|
1
|
Mettikanont P, Bunchorntavakul C, Reddy KR. Systematic review: epidemiology and response to direct-acting antiviral therapy in genotype 6 chronic hepatitis C virus infection. Aliment Pharmacol Ther 2019; 49:492-505. [PMID: 30687952 DOI: 10.1111/apt.15100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/07/2018] [Accepted: 11/27/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) genotype 6 (GT6) is predominantly encountered in Southeast Asia and data on GT6 response to direct-acting antiviral (DAA) therapy are relatively limited. AIM To review the epidemiology and virologic outcome of DAA regimens in HCV GT6 patients. METHODS Electronic literature search of PubMed, EMBASE, and The Cochrane Library databases were conducted. RESULTS Hepatitis C virus genotype 6 is the most genetically diverse, has a prevalence of 19.9%-95.6% in HCV infected patients in Southeast Asia and has been associated with a higher risk of HCC in those with cirrhosis. After an extensive literature review, a total of 20 studies were selected to assess study population and treatment outcomes (total of 938 GT6 patients were included); 12 were clinical trials and eight were observational studies. Sustained virologic response at week 12 (SVR 12) following glecaprevir/pibrentasvir (n = 4; 108 patients), ledipasvir/sofosbuvir (n = 8; 427 patients), sofosbuvir/velpatasvir with or without voxilaprevir (n = 5; 171 patients), sofosbuvir/daclatasvir (n = 3; 172 patients) and sofosbuvir with ribavirin (n = 3; 60 patients) was 98%-100%, 64%-100%, 100%, 88%-94% and 100%, respectively. Failure was mostly in those with cirrhosis and prior treatment experience. DAA therapy was well tolerated and with a serious adverse event rate of <5%. CONCLUSIONS Hepatitis C virus genotype 6 is genetically diverse and is highly prevalent in Asia. While SVR rates have been high, cirrhosis and prior treatment experience marginally compromise response to DAAs. Large scale and exclusive studies in HCV genotype 6 prevalent areas are needed, while the current evidence suggests that DAAs are highly effective and safe.
Collapse
Affiliation(s)
| | - Chalermrat Bunchorntavakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Rajavithi Hospital, College of Medicine, Rangsit University, Bangkok, Thailand
| | - K Rajender Reddy
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
|
2
|
Camarasa CG, Cobo F. Application of MALDI-TOF Mass Spectrometry in Clinical Virology. THE USE OF MASS SPECTROMETRY TECHNOLOGY (MALDI-TOF) IN CLINICAL MICROBIOLOGY 2018. [PMCID: PMC7150354 DOI: 10.1016/b978-0-12-814451-0.00012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a diagnostic tool of microbial identification and characterization based on the detection of the mass of molecules. In the majority of clinical laboratories, this technology is currently being used mainly for bacterial diagnosis, but several approaches in the field of virology have been investigated. The introduction of this technology in clinical virology will improve the diagnosis of infections produced by viruses but also the discovery of mutations and variants of these microorganisms as well as the detection of antiviral resistance. This chapter is focused on the main current applications of MALDI-TOF MS techniques in clinical virology showing the state of the art with respect to this exciting new technology.
Collapse
|
|
3
|
Shin SR, Kim YS, Lim YS, Lee JS, Lee JW, Kim SM, Jeong SH, Sohn JH, Lee MS, Park SH. Clinical Characteristics and Treatment Outcome of Peginterferon Plus Ribavirin in Patients Infected with Genotype 6 Hepatitis C Virus in Korea: A Multicenter Study. Gut Liver 2017; 11:270-275. [PMID: 27728965 PMCID: PMC5347652 DOI: 10.5009/gnl16163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 12/29/2022] Open
Abstract
Background/Aims Because of the limited geographic distribution, there have been insufficient data regarding hepatitis C virus (HCV) genotype 6 in Korea. This study aimed to investigate the clinical characteristics and available treatment outcomes of patients with genotype 6 HCV in Korea. Methods From 2004 to 2014, data were collected from Korean patients infected with genotype 6 HCV in eight hospitals. Results Thirty-two patients had genotype 6 HCV. The median age was 44 years, and 6c was the most common subtype. The baseline median alanine transaminase level was 88 (21 to 1,019) IU/mL, and the HCV RNA level was 1,405,000 (96,500 to 28,844,529) IU/mL. Twenty-five patients were treated with peginterferon (PEG-IFN) and ribavirin. Three follow-up losses occurred. Additionally, 13 patients attained a sustained virologic response (SVR), seven patients relapsed, and two patients exhibited a null response. The SVR rates were 40% and 75% for the 24- and more than 48-week treatments, respectively, and five of the six patients who achieved a rapid virologic response (RVR) attained a SVR. Conclusions Korean patients infected with genotype 6 HCV are relatively young, and 6c is the most common subtype. When treated with PEG-IFN and ribavirin, the SVR rate was 52%. Similar to other genotypes, a longer duration of treatment and attainment of RVR are important for SVR.
