Evidence map›Paper›PMID 31438880›Full record

ArticleBMC infectious diseases2019

Comparison of Sanger sequencing for hepatitis C virus genotyping with a commercial line probe assay in a tertiary hospital.

Sylvie Goletti, Siméon Zuyten, Léonie Goeminne, Chris Verhofstede, Hector Rodriguez-Villalobos, Monique Bodeus, Peter Stärkel, Yves Horsmans, Benoît Kabamba-Mukadi

Open access · goldAbstract readComparative StudyEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC infectious diseases, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.7field-weighted citation impact, top 29% 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

3 citing papers in PubMed, 8 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

9 authors at 3 institutions in 1 country.

Sylvie GolettiMicrobiology Department, Cliniques universitaires St Luc, Université catholique de Louvain, Brussels, Belgium. sylviegoletti@hotmail.com.ORCID http://orcid.org/0000-0002-5884-237X
Siméon ZuytenPôle de Microbiologie médicale, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain , Brussels, Belgium.
Léonie GoeminnePôle de Microbiologie médicale, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain , Brussels, Belgium.
Chris VerhofstedeAIDS Reference Laboratory, Clinical Chemistry, Microbiology and Immunology Department, Ghent University, Ghent, Belgium.
Hector Rodriguez-VillalobosMicrobiology Department, Cliniques universitaires St Luc, Université catholique de Louvain, Brussels, Belgium.
Monique BodeusMicrobiology Department, Cliniques universitaires St Luc, Université catholique de Louvain, Brussels, Belgium.
Peter StärkelHepatoGastroenterology Department, Cliniques universitaires St Luc, Université catholique de Louvain, Brussels, Belgium.
Yves HorsmansHepatoGastroenterology Department, Cliniques universitaires St Luc, Université catholique de Louvain, Brussels, Belgium.
Benoît Kabamba-MukadiMicrobiology Department, Cliniques universitaires St Luc, Université catholique de Louvain, Brussels, Belgium.
Cliniques Universitaires Saint-Luc · BEUCLouvain · BEGhent University · BE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe technique most frequently used to genotype HCV is quantitative RT-PCR. This technique is unable to provide an accurate genotype/subtype for many samples; we decided to develop an in-house method with the goal of accurately identifying the genotype of all samples. As a Belgium National Centre of reference for hepatitis, we developed in-house sequencing not only for 5'UTR and core regions starting from VERSANT LiPA amplicons but also for NS5B regions. The sequencing of VERSANT LiPA amplicons might be useful for many laboratories worldwide using the VERSANT LiPA assay to overcome undetermined results.

methods100 samples from Hepatitis C virus infected patients analysed by the VERSANT HCV Genotype 2.0 LiPA Assay covering frequent HCV types and subtypes were included in this study. NS5B, 5'UTR and Core home-made sequencing were then performed on these samples. The sequences obtained were compared with the HCV genomic BLAST bank.

resultsAll the samples were characterised by the VERSANT LiPA assay (8 G1a, 17 G1b, 6 G2, 11 G3, 13 G4, and 10 G6). It was not possible to discriminate between G6 and G1 by the VERSANT LiPA assay for 8 samples and 27 had an undetermined genotype. Forty-one samples were sequenced for the three regions: NS5B, 5'UTR and Core. Twenty-three samples were sequenced for two regions: 5' UTR and Core and 36 samples were sequenced only for NS5B. Of the 100 samples included, 64 samples were analysed for 5'UTR and Core sequencing and 79 samples were analysed for NS5B sequencing. The global agreement between VERSANT LiPA assay and sequencing was greater than 95%.

conclusionsIn this study, we describe a new, original method to confirm HCV genotypes of samples not discriminated by a commercial assay, using amplicons already obtained by the screening method, here the VERSANT LiPA assay. This method thus saves one step if a confirmation assay is needed and might be of usefulness for many laboratories worldwide performing VERSANT LiPA assay in particular.

Indexed as

Molecular Probe TechniquesReagent Kits, Diagnostic5' Untranslated RegionsBase SequenceCommerceGenomicsGenotypeGenotyping TechniquesHepacivirusHepatitis CHumansPhylogenyRetrospective StudiesRNA, ViralSequence Analysis, RNATertiary Care Centers5' Untranslated RegionsReagent Kits, DiagnosticRNA, ViralGenotypingHepatitis C virusSequencing

Identifiers

PMID31438880
PMCPMC6704641
OpenAlexW2969517596

What OpenQuestion holds

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LicenceCC BY
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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.