Evidence map›Paper›PMID 29322922›Full record

ArticleBMC medical genomics2017

Analysis of viral diversity for vaccine target discovery.

Asif M Khan, Yongli Hu, Olivo Miotto, Natascha M Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J Thomas August

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC medical genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Article
  9. Review
  10. Article
  11. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018
    Review
  12. A bioinformatics potpourri.BMC genomics · 2018
    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

9 authors.

Asif M KhanCentre for Bioinformatics, School of Data Sciences, Perdana University, Jalan MAEPS Perdana, Serdang, Selangor Darul Ehsan, 43400, Malaysia. asif@perdanauniversity.edu.my.
Yongli HuDepartment of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
Olivo MiottoCentre for Genomics and Global Health, University of Oxford, Oxford, UK.
Natascha M ThevasagayamDepartment of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
Rashmi SukumaranDepartment of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
Hadia Syahirah Abd RamanCentre for Bioinformatics, School of Data Sciences, Perdana University, Jalan MAEPS Perdana, Serdang, Selangor Darul Ehsan, 43400, Malaysia.
Vladimir BrusicMenzies Health Institute Queensland, Griffith University, Parklands Dr, Southport, 4215, QLD, Australia.
Tin Wee TanDepartment of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
J Thomas AugustDepartment of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA.

Funding

Dengue Epitope Vaccine,Tetravalent &MHCII-TargetedU19AI056541 · NIAID · JOHNS HOPKINS UNIVERSITY · PI AUGUST, J. THOMAS · 2003 to 2007
$6.8M
HIV-1 Gene Products/Targeted/MHC II Antigen PresentationR37AI041908 · NIAID · JOHNS HOPKINS UNIVERSITY · PI AUGUST, J. THOMAS · 2002 to 2011
$4.1M
NIAID NIH HHS R37 AI041908NIAID NIH HHS U19 AI056541
6 · The paper itself

Abstract

backgroundViral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets.

resultsThis work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Our methodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis.

conclusionThese steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation.

Indexed as

Amino Acid SequenceComputational BiologyConserved SequenceGenetic VariationSpecies SpecificityVaccinologyViral ProteinsViral VaccinesViral ProteinsViral VaccinesBioinformaticsDatabaseReverse vaccinologyTarget discoveryToolsVaccine designViral diversity

Identifiers

PMID29322922
PMCPMC5763473

What OpenQuestion holds

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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.