Collapse
Affiliation(s)
- Su Rin Shin
- Health Care Center, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea.,Department of Internal Medicine, Kangwon National University College of Medicine, Chuncheon, Korea
| | - Young Seok Kim
- Department of Internal Medicine, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Young-Seok Lim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - June Sung Lee
- Department of Internal Medicine, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang, Korea
| | - Jin Woo Lee
- Department of Internal Medicine, Inha University School of Medicine, Incheon, Korea
| | - Sun Myung Kim
- Department of Internal Medicine, Gimpo Woori Hospital, Gimpo, Korea
| | - Sook-Hyang Jeong
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Joo Hyun Sohn
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - Myung Seok Lee
- Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Sang Hoon Park
- Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| |
Collapse
|
|
4
|
Han MS, Park Y, Kim HS. Comparison of Abbott RealTime genotype II, GeneMatrix restriction fragment mass polymorphism and Sysmex HISCL HCV Gr assays for hepatitis C virus genotyping. ACTA ACUST UNITED AC 2017; 55:1122-1128. [DOI: 10.1515/cclm-2016-0130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022]
Abstract
AbstractBackground:Hepatitis C virus (HCV) genotype is a predictive marker for treatment response. We sequentially evaluated the performances of two nucleic acid amplification tests (NAATs) and one serology assay for HCV genotype: Abbott RealTimegenotype II (RealTimeII), GeneMatrix restriction fragment mass polymorphism (RFMP), and Sysmex HISCL HCV Gr (HISCL Gr).Methods:We examined 281 clinical samples with three assays. The accuracy was assessed using the HCV Genotype Performance Panel PHW204 (SeraCare Life Sciences) for two NAATs. Discrepant cases were re-genotyped by the Versant HCV v.2.0 (line probe 2.0) assay.Results:With the RealTimeII assay, clinic samples were analyzed as follows: genotypes 1b (43.1%), 2 (40.2%), 1 subtypes other than 1a and 1b (12.5%), 3 (1.8%), 4 (1.4%), 1a (0.7%), 6 (0.4%), and mixed (1.1%). The RealTimeII and RFMP assays showed a type concordance rate of 97.5% (274/281) (κ=0.80) and no significant discordance (p=0.25). Both assays accurately genotyped all samples in the Performance Panel by the subtype level. The HISCL Gr assay showed concordance rates of about 91% (κ<0.40) and statistically significant discordances with two NAATs (p<0.05). In confirmation tests, the results of RFMP assay were the most consistent with those of Versant 2.0 assay.Conclusions:The three HCV assays provided genotyping and serotyping results with good concordance rates. The two NAATs (RealTimeII and RFMP) showed comparable performance and good agreement. However, the results of the HISCL Gr assay showed statistically significant differences with those of the NAATs.
