Evidence map›Paper›PMID 34570820›Full record

ArticlePLoS pathogens2021

Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome.

Yuta Shirogane, Elsa Rousseau, Jakub Voznica, Yinghong Xiao, Weiheng Su, Adam Catching, Zachary J Whitfield, Igor M Rouzine, Simone Bianco, Raul Andino

Abstract read
In one paragraph

Article in PLoS pathogens, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing 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

18 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Review
  6. Open questions in the social lives of viruses.Journal of evolutionary biology · 2023
    Review
  7. Article
  8. Article
  9. High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  10. Review
  11. Article
  12. Article
  13. Article
  14. Article
  15. The evolution of cheating in viruses.Nature communications · 2021
    Review
  16. Article
  17. Article
  18. 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

10 authors.

Yuta ShiroganeDepartment of Microbiology and Immunology, University of California, San Francisco, California, United States of America.ORCID 0000-0002-4284-0310
Elsa RousseauDepartment of Industrial and Applied Genomics, AI and Cognitive Software Division, IBM Almaden Research Center, San Jose, California, United States of America.ORCID 0000-0001-7013-6024
Jakub VoznicaDepartment of Microbiology and Immunology, University of California, San Francisco, California, United States of America.ORCID 0000-0002-0530-5837
Yinghong XiaoDepartment of Microbiology and Immunology, University of California, San Francisco, California, United States of America.
Weiheng SuDepartment of Microbiology and Immunology, University of California, San Francisco, California, United States of America.
Adam CatchingDepartment of Microbiology and Immunology, University of California, San Francisco, California, United States of America.ORCID 0000-0002-9797-7701
Zachary J WhitfieldDepartment of Microbiology and Immunology, University of California, San Francisco, California, United States of America.
Igor M RouzineDepartment of Microbiology and Immunology, University of California, San Francisco, California, United States of America.
Simone BiancoDepartment of Industrial and Applied Genomics, AI and Cognitive Software Division, IBM Almaden Research Center, San Jose, California, United States of America.
Raul AndinoDepartment of Microbiology and Immunology, University of California, San Francisco, California, United States of America.ORCID 0000-0001-5503-9349

Funding

STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
RNA PROTEIN INTERACTIONS IN POLIOVIRUS REPLICATIONR01AI040085 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANDINO, RAUL · 1998 to 2019
$5.8M
Targeting Covid-19 with a Therapeutic Interfering ParticleR41AI157129 · NIAID · ALEPH THERAPEUTICS, INC. · PI ANDINO, RAUL · 2021 to 2022
$596k
Genetic Diversity as a determinant of viral adaptation and pathogenesisR56AI036178 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANDINO, RAUL · 2014 to 2014
$531k
EV71 intra-host evolution, attenuation and vaccine developmentR21AI144144 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANDINO, RAUL · 2019 to 2020
$442k
A Vaccine for Acute Flaccid MyelitisR41AI155100 · NIAID · ALEPH THERAPEUTICS, INC. · PI ANDINO, RAUL · 2020 to 2020
$250k
NIAID NIH HHS R01 AI040085NIAID NIH HHS R21 AI144144NIAID NIH HHS R41 AI155100NIAID NIH HHS R41 AI157129NIAID NIH HHS R56 AI036178NIAID NIH HHS T32 AI060537NIGMS NIH HHS T32 GM008284
6 · The paper itself

Abstract

During replication, RNA viruses accumulate genome alterations, such as mutations and deletions. The interactions between individual variants can determine the fitness of the virus population and, thus, the outcome of infection. To investigate the effects of defective interfering genomes (DI) on wild-type (WT) poliovirus replication, we developed an ordinary differential equation model, which enables exploring the parameter space of the WT and DI competition. We also experimentally examined virus and DI replication kinetics during co-infection, and used these data to infer model parameters. Our model identifies, and our experimental measurements confirm, that the efficiencies of DI genome replication and encapsidation are two most critical parameters determining the outcome of WT replication. However, an equilibrium can be established which enables WT to replicate, albeit to reduced levels.

Indexed as

Defective VirusesModels, TheoreticalPoliovirusCoinfectionHumansVirus Replication

Identifiers

PMID34570820
PMCPMC8496841

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.