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Ozefe F, Arslan Yildiz A. Smartphone-assisted Hepatitis C detection assay based on magnetic levitation. Analyst 2020; 145:5816-5825. [DOI: 10.1039/d0an01111h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This work describes development of smartphone-assisted magnetic levitation assay for Point-of-Care (PoC) applications.
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Affiliation(s)
- Fatih Ozefe
- Department of Bioengineering
- Izmir Institute of Technology (IZTECH)
- Izmir
- Turkey
| | - Ahu Arslan Yildiz
- Department of Bioengineering
- Izmir Institute of Technology (IZTECH)
- Izmir
- Turkey
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Uribe-Noguez LA, Mata-Marín JA, Ocaña-Mondragón A, Pompa-Mera EN, Ribas-Aparicio RM, Arroyo-Anduiza CI, Gomez-Torres ME, Chaparro-Sánchez A, Gaytán-Martínez J, Mauss S. Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico. J Infect Chemother 2019; 26:205-210. [PMID: 31537472 DOI: 10.1016/j.jiac.2019.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) infection affects an estimated 71 million people worldwide. HCV is classified into eight genotypes and >70 subtypes. Determination of HCV genotype is important for selection of type and duration of antiviral therapy, and genotype is also a predictor of treatment response. The most commonly used HCV genotyping method in clinical laboratories is a hybridization-based line probe assay (LiPA; Versant HCV Genotype 2.0). However, these methods have a lack of specificity in genotype identification and subtype assignment. Here, we compared the performance of Versant HCV Genotype 2.0 with the gold standard direct sequencing of the NS5B region, in 97 samples from Mexican patients. We found a genotypic concordance of 63.9% between these methods. While 68 samples (70%) were classified into HCV genotype 1 (GT1) by NS5B sequencing, it was not true for 17 samples (17.5%), which were not match HCV subtype by LiPA. Furthermore, nine of the 33 samples classified by NS5B sequencing as GT1a were not identified by LiPA. Use of direct sequencing could improve selection of the optimal therapy, avoid possible failures of therapy and avoid high costs resulting from incorrect genotyping tests in settings without broad access to pangenotypic regimens.
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Affiliation(s)
- Luis Antonio Uribe-Noguez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico; Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico; Centro de Simulación Médica, Facultad Mexicana de Medicina, Universidad La Salle, Mexico City, Mexico.
| | - José Antonio Mata-Marín
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alicia Ocaña-Mondragón
- Laboratorio Central de Epidemiología, División de Laboratorios de Vigilancia e Investigación Epidemiológica, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Ericka Nelly Pompa-Mera
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico
| | - Carla Ileana Arroyo-Anduiza
- Departamento de Patología Clínica, Banco Central de Sangre, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - María Elena Gomez-Torres
- Laboratorio de Urgencias, Hospital de Infectología, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alberto Chaparro-Sánchez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Jesus Gaytán-Martínez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Stefan Mauss
- Center for HIV and Hepatogastroenterology, Duesseldorf, Germany
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Warkad SD, Nimse SB, Song KS, Kim T. HCV Detection, Discrimination, and Genotyping Technologies. SENSORS (BASEL, SWITZERLAND) 2018; 18:E3423. [PMID: 30322029 PMCID: PMC6210034 DOI: 10.3390/s18103423] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
Abstract
According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.
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Affiliation(s)
- Shrikant Dashrath Warkad
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Keum-Soo Song
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
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Warkad SD, Nimse SB, Song KS, Chantratita W, Pongthanapisith V, Nawale LU, Kim T. Performance of 6 HCV genotyping 9G test for HCV genotyping in clinical samples. Virol J 2018; 15:107. [PMID: 29996859 PMCID: PMC6042330 DOI: 10.1186/s12985-018-1017-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/21/2018] [Indexed: 12/17/2022] Open
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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Affiliation(s)
- Shrikant Dasharath Warkad
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea
| | - Keum-Soo Song
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea
| | - Wasun Chantratita
- Department of Pathology, Faculty of Medicine, Virology Laboratory, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Viroj Pongthanapisith
- Department of Pathology, Faculty of Medicine, Virology Laboratory, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Laxman Uddhav Nawale
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea.
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Yusrina F, Chua CW, Lee CK, Chiu L, Png TSY, Khoo MJ, Yan G, Lee GH, Yan B, Lee HK. Comparison of cobas HCV GT against Versant HCV Genotype 2.0 (LiPA) with confirmation by Sanger sequencing. J Virol Methods 2018; 255:8-13. [PMID: 29428399 DOI: 10.1016/j.jviromet.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/29/2018] [Accepted: 02/04/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Correct identification of infecting hepatitis C virus (HCV) genotype is helpful for targeted antiviral therapy. OBJECTIVES Here, we compared the HCV genotyping performance of the cobas HCV GT assay against the Versant HCV Genotype 2.0 (LiPA) assay, using 97 archived serum samples. STUDY DESIGN In the event of discrepant or indeterminate results produced by either assay, the core and NS5B regions were sequenced. RESULTS Of the 97 samples tested by the cobas, 25 (26%) were deemed indeterminate. Sequencing analyses confirmed 21 (84%) of the 25 samples as genotype 6 viruses with either subtype 6m, 6n, 6v, 6xa, or unknown subtype. Of the 97 samples tested by the LiPA, thirteen (13%) were deemed indeterminate. Seven (7%) were assigned with genotype 1, with unavailable/inconclusive results from the core region of the LiPA. Notably, the 7 samples were later found to be either genotype 3 or 6 by sequencing analyses. Moreover, 1 sample by the LiPA was assigned as genotypes 4 (cobas: indeterminate) but were later found to be genotype 3 by sequencing analyses, highlighting its limitation in assigning the correct genotype. CONCLUSIONS The cobas showed similar or slightly higher accuracy (100%; 95% CI 94-100%) compared to the LiPA (99%; 95% CI 92-100%). Twenty-six percent of the 97 samples tested by the cobas had indeterminate results, mainly due to its limitation in identifying genotype 6 other than subtypes 6a and 6b. This presents a significant assay limitation in Southeast Asia, where genotype 6 infection is highly prevalent.