Collapse
|
|
5
|
Shin SK, Park SY, Jung YK, Kim EJ, Lee HN, Lee JJ, Kwon OS, Choi DJ, Kim YS, Kim JH. [Prevalence, risk factors and clinical characteristics in patients with genotype 6 chronic hepatitis C: a single institute experience]. THE KOREAN JOURNAL OF GASTROENTEROLOGY 2017; 65:105-11. [PMID: 25716713 DOI: 10.4166/kjg.2015.65.2.105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND/AIMS Hepatitis C genotypes 1 and 2 are widely distributed globally. In contrast, genotype 6 is found mainly in Southeast Asia, while genotype 6 is rare in Korea. This study aims to investigate the prevalence, risk factors and clinical characteristics of patients with genotype 6 chronic hepatitis C. METHODS We retrospectively identified 133 HCV-infected patients who underwent HCV genotype analysis between January 2012 and December 2012, and analyzed the prevalence, risk factors and clinical characteristics of patients diagnosed with genotype 6 chronic hepatitis C. RESULTS Among 133 patients, 53 patients (39.8%) were infected with genotype 1, 62 patients (46.6%) with genotype 2, 2 patients (1.5%) with genotype 3, 14 patients (10.5%) with genotype 6, and 2 patients (1.5%) with mixed genotypes (genotype 1 and 6). The risk factors associated with genotype 6 were acupuncture (n=4, 28.6%), intravenous drug use (n=3, 21.4%), tattoo (n=2, 14.3%), and transfusion (n=2, 14.3%). Of the 14 patients with genotype 6, 6 patients were treated with pegylated interferon and ribavirin. Five patients had reached the end of treatment. All patients reaching end of treatment for genotype 6 showed early virological response and sustained virological response. CONCLUSIONS The prevalence of genotype 6 is 10.5% and mixed infections of genotype 1 and 6 are 1.5% in patients with chronic hepatitis C. A major potential risk factor is intravenous drug use and the treatment response rate to pegylated interferon plus ribavirin is high in patients with genotype 6 chronic hepatitis C. Large scale multicenter studies are needed.
Collapse
Affiliation(s)
- Seung Kak Shin
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Soo Yong Park
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Young Kul Jung
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Eui Joo Kim
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Heon Nam Lee
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Jong Joon Lee
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Oh Sang Kwon
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Duck Joo Choi
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Yun Soo Kim
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Ju Hyun Kim
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| |
Collapse
|
|
6
|
Papastergiou V, Karatapanis S. Current status and emerging challenges in the treatment of hepatitis C virus genotypes 4 to 6. World J Clin Cases 2015; 3:210-20. [PMID: 25789294 PMCID: PMC4360493 DOI: 10.12998/wjcc.v3.i3.210] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/01/2014] [Accepted: 12/29/2014] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) genotypes 4, 5 and 6 are mainly present in Africa, the Middle East and Asia and they have been less extensively studied with respect to epidemiology, natural disease history and therapeutic endpoints. Response rates to a 48-wk combined peginterferon/ribavirin treatment range to 40%-69% for HCV 4, 55%-60% for HCV 5 and 60%-90% for HCV 6. Response-guided schedules are recommended to optimize the outcomes of peginterferon/ribavirin treatment in HCV 4 and, in form of preliminary data, for HCV 6, but no data are yet available to support such an individualization of therapy for HCV 5. Recently, the direct-acting antivirals (DAAs) with pan-genotypic activities simeprevir, sofosbuvir and daclatasvir have been recommended in triple regimens with peginterferon/ribavirin for the treatment of HCV genotypes 4 to 6 infections. In the future, DAA-based interferon-free therapies are awaited to drastically improve treatment outcomes in HCV. However, efforts to improve treatment outcomes with peginterferon/ribavirin should continue, as the HCV 4-6 infected population is mainly based in resource-limited settings with restricted access to the costly DAAs.
