Evidence map›Paper›PMID 30578702›Full record

ArticleJournal of viral hepatitis2019

Genomic variability of within-host hepatitis C variants in acute infection.

Chaturaka Rodrigo, Preston Leung, Andrew R Lloyd, Rowena A Bull, Fabio Luciani, Jason Grebely, Gregory J Dore, Tanya Applegate, Kimberly Page, Julie Bruneau and 11 more

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

Article in Journal of viral hepatitis, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
0.9field-weighted citation impact, top 23% 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

7 citing papers in PubMed, 9 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

21 authors at 7 institutions in 4 countries.

Chaturaka RodrigoSchool of Medical Sciences, UNSW, Sydney, New South Wales, Australia.ORCID 0000-0003-2189-9177
Preston LeungThe Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.
Andrew R LloydThe Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.
Rowena A BullSchool of Medical Sciences, UNSW, Sydney, New South Wales, Australia.
Fabio LucianiSchool of Medical Sciences, UNSW, Sydney, New South Wales, Australia.
Jason GrebelyThe Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.ORCID 0000-0002-1833-2017
Gregory J DoreThe Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.
Tanya ApplegateThe Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.
Kimberly PageUniversity of New Mexico, Albuquerque, New Mexico.
Julie BruneauCentre de Recherche du Centre hospitalier de l', Université de Montréal (CRCHUM), Montreal, Quebec, Canada.
Andrea L CoxJohns Hopkins Medical Institutions, Baltimore, Maryland.
William OsburnJohns Hopkins Medical Institutions, Baltimore, Maryland.
Arthur Y KimHarvard Medical School, Boston, Massachusetts.
Naglaa H ShoukryCentre de Recherche du Centre hospitalier de l', Université de Montréal (CRCHUM), Montreal, Quebec, Canada.
Georg M LauerHarvard Medical School, Boston, Massachusetts.
Lisa MaherThe Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.
Janke SchinkelAcademic Medical Center, Amsterdam, The Netherlands.
Maria PrinsAcademic Medical Center, Amsterdam, The Netherlands.
Margaret HellardBurnet Institute, Melbourne, Victoria, Australia.ORCID 0000-0002-5055-3266
Auda A EltahlaSchool of Medical Sciences, UNSW, Sydney, New South Wales, Australia.
InC3 Collaborative
UNSW Sydney · AUAmsterdam UMC Location University of Amsterdam · NLCentre Hospitalier de l’Université de Montréal · CAHarvard University · USJohns Hopkins University · USBurnet Institute · AUUniversity of New Mexico · US

Funding

Acute Hepatitis C Infection in Young InjectorsR01DA016017 · NIDA · UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR · PI PAGE, KIMBERLY · 2002 to 2018
$14.0M
The role of NK cells during acute HCV infection and antiviral therapyU19AI066345 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI KIM, ARTHUR Y · 2005 to 2014
$8.5M
Scientific CoreU19AI088791 · NIAID · JOHNS HOPKINS UNIVERSITY · PI COX, ANDREA L · 2010 to 2020
$8.2M
Treatment of recently acquired hepatitis C virus infectionR01DA015999 · NIDA · UNIVERSITY OF NEW SOUTH WALES · PI DORE, GREGORY JOHN · 2003 to 2014
$3.7M
International Collaborative of prospective studies of HIV and Hepatitis in IDUR01DA031056 · NIDA · UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR · PI PAGE, KIMBERLY · 2011 to 2015
$2.2M
Immune Control and Evadion during Acute HCV InfectionU01AI131314 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI LAUER, GEORG MICHAEL · 2016 to 2020
$1.4M
NIAID NIH HHS U01 AI131314NIAID NIH HHS U19 AI066345NIAID NIH HHS U19 AI088791NIDA NIH HHS R01 DA015999NIDA NIH HHS R01 DA016017NIDA NIH HHS R01 DA031056
6 · The paper itself

Abstract

Interactions between the host immune system and the viral variants determine persistence of hepatitis C virus (HCV) infection after the acute phase of infection. This study describes the genetic variability of within-host HCV viral variants in acute infection and correlates it with host- and virus-related traits and infection outcome. Next generation sequence data (Illumina, MiSeq platform) of viral genomes from 116 incident acute infections (within 180 days of infection) were analysed to determine all the single nucleotide polymorphism (SNP) frequencies above a threshold of 0.1%. The variability of the SNPs for the full open reading frame of the genome as well as for each protein coding region were compared using mean standardized Shannon entropy (SE) values calculated separately for synonymous and nonsynonymous mutations. The envelope glycoproteins regions (E1 and E2) had the highest SE values (indicating greater variability) followed by the NS5B region. Nonsynonymous mutations rather than synonymous mutations were the main contributors to genomic variability in acute infection. The mean difference of Shannon entropy was also compared between subjects after categorizing the samples according to host and virus-related traits. Host IFNL3 allele CC polymorphism at rs12979860 (vs others) and viral genotype 1a (vs 3a) were associated with higher genomic variability across the viral open reading frame. Time since infection, host gender or continent of origin was not associated with the viral genomic variability. Viral genomic variability did not predict spontaneous clearance.

Indexed as

FemaleGenome, ViralGenotypeHepacivirusHepatitis CHepatitis C, ChronicHumansInterferon LambdaInterferonsInterleukinsMaleMutationPolymorphism, Single NucleotideViral ProteinsInterferon Lambdainterferon-lambda, humanInterferonsInterleukinsViral Proteinshepatitis C virusIFNL3InC3 studyShannon entropyspontaneous clearance

Identifiers

PMID30578702
PMCPMC6417964
OpenAlexW2905838688

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.