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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.
J Virol Methods. 2015 Oct; 223:105-8.JV

Abstract

Many studies have reported the use of the NS5B gene to subtype hepatitis C virus (HCV). Other HCV genes, such as HCV-5' UTR, Core (C) and E1, have also been used. In some studies, NS5B have been used together with 5'-UTR or C genes to improve genotyping results obtained using commercial procedures. Only two studies in Spain have compared molecular techniques versus commercial procedures regarding the efficacy of HCV subtyping. The aim of this study was to determine whether nested PCR and sequencing of a NS5B region was more reliable than commercial procedures to subtype HCV. We analyzed the results of HCV genotyping in [726] serum specimens collected from 2001 to 2013. From 2001 to 2011, we used PCR and INNO-LiPA hybridization or its new version Versant HCV Genotype 2.0 assay (471 samples). From 2012 to 2013, we used nested PCR and sequencing of a NS5B region (255 cases). This method used two pairs of primers to amplify the RNA of the sample converted to DNA by retrotranscription. The amplification product of 270 base pairs was further sequenced. To identify the subtype, the sequences obtained were compared to those in the international database: http://hcv.lanl.gov./content/sequence/, HCV/ToolsOutline.html and Geno2pheno[hcv] http://hcv.bioinf.mpi-inf.mpg.de/index.php. Nested PCR of a NS5B region and sequencing identified all but one subtype (0.4%, 1/255), differentiated all 1a subtypes from 1b subtypes, and characterized all HCV 2-4 subtypes. This approach also distinguished two subtypes, 2j and 2q, that had rarely been detected previously in Spain. However, commercial procedures failed to subtype 12.7% (60/471) of samples and to genotype 0.6% of specimens (3/471). Nested PCR and sequencing of a NS5B region improved the subtyping of HCV in comparison with classical procedures and identified two rare subtypes in Spain: 2j and 2q. However, full length genome sequencing is recommended to confirm HCV 2j and 2q subtypes.

Authors+Show Affiliations

Servei de Microbiología, Fundació de Gestió de l'Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08026 Barcelona, Spain. Electronic address: nmargall@santpau.cat.Servei de Microbiología, Fundació de Gestió de l'Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08026 Barcelona, Spain.Servei de Microbiología, Fundació de Gestió de l'Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08026 Barcelona, Spain.Servei de Digestiu, Fundació de Gestió de l' Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.Servei de Digestiu, Fundació de Gestió de l' Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.Servei de Microbiología, Fundació de Gestió de l'Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08026 Barcelona, Spain; Departament de Genètica i Microbiología, Universitat Autònoma de Barcelona, Edifici C 08193, Bellaterra, Cerdanyola del Vallès, Spain.

Pub Type(s)

Case Reports
Evaluation Study
Journal Article

Language

eng

PubMed ID

26253334

Citation

Margall, N, et al. "Two Unusual Hepatitis C Virus Subtypes, 2j and 2q, in Spain: Identification By nested-PCR and Sequencing of a NS5B Region." Journal of Virological Methods, vol. 223, 2015, pp. 105-8.
Margall N, March F, Español M, et al. Two unusual hepatitis C virus subtypes, 2j and 2q, in Spain: Identification by nested-PCR and sequencing of a NS5B region. J Virol Methods. 2015;223:105-8.
Margall, N., March, F., Español, M., Torras, X., Gallego, A., & Coll, P. (2015). Two unusual hepatitis C virus subtypes, 2j and 2q, in Spain: Identification by nested-PCR and sequencing of a NS5B region. Journal of Virological Methods, 223, 105-8. https://doi.org/10.1016/j.jviromet.2015.07.022
Margall N, et al. Two Unusual Hepatitis C Virus Subtypes, 2j and 2q, in Spain: Identification By nested-PCR and Sequencing of a NS5B Region. J Virol Methods. 2015;223:105-8. PubMed PMID: 26253334.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Two unusual hepatitis C virus subtypes, 2j and 2q, in Spain: Identification by nested-PCR and sequencing of a NS5B region. AU - Margall,N, AU - March,F, AU - Español,M, AU - Torras,X, AU - Gallego,A, AU - Coll,P, Y1 - 2015/08/05/ PY - 2014/11/24/received PY - 2015/07/31/revised PY - 2015/07/31/accepted PY - 2015/8/9/entrez PY - 2015/8/9/pubmed PY - 2016/5/24/medline KW - HCV PCR KW - NS5B region sequencing KW - Subtype 2j KW - Subtype 2q SP - 105 EP - 8 JF - Journal of virological methods JO - J Virol Methods VL - 223 N2 - Many studies have reported the use of the NS5B gene to subtype hepatitis C virus (HCV). Other HCV genes, such as HCV-5' UTR, Core (C) and E1, have also been used. In some studies, NS5B have been used together with 5'-UTR or C genes to improve genotyping results obtained using commercial procedures. Only two studies in Spain have compared molecular techniques versus commercial procedures regarding the efficacy of HCV subtyping. The aim of this study was to determine whether nested PCR and sequencing of a NS5B region was more reliable than commercial procedures to subtype HCV. We analyzed the results of HCV genotyping in [726] serum specimens collected from 2001 to 2013. From 2001 to 2011, we used PCR and INNO-LiPA hybridization or its new version Versant HCV Genotype 2.0 assay (471 samples). From 2012 to 2013, we used nested PCR and sequencing of a NS5B region (255 cases). This method used two pairs of primers to amplify the RNA of the sample converted to DNA by retrotranscription. The amplification product of 270 base pairs was further sequenced. To identify the subtype, the sequences obtained were compared to those in the international database: http://hcv.lanl.gov./content/sequence/, HCV/ToolsOutline.html and Geno2pheno[hcv] http://hcv.bioinf.mpi-inf.mpg.de/index.php. Nested PCR of a NS5B region and sequencing identified all but one subtype (0.4%, 1/255), differentiated all 1a subtypes from 1b subtypes, and characterized all HCV 2-4 subtypes. This approach also distinguished two subtypes, 2j and 2q, that had rarely been detected previously in Spain. However, commercial procedures failed to subtype 12.7% (60/471) of samples and to genotype 0.6% of specimens (3/471). Nested PCR and sequencing of a NS5B region improved the subtyping of HCV in comparison with classical procedures and identified two rare subtypes in Spain: 2j and 2q. However, full length genome sequencing is recommended to confirm HCV 2j and 2q subtypes. SN - 1879-0984 UR - https://www.unboundmedicine.com/medline/citation/26253334/Two_unusual_hepatitis_C_virus_subtypes_2j_and_2q_in_Spain:_Identification_by_nested_PCR_and_sequencing_of_a_NS5B_region_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0166-0934(15)00265-7 DB - PRIME DP - Unbound Medicine ER -