Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico

Background: Hepatitis C virus (HCV) is a major cause of liver diseases. Transmission of HCV, as a blood-borne virus, is a major concern for the safety of blood products. In Iran, intravenous drug abuse is a major risk factor for HCV transmission. Recently a change in the distribution of HCV genotype among Iranian blood donors has been reported, and genotype 3a is reported as the most frequent genotype. Also, genotype 3a is the dominant genotype among IDUs. Objective: To investigate the association between HCV genotype 3a circulating in the community, sequences of HCV genotype 3a were analyzed among different risk groups in Iran. Methods: In this cross-sectional study, a partial sequence of the NS5B region of the HCV genome was isolated from 58 blood donors, 48 intravenous drug users (IDUs), and 31 patients with inherited bleeding disorders (IBDs) infected with HCV genotype 3a were included. The published sequence data were obtained from the Gen Bank database and were compared to construct the phylogenetic trees. Results: Of 58 blood donors infected with subtype 3a, 31 (53.5%) reported the risk of intravenous drug abuse. In the phylogenetic tree, no separate cluster was formed to differentiate between HCV sequences in blood donors and IDUs. A cluster at the middle level was found in the phylogenetic tree formed by sequences from blood donors, IDUs, and patients with inherited bleeding disorders. Conclusions: The phylogenetic tree showed the phylogenetic mixing of genotype 3a sequences in BDs, IBD patients, and IDUs. The results confirmed the extensive transmission of IDU-related genotype 3a towards the general population.

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Clinical relevance of accurate HCV genotype and subtype assignment by NS3/NS5A/NS5B direct sequencing in the era of new direct acting antiviral agents

Digestive and Liver Disease ◽

10.1016/j.dld.2015.12.019 ◽

2016 ◽

Vol 48 ◽

pp. e1-e2

Author(s):

M. Aragri ◽

V.C. Di Maio ◽

D. Di Paolo ◽

V. Cento ◽

F. De Leonardis ◽

...

Keyword(s):

Clinical Relevance ◽

Direct Sequencing ◽

Antiviral Agents ◽

Hcv Genotype ◽

Direct Acting Antiviral ◽

Subtype Assignment ◽

Direct Acting ◽

Direct Acting Antiviral Agents

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An outbreak of HCV genotype 6a and 2a infection in South China: Confirmation of iatrogenic transmission by phylogenetic analysis of the NS5B region

Molecular Medicine Reports ◽

10.3892/mmr.2016.5737 ◽

2016 ◽

Vol 14 (5) ◽

pp. 4285-4292 ◽

Cited By ~ 1

Author(s):

Xiaoqiong Shao ◽

Qiumin Luo ◽

Qingxian Cai ◽

Fulong Zhang ◽

Jiangyun Zhu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

South China ◽

Ns5b Region ◽

Hcv Genotype ◽

Iatrogenic Transmission

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High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods

Journal of Clinical Microbiology ◽

10.1128/jcm.02093-14 ◽

2014 ◽

Vol 53 (1) ◽

pp. 219-226 ◽

Cited By ~ 56

Author(s):

Josep Quer ◽

Josep Gregori ◽

Francisco Rodríguez-Frias ◽

Maria Buti ◽

Antonio Madejon ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Real Time ◽

Deep Sequencing ◽

Direct Sequencing ◽

Treatment Strategies ◽

Dual Infection ◽

Genotype 1 ◽

Hcv Genotype ◽

Genotype Ii

Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.

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