HCV inter-subtype 1a/1b recombinant detected by complete-genome next-generation sequencing

Gaspareto, Karine Vieira; Ribeiro, Roberto; Malta, Fernanda de Mello; Gomes‐Gouvêa, Michele Soares; Muto, Nair Hideko; Mendes‐Correa, Maria Cássia; Rozanski, Andrei; Carrilho, Flair José; Sabino, Éster Cerdeira; Pinho, João Renato Rebello

doi:10.1007/s00705-016-2889-5

Cited by 9 publications

(4 citation statements)

References 38 publications

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“…However, Roche-NGS protocols are very laborious and time consuming, and are difficult to implement, so far, in the routine laboratory. In addition, Roche-NGS targets only the NS5B region 32,33 , therefore, HCV infections that are due to HCV recombinants may be missed.…”

Section: Discussionmentioning

confidence: 99%

Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing

Fernández-Caso

Fernández-Caballero

Chueca

et al. 2019

Sci Rep

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Current HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencing assay (Roche-NGS). Plasma samples collected from 139 HCV-infected patients tested with Abbott-RT-PCR, 114 with single genotype (GT) and 25 with mixed GTs were genotyped using Roche-NGS. Roche-NGS confirmed all single GTs obtained with Abbott-RT-PCR. One case of Abbott GT 4 was found as GT 1a using Roche-NGS. Genotype 5 was confirmed using Roche-NGS in 75% cases (3 out of 4 cases). Twenty-five patients were identified as having mixed HCVinfections using Abbott-RT-PCR. The concordance between Abbott-RT-PCR and Roche-NGS was 76% (19 out of 25 cases). Three mixed-GT infections identified with the Abbott assay (two (1b + 4); one (1a + 3)) were reported as pure 1b using Roche-NGS. Very divergent results were found for the other three samples. When compared to Roche-NGS, Abbott-RT-PCR has performed excellently for the determination of patients infected with single GTs. For patients that are categorized as having a mixed infection using Abbott-RT-PCR, we recommend an NGS assay as a confirmation test.

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Section: Discussionmentioning

confidence: 99%

Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing

Fernández-Caso

Fernández-Caballero

Chueca

et al. 2019

Sci Rep

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“…Other studies complete de novo assembly with tools such as Geneious [ 38 ], CLC Main Workbench (Qiagen) [ 16 , 39 , 40 ], and Iterative Virus Assembler (IVA) [ 22 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ]. HCV studies follow similar patterns to those of HIV-1 [ 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 ]. A combination of both assembly approaches has been implemented to construct a consensus sequence by first mapping the reads to a reference sequence and then completing de novo assembly of those mapped reads [ 53 , 60 ].…”

Section: Introductionmentioning

confidence: 73%

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses

Gibson

Steiner

Rentia

et al. 2020

Viruses

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Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options.

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“…To obtain more accurate results, we recommend ≥2 HCV genomic regions be adopted for classification. 2b/1a 5'UTR/NS5B Virology Journal United States 2011 0.8% [31] 1a/1b Full length Arch Virol Brazil 2016 2% [32] 2b/6w E1/NS5B J Med Virol Taiwan 2010 1.7% [33] 2/5 E2/NS5B J Viro French 2007 3.8% [34] 4a/4d E1/NS5B J Med Virol Portugal 2011 0.8% [50] 1a/1c Full length J Viro Japan 2006 1.1%. [21] Cheng et al Medicine (2021) 100:18 www.md-journal.com…”

Section: Discussionmentioning

confidence: 99%

The genotype analysis of the hepatitis C virus in Heilongjiang Province, China

Cheng

Feng

et al. 2021

Medicine

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Introduction: Hepatitis C virus (HCV) infection is a major public health issue. HCV genotype identification is clinically important to tailor the dosage and duration of treatment, and recombination in intra-patient populations of HCV may lead to the generation of escape mutants, as previously observed for other RNA viruses. Up to now, there is no study assessing HCV genotypes and subtypes in Heilongjiang Province, China. Methods: To determine genotype and phylogenetic analysis of HCV in Heilongjiang Province is crucial. In this study, we amplified 3 genome regions (5’UTR, E1, and NS5B) of 30 HCV patients in Heilongjiang Province, amplified products were analyzed by bioinformatics. Results: We found that 23 specimens had concordant subtypes in the 3 gene regions (2a and 1b), 7 HCV patients were considered the recombinants, the recombination pattern of the 7 HCV patients in the 5’UTR, E1, and NS5B region as followed: 1b/2a/1b, 2a/2a/1b, 1b/2a/2a, 1b/2a/1b, 1b/2a/1b, 1b/2a/1b, 2a/2a/1b. Conclusions: The findings in the present study showed that a higher recombination rate (23%) than other researches, and the recombination of 2a/1b in the 5’UTR, E1, and NS5B region was only found in the present study up to now.

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HCV inter-subtype 1a/1b recombinant detected by complete-genome next-generation sequencing

Cited by 9 publications

References 38 publications

Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing

Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses

The genotype analysis of the hepatitis C virus in Heilongjiang Province, China

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