Two unusual hepatitis C virus subtypes, 2j and 2q, in Spain: Identification by nested-PCR and sequencing of a NS5B region

Margall, N; March, Francesca; Español, Montserrat; Torras, Xavier; Gallego, Adolfo; Coll, Pere

doi:10.1016/j.jviromet.2015.07.022

Cited by 4 publications

(4 citation statements)

References 30 publications

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“…GT‐2j was identified in Japan but has been found in Europe (Bosnia, France, and Spain) and in North and South America (Canada, Argentina, and Venezuela). GT‐2j prevalence is 0.4% in Spain, 5% in Argentina and 21% in Venezuela . In this study, we found two patients (4%) had GT‐2j and one (2%) had a mixed infection with GT‐2k + 2j.…”

Section: Discussionmentioning

confidence: 47%

“…In our study, patients with GT 2j, 2k, and 2r showed no increases in transaminases levels (ALT <40 IU/L and AST <35 IU/L), had normal platelet (150‐450 × 10 9 /l) and albumin (3.5‐5.0 g/dL) levels, and showed no fibrosis as determined by APRI (>1 presence of fibrosis) . However, GT‐2j has been reported to evolve to cirrhosis . Two patients ( Exk and Pk ) presented data compatible with steatosis by ultrasound.…”

Section: Discussionmentioning

confidence: 50%

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Presence of rare hepatitis C virus subtypes, 2j, 2k, and 2r in Mexico City as identified by sequencing

Uribe-Noguez

Ocaña-Mondragón

Mata‐Marín

et al. 2018

Journal of Medical Virology

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The HCV 5'UTR, Core/E1, and NS5B regions of samples from fifty patients infected with the hepatitis C virus (HCV) were analyzed. Seventeen patients were identified with genotype (GT) 1b, eleven with GT-1a, nine with GT-2b and four with GT-3a. Two rare subtypes were detected: GT-2j in two patients and GT-2r in one patient. Three patients had mixed infections: one with GT-2k + 2j and two with GT-1b + 2b. This work identifies HCV GTs, 2j, 2k, and 2r for the first time in Mexico.

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Section: Discussionmentioning

confidence: 47%

Section: Discussionmentioning

confidence: 50%

Presence of rare hepatitis C virus subtypes, 2j, 2k, and 2r in Mexico City as identified by sequencing

Uribe-Noguez

Ocaña-Mondragón

Mata‐Marín

et al. 2018

Journal of Medical Virology

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“…The extracted nucleic acid was eluted using 50 μL of elution buffer, HCV RNA was denaturised and reverse-transcribed. NS5B amplification was achieved using a KOD Hot Start DNA polymerase (Merck, Darmstadt, Germany) and specific NS5B amplification-FOR and REV primers describe by Margall et al [15] (Table 1). The PCR was conducted using the following protocol: 2 min at 95 °C, 40 cycles of 20 s at 95 °C, 10 s at 60 °C and 5 s at 70 °C, and finally 5 min at 70 °C.…”

Section: Methodsmentioning

confidence: 99%

“…The primers used for sequencing of 5’UTR and core regions were designed in our laboratory. The primers used for sequencing of NS5B regions were describe by Margall et al [15]. The sequencing protocol was as follows: 2 min at 96 °C, 40 cycles of 20 s at 96 °C, 10 s at 50 °C and 5 s at 60 °C, and finally the sequences were maintained at 40 °C.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2019

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Background The 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. Methods 100 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. Results All 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%. Conclusions In 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.

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Development and Evaluation of a Loop-mediated Isothermal Amplification Assay for the Rapid Detection and Identification of Pectobacterium carotovorum on Celery in the Field

Shi¹,

Jin²,

Meng³

et al. 2020

Horticultural Plant Journal

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Two unusual hepatitis C virus subtypes, 2j and 2q, in Spain: Identification by nested-PCR and sequencing of a NS5B region

Cited by 4 publications

References 30 publications

Presence of rare hepatitis C virus subtypes, 2j, 2k, and 2r in Mexico City as identified by sequencing

Presence of rare hepatitis C virus subtypes, 2j, 2k, and 2r in Mexico City as identified by sequencing

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

Development and Evaluation of a Loop-mediated Isothermal Amplification Assay for the Rapid Detection and Identification of Pectobacterium carotovorum on Celery in the Field

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