Evidence map›Paper›PMID 34541061›Full record

ArticleBio-protocol2017

Ultradeep Pyrosequencing of Hepatitis C Virus to Define Evolutionary Phenotypes.

Brendan A Palmer, Zoya Dimitrova, Pavel Skums, Orla Crosbie, Elizabeth Kenny-Walsh, Liam J Fanning

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

Article in Bio-protocol, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact, top 90% 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

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

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

6 authors at 3 institutions in 2 countries.

Brendan A PalmerMolecular Virology Diagnostic & Research Laboratory, Department of Medicine, University College Cork, Cork, Ireland.
Zoya DimitrovaDivision of Viral Hepatitis, Centers of Disease Control and Prevention, Atlanta, Georgia, USA.
Pavel SkumsDivision of Viral Hepatitis, Centers of Disease Control and Prevention, Atlanta, Georgia, USA.
Orla CrosbieDepartment of Gastroenterology, Cork University Hospital, Cork, Ireland.
Elizabeth Kenny-WalshDepartment of Gastroenterology, Cork University Hospital, Cork, Ireland.
Liam J FanningMolecular Virology Diagnostic & Research Laboratory, Department of Medicine, University College Cork, Cork, Ireland.
Centers for Disease Control and Prevention · USCork University Hospital · IEUniversity College Cork · IE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Analysis of hypervariable regions (HVR) using pyrosequencing techniques is hampered by the ability of error correction algorithms to account for the heterogeneity of the variants present. Analysis of between-sample fluctuations to virome sub-populations, and detection of low frequency variants, are unreliable through the application of arbitrary frequency cut offs. Cumulatively this leads to an underestimation of genetic diversity. In the following technique we describe the analysis of Hepatitis C virus (HCV) HVR1 which includes the E1/E2 glycoprotein gene junction. This procedure describes the evolution of HCV in a treatment naïve environment, from 10 samples collected over 10 years, using ultradeep pyrosequencing (UDPS) performed on the Roche GS FLX titanium platform ( Palmer

Indexed as

HypervariabilityQuasispeciesUltradeep pyrosequencingVirus

Identifiers

PMID34541061
PMCPMC8410299
OpenAlexW2620511597

What OpenQuestion holds

Textmetadata
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.