · NIAID · UNIVERSITY OF WASHINGTON · PI WALD, ANNA · 2012 to 2013
$413k
NIAID NIH HHS P01 AI030731NIAID NIH HHS R01 AI094019NIAID NIH HHS R21 AI096058
6 · The paper itself

Abstract

introductionUnderstanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines.

methodsGenital lesion swabs containing ≥ 10

resultsAmong 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated U

conclusionsUnenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens.

Indexed as

Conserved SequenceGenes, ViralGenetic VariationAfricaCluster AnalysisGenitaliaHerpes GenitalisHerpesvirus 2, HumanHigh-Throughput Nucleotide SequencingPhylogenySequence HomologySouth AmericaUnited StatesGenital herpesGenomicsHerpes simplex virus type 2Sequencing

Identifiers

PMID28711653
PMCPMC5565707

What OpenQuestion holds

Textmetadata
LicenceTDM
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.