Performance of 6 HCV genotyping 9G test for HCV genotyping in clinical samples

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Abstract

Background

A treatment of HCV infection depends on the genotype and sub-genotype. Therefore, accurate HCV genotyping is critical for selecting the appropriate treatment regimen.

Method

This study included 280 plasma samples to evaluate the performance of 6 HCV Genotyping 9G test. The performance of 6 HCV Genotyping 9G test for accurate detection of HCV 1a, 1b, 2, 3, 4, and 6 genotypes was evaluated by comparing it with LiPA 2.0 assay and sequencing.

Results

6 HCV Genotyping 9G test and LiPA 2.0 assay demonstrated 83.9% ( n = 235) agreement. 39/45 samples that showed discrepant results between the two tests were analyzed by sequencing. Sequencing genotyped 39 discrepant samples as 0 (HCV 1a), 24 (HCV 1b), 1 (HCV 6f), 12 (HCV 6i), and 2 (HCV-negative). Results of 6 HCV Genotyping 9G test were very similar to the sequencing as it detected 1, 23, 1, 12, and 2 samples as HCV 1a, 1b, 3 & 6a or 6f, 6i or 6n, and negative, respectively. However, LiPA 2.0 assay showed complete disagreement with sequencing, as it did not detect any of these 39 samples correctly. These results indicate that LiPA 2.0 assay has limitations in identifying HCV genotypes 1b, and 6. The sensitivity, specificity, PPV, and NPV of 6 HCV Genotyping 9G test were 99.5, 98.8, 99.5, and 98.8%, respectively. It is important to note that HCV Genotyping 9G test showed 98.3 and 100% sensitivity for HCV 1b and 6 genotyping, respectively. However, LiPA 2.0 assay demonstrated 57.9 and 71.7% sensitivity for these genotypes.

Conclusions

6 HCV Genotyping 9G test identifies HCV 1a, 1b, 2, 3, and 6 with good agreement with sequencing. Hence, 6 HCV Genotyping 9G test has a high clinical value because it can provide critical information to physicians and assist them to use the correct drug for efficient hepatitis C treatment.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-1017-4) contains supplementary material, which is available to authorized users.

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Most cited references 22

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Global epidemiology of hepatitis C virus infection: new estimates of age-specific antibody to HCV seroprevalence.

Khayriyyah Mohd Hanafiah, Justina Groeger, Abraham Flaxman … (2013)

In efforts to inform public health decision makers, the Global Burden of Diseases, Injuries, and Risk Factors 2010 (GBD2010) Study aims to estimate the burden of disease using available parameters. This study was conducted to collect and analyze available prevalence data to be used for estimating the hepatitis C virus (HCV) burden of disease. In this systematic review, antibody to HCV (anti-HCV) seroprevalence data from 232 articles were pooled to estimate age-specific seroprevalence curves in 1990 and 2005, and to produce age-standardized prevalence estimates for each of 21 GBD regions using a model-based meta-analysis. This review finds that globally the prevalence and number of people with anti-HCV has increased from 2.3% (95% uncertainty interval [UI]: 2.1%-2.5%) to 2.8% (95% UI: 2.6%-3.1%) and >122 million to >185 million between 1990 and 2005. Central and East Asia and North Africa/Middle East are estimated to have high prevalence (>3.5%); South and Southeast Asia, sub-Saharan Africa, Andean, Central, and Southern Latin America, Caribbean, Oceania, Australasia, and Central, Eastern, and Western Europe have moderate prevalence (1.5%-3.5%); whereas Asia Pacific, Tropical Latin America, and North America have low prevalence (<1.5%). The high prevalence of global HCV infection necessitates renewed efforts in primary prevention, including vaccine development, as well as new approaches to secondary and tertiary prevention to reduce the burden of chronic liver disease and to improve survival for those who already have evidence of liver disease. Copyright © 2012 American Association for the Study of Liver Diseases.

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(2015)

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Genotypic Distribution of Hepatitis C Virus in Thailand and Southeast Asia

Rujipat Wasitthankasem, Sompong Vongpunsawad, Nipaporn Siripon … (2015)

The majority of hepatitis C virus (HCV) infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV) is estimated at 150 million individuals, or 3% of the world’s population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5’ untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%), followed by 1a (19.9%), 1b (12.6%), 3b (9.7%) and 2a (0.5%). While genotype 1 was prevalent throughout Thailand (27–36%), genotype 3 was more common in the south. Genotype 6 (20.9%) constituted subtype 6f (7.8%), 6n (7.7%), 6i (3.4%), 6j and 6m (0.7% each), 6c (0.3%), 6v and 6xa (0.2% each) and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively). Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread.

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Author and article information

Contributors

Shrikant Dasharath Warkad: shrikant.warkad@gmail.com

Satish Balasaheb Nimse: satish_nimse@hallym.ac.kr

Keum-Soo Song: hanlimsk@empas.com

Wasun Chantratita: wasun.cha@mahidol.ac.th

Viroj Pongthanapisith: viroj.pon@mahidol.ac.th

Laxman Uddhav Nawale: lax01nawale@gmail.com

Taisun Kim:

ORCID: http://orcid.org/0000-0002-7834-575X

+82-033-248-2078 , tskim@hallym.ac.kr

Journal

Journal ID (nlm-ta): Virol J

Journal ID (iso-abbrev): Virol. J

Title: Virology Journal

Publisher: BioMed Central (London )

ISSN (Electronic): 1743-422X

Publication date (Electronic): 11 July 2018

Publication date PMC-release: 11 July 2018

Publication date Collection: 2018

Volume: 15

Electronic Location Identifier: 107

Affiliations

[1 ]ISNI 0000 0004 0470 5964, GRID grid.256753.0, Institute for Applied Chemistry and Department of Chemistry, , Hallym University, ; 1 Okcheon-dong, Chuncheon, 200-702 South Korea

[2 ]ISNI 0000 0004 1937 0490, GRID grid.10223.32, Department of Pathology, Faculty of Medicine, Virology Laboratory, Ramathibodi Hospital, , Mahidol University, ; Bangkok, 10400 Thailand

Author information

Taisun Kim http://orcid.org/0000-0002-7834-575X

Article

Publisher ID: 1017

DOI: 10.1186/s12985-018-1017-4

PMC ID: 6042330

PubMed ID: 29996859

SO-VID: 6563ce6f-fff9-48e3-a1f7-659b8d202e04

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 6 April 2018

Date accepted : 21 May 2018

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100003052, Ministry of Trade, Industry and Energy;

Award ID: R0004191

Award Recipient : Taisun Kim

Custom metadata

ScienceOpen disciplines: Microbiology & Virology

Keywords: hcv,hcv genotyping,9g dna technology,inno-lipa, liver cirrhosis, hepatocellular carcinoma

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ScienceOpen disciplines: Microbiology & Virology

Keywords: hcv, hcv genotyping, 9g dna technology, inno-lipa, liver cirrhosis, hepatocellular carcinoma

Performance of 6 HCV genotyping 9G test for HCV genotyping in clinical samples

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Method

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Conclusions

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Most cited references 22

Global epidemiology of hepatitis C virus infection: new estimates of age-specific antibody to HCV seroprevalence.

EASL Recommendations on Treatment of Hepatitis C 2015.

Genotypic Distribution of Hepatitis C Virus in Thailand and Southeast Asia

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