Collapse
|
|
7
|
Choi HS, Min KT, Cha YS, Hong SP. Multiplex detection of KRAS mutations by a matrix-assisted laser desorption/ionization-time of flight mass spectrometry assay. Clin Biochem 2014; 47:1091-7. [PMID: 24726492 DOI: 10.1016/j.clinbiochem.2014.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/26/2014] [Accepted: 03/31/2014] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Mutations of the Kirsten rat sarcoma viral oncogene (KRAS) gene are known to be important in the pathogenesis of a variety of cancers. Patients with mutant KRAS tumors do not respond to epidermal growth factor receptor (EGFR) inhibitors and fail to benefit from adjuvant chemotherapy. Testing for KRAS mutations is now being recommended as a tailored therapeutic strategy prior to anti-EGFR treatment; however, the low sensitivity of direct sequencing frequently leads to failure of detection of KRAS mutations in clinical samples. DESIGN AND METHODS We developed restriction fragment mass polymorphism (RFMP) assays, to detect KRAS mutations in codons 12, 13, and 61. We performed RFMP analysis for KRAS on DNA isolated from eight different KRAS mutant cell lines and 34 formalin-fixed paraffin-embedded (FFPE) lung cancer tissues. RESULTS Overall, the RFMP assay was in good concordance with direct sequencing analysis in the detection of KRAS mutations. By using dilutions of KRAS mutant DNA in wild type DNA from mutation cell lines with a known KRAS status, we confirmed that the RFMP assay has a higher analytical sensitivity, requiring only 3% of cells in a sample to have mutant alleles, compared to direct sequencing, which had a detection threshold of ~25%. In the FFPE samples, RFMP successfully detected KRAS genotypes in codons 12, 13, and 61. CONCLUSION The RFMP might be efficiently applicable for the detection of KRAS mutations in a clinical setting, particularly for tumor samples containing abundant non-neoplastic cells.
Collapse
Affiliation(s)
- Hee Sook Choi
- Research and Development Center, GeneMatrix Inc., Seongnam, South Korea
| | - Kyung Tae Min
- Research and Development Center, GeneMatrix Inc., Seongnam, South Korea
| | - Yoon Seok Cha
- Research and Development Center, GeneMatrix Inc., Seongnam, South Korea
| | - Sun Pyo Hong
- Research and Development Center, GeneMatrix Inc., Seongnam, South Korea.
| |
Collapse
|
|
8
|
Epidemiology and treatment of hepatitis C genotypes 5 and 6. CANADIAN JOURNAL OF GASTROENTEROLOGY = JOURNAL CANADIEN DE GASTROENTEROLOGIE 2014; 27:e8-12. [PMID: 23378985 DOI: 10.1155/2013/624986] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chronic hepatitis C infection is a major global health problem. The WHO estimates the number of infected people worldwide to be approximately 170 million. The estimated number of hepatitis C virus (HCV)-infected people in Canada is approximately 250,000, with approximately 5000 Canadians newly infected each year. Based on the identification of genomic differences, HCV has been classified into six genotypes; genotype may influence the outcome of antiviral therapy. HCV genotypes 1, 2 and 3 are widely distributed throughout the world and have been the focus of the majority of epidemiological, natural course and treatment studies. Although HCV genotypes 5 and 6 are prevalent in certain geographical areas, they are studied less extensively. HCV genotypes 5 and 6 are uncommon in Canada and account for less than 5% of HCV-infected Canadians. However, immigration and travel can alter the epidemiology of these uncommon genotypes. The present article reviews and summarizes the available data regarding the epidemiology and treatment of HCV genotypes 5 and 6. Genotype 5 is endemic in the northern part of South Africa while genotype 6 is reported primarily in Asia. Available data show that 48 weeks of treatment with a combination of pegylated interferon and ribavirin lead to a higher sustained virological response compared with HCV genotypes 1 and 4. None of the approved direct-acting antiviral agents is currently recommended for the treatment of HCV genotypes 5 or 6.