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Affiliation(s)
- Falah Yusrina
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Cui Wen Chua
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Chun Kiat Lee
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Lily Chiu
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Tracy Si-Yu Png
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Mui Joo Khoo
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Gabriel Yan
- Department of Medicine, National University Hospital, National University Health System, Singapore
| | - Guan Huei Lee
- Department of Medicine, National University Hospital, National University Health System, Singapore
| | - Benedict Yan
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore; Translational Centre for Development and Research, National University Health System, Singapore
| | - Hong Kai Lee
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore.
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Neukam K, Martínez AP, Culasso ACA, Ridruejo E, García G, Di Lello FA. NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b. PLoS One 2017; 12:e0182193. [PMID: 28753662 PMCID: PMC5533332 DOI: 10.1371/journal.pone.0182193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/13/2017] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE To evaluate the use of hepatitis C virus (HCV) NS3 sequencing as alternative to the comercially available Versant HCV 2.0 reverse hybridization line-probe assay (LiPA 2.0) to determine HCV genotype 1 (HCV-1) subtypes. PATIENTS AND METHODS A cohort of 104 patients infected by HCV-1 according to LiPA 2.0 was analyzed in a cross-sectional study conducted in patients seen from January 2012 to June 2016 at an outpatient clinic in Buenos Aires, Argentina. RESULTS The samples were included within well supported subtype clades: 64 with HCV-1b and 39 with HCV-1a infection. Twenty of the HCV-1a infected patientes were included in a supported sub-clade "1" and 19 individuals were among the basal sub-clade "2". LiPA 2.0 failed to subtype HCV-1 in 20 (19.2%) individuals. Subtype classification determined by NS3 direct sequencing showed that 2/18 (11.1%) of the HCV-1a-infected patients as determined by LiPA 2.0 were in fact infected by HCV-1b. Of the HCV-1b-infected according to LiPA 2.0, 10/66 (15.2%) patients showed HCV-1a infection according to NS3 sequencing. Overall misclassification was 14.3% (κ-index for the concordance with NS3 sequencing = 0.635). One (1%) patient was erroneously genotyped as HCV-1 and was revealed as HCV genotype 4 infection. CONCLUSIONS Genomic sequencing of the HCV NS3 region represents an adequate alternative since it provides reliable genetic information. It even distinguishes between HCV-1a clades related to resistance-associated substitutions to HCV protease inhibitors, it provides reliable genetic information for genotyping/subgenotyping and simultaneously allows to determine the presence of resistance-associated substitutions to currently recommended DAAs.
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Affiliation(s)
- Karin Neukam
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Virología, Buenos Aires, Argentina
- Instituto de Biomedicina de Sevilla / Hospital Universitario Virgen del Rocío / CSIC / Universidad de Sevilla, Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
- Hospital Universitario de Valme, Unit of Infectious Diseases and Mirobiology, Seville, Spain
| | - Alfredo P. Martínez
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Virology Section, Buenos Aires, Argentina
| | - Andrés C. A. Culasso
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Virología, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Ridruejo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Hepatology Section, Department of Medicine, Buenos Aires, Argentina
| | - Gabriel García
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Virología, Buenos Aires, Argentina
| | - Federico A. Di Lello
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Virología, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Win NN, Nakamoto S, Kanda T, Takahashi H, Takahashi-Nakaguchi A, Yasui S, Nakamura M, Wu S, Imazeki F, Mikami S, Yokosuka O, Gonoi T, Shirasawa H. Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences. Int J Mol Sci 2017; 18:ijms18010172. [PMID: 28106726 PMCID: PMC5297804 DOI: 10.3390/ijms18010172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 01/31/2023] Open
Abstract
Determination of hepatitis C virus (HCV) genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4) region and 5'-untranslated region (5'-UTR), respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results. Deep sequencing was also performed for the corresponding HCV NS4 regions. Seventeen out of 18 discrepant samples could be sequenced by the Sanger method. Both HCV core and NS4 sequences were concordant with that of genotyping in the 5'-UTR in all 17 samples. In cloning analysis of the HCV NS4 region, there were several amino acid variations, but each sequence was much closer to the peptide with the same genotype. Deep sequencing revealed that minor clones with different subgenotypes existed in two of the 17 samples. Genotyping by genome amplification showed high consistency, while several false reactions were detected by serotyping. The deep sequencing method also provides accurate genotyping results and may be useful for analyzing discrepant cases. HCV genotyping should be correctly determined before antiviral treatment.
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Affiliation(s)
- Nan Nwe Win
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Shingo Nakamoto
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Tatsuo Kanda
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.
| | | | - Shin Yasui
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Masato Nakamura
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Shuang Wu
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Fumio Imazeki
- Safety and Health Organization, Chiba University, Chiba 263-8522, Japan.
| | - Shigeru Mikami
- Department of Gastroenterology, Kikkoman General Hospital, Noda 278-0005, Japan.
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.
| | - Hiroshi Shirasawa
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
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