Collapse
|
|
9
|
Ahn SH, Chun JY, Shin SK, Park JY, Yoo W, Hong SP, Kim SO, Han KH. Performance evaluation of the HepB Typer-Entecavir kit for detection of entecavir resistance mutations in chronic hepatitis B. Clin Mol Hepatol 2014; 19:399-408. [PMID: 24459645 PMCID: PMC3894440 DOI: 10.3350/cmh.2013.19.4.399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/31/2013] [Accepted: 11/07/2013] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND/AIMS Molecular diagnostic methods have enabled the rapid diagnosis of drug-resistant mutations in hepatitis B virus (HBV) and have reduced both unnecessary therapeutic interventions and medical costs. In this study we evaluated the analytical and clinical performances of the HepB Typer-Entecavir kit (GeneMatrix, Korea) in detecting entecavir-resistance-associated mutations. METHODS The HepB Typer-Entecavir kit was evaluated for its limit of detection, interference, cross-reactivity, and precision using HBV reference standards made by diluting high-titer viral stocks in HBV-negative human serum. The performance of the HepB Typer-Entecavir kit for detecting mutations related to entecavir resistance was compared with direct sequencing for 396 clinical samples from 108 patients. RESULTS Using the reference standards, the detection limit of the HepB Typer-Entecavir kit was found to be as low as 500 copies/mL. No cross-reactivity was observed, and elevated levels of various interfering substances did not adversely affect its analytical performance. The precision test conducted by repetitive analysis of 2,400 replicates with reference standards at various concentrations showed 99.9% agreement (2398/2400). The overall concordance rate between the HepB Typer-Entecavir kit and direct sequencing assays in 396 clinical samples was 99.5%. CONCLUSIONS The HepB Typer-Entecavir kit showed high reliability and precision, and comparable sensitivity and specificity for detecting mutant virus populations in reference and clinical samples in comparison with direct sequencing. Therefore, this assay would be clinically useful in the diagnosis of entecavir-resistance-associated mutations in chronic hepatitis B.
Collapse
Affiliation(s)
- Sang Hoon Ahn
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea. ; Liver Cirrhosis Clinical Research Center, Seoul, Korea. ; Brain Korea 21 Project for Medical Science, Seoul, Korea
| | - Ji-Yong Chun
- Research and Development Center, GeneMatrix Inc., Seongnam, Korea
| | - Soo-Kyung Shin
- Research and Development Center, GeneMatrix Inc., Seongnam, Korea
| | - Jun Yong Park
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea. ; Liver Cirrhosis Clinical Research Center, Seoul, Korea
| | - Wangdon Yoo
- Research and Development Center, GeneMatrix Inc., Seongnam, Korea
| | - Sun Pyo Hong
- Research and Development Center, GeneMatrix Inc., Seongnam, Korea
| | - Soo-Ok Kim
- Research and Development Center, GeneMatrix Inc., Seongnam, Korea
| | - Kwang-Hyub Han
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea. ; Liver Cirrhosis Clinical Research Center, Seoul, Korea. ; Brain Korea 21 Project for Medical Science, Seoul, Korea
| |
Collapse
|
|
10
|
Cobo F. Application of maldi-tof mass spectrometry in clinical virology: a review. Open Virol J 2013; 7:84-90. [PMID: 24222805 PMCID: PMC3821086 DOI: 10.2174/1874357920130927003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 01/05/2023] Open
Abstract
MALDI-TOF mass spectrometry is a diagnostic tool of microbial identification and characterization based on the detection of the mass of molecules. In the majority of clinical laboratories, this technology is currently being used mainly for bacterial diagnosis, but several approaches in the field of virology have been investigated. The introduction of this technology in clinical virology will improve the diagnosis of infections produced by viruses but also the discovery of mutations and variants of these microorganisms as well as the detection of antiviral resistance. This review is focused on the main current applications of MALDI-TOF MS techniques in clinical virology showing the state of the art with respect to this exciting new technology.
Collapse
Affiliation(s)
- Fernando Cobo
- Section of Microbiology (Integrated Biotechnology Area), Hospital de Poniente. El Ejido, Almería, Spain
| |
Collapse
|
|
11
|
Heo NY, Lim YS, Lee HC, Lee YS, Kim KM, Byun KS, Han KH, Lee KS, Paik SW, Yoon SK, Suh DJ. High effectiveness of peginterferon alfa-2a plus ribavirin therapy in Korean patients with chronic hepatitis C in clinical practice. Clin Mol Hepatol 2013; 19:60-9. [PMID: 23593611 PMCID: PMC3622857 DOI: 10.3350/cmh.2013.19.1.60] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/27/2012] [Accepted: 01/10/2013] [Indexed: 02/07/2023] Open
Abstract
Background/Aims Identifying the impact of a patient's ethnicity on treatment responses in clinical practice may assist in providing individualized treatment regimens for chronic hepatitis C (CHC). The effectiveness of standard peginterferon plus ribavirin therapy and the need for triple combination therapy with protease inhibitors in Koreans remain matters of debate. These issues were investigated in the present study. Methods The clinical data of 272 treatment-naïve Korean CHC patients who were treated in a community-based clinical trial (Clinical Trial group; n=51) and in clinical practice (Cohort group; n=221), were analyzed and compared. All were treated with standard protocols of peginterferon alfa-2a plus ribavirin therapy. Results For patients with hepatitis C virus (HCV) genotype 1, the sustained virological response (SVR) rates in the Clinical Trial and Cohort groups were 81% (21/26) and 55% (58/106), respectively, by intention-to-treat (ITT) analysis (P=0.02), and 100% (13/13) and 80% (32/40), respectively, in treatment-adherent patients (P=0.18). For patients with HCV genotype 2, the SVR rates in these two groups were 96% (24/25) and 88% (101/115), respectively, by ITT analysis (P=0.31). Adherence and treatment duration were independent predictors of SVR for genotypes 1 and 2, respectively (P<0.01 for each). Korean patients with CHC achieved high SVR rates with peginterferon alfa-2a plus ribavirin in both the clinical trial and clinical practice settings. Conclusions Measures to raise adherence to standard therapy in clinical practice may improve the SVR rates in these patients as effectively as adding protease inhibitors, thus obviating the need for the latter.
Collapse
Affiliation(s)
- Nae-Yun Heo
- Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
12
|
Lee JH, Hachiya A, Shin SK, Lee J, Gatanaga H, Oka S, Kirby KA, Ong YT, Sarafianos SG, Folk WR, Yoo W, Hong SP, Kim SO. Restriction fragment mass polymorphism (RFMP) analysis based on MALDI-TOF mass spectrometry for detecting antiretroviral resistance in HIV-1 infected patients. Clin Microbiol Infect 2013; 19:E263-70. [PMID: 23480551 DOI: 10.1111/1469-0691.12167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 01/04/2013] [Accepted: 01/15/2013] [Indexed: 02/07/2023]
Abstract
Viral genotype assessment is important for effective clinical management of HIV-1 infected patients, especially when access and/or adherence to antiretroviral treatment is reduced. In this study, we describe development of a matrix-assisted laser desorption/ionization-time of flight mass spectrometry-based viral genotyping assay, termed restriction fragment mass polymorphism (RFMP). This assay is suitable for sensitive, specific and high-throughput detection of multiple drug-resistant HIV-1 variants. One hundred serum samples from 60 HIV-1-infected patients previously exposed to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) were analysed for the presence of drug-resistant viruses using the RFMP and direct sequencing assays. Probit analysis predicted a detection limit of 223.02 copies/mL for the RFMP assay and 1268.11 copies/mL for the direct sequencing assays using HIV-1 RNA Positive Quality Control Series. The concordance rates between the RFMP and direct sequencing assays for the examined codons were 97% (K65R), 97% (T69Ins/D), 97% (L74VI), 97% (K103N), 96% (V106AM), 97% (Q151M), 97% (Y181C), 97% (M184VI) and 94% (T215YF) in the reverse transcriptase coding region, and 100% (D30N), 100% (M46I), 100% (G48V), 100% (I50V), 100% (I54LS), 99% (V82A), 99% (I84V) and 100% (L90M) in the protease coding region. Defined mixtures were consistently and accurately identified by RFMP at 5% relative concentration of mutant to wild-type virus while at 20% or greater by direct sequencing. The RFMP assay based on mass spectrometry proved to be sensitive, accurate and reliable for monitoring the emergence and early detection of HIV-1 genotypic variants that lead to drug resistance.
Collapse
Affiliation(s)
- J-H Lee
- Research and Development Center, GeneMatrix Inc, Seongnam, South Korea
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
13
|
Evaluation of two hepatitis C virus genotyping assays based on the 5' untranslated region (UTR): the limitations of 5' UTR-based assays and the need for a supplementary sequencing-based approach. J Clin Microbiol 2012; 50:3741-3. [PMID: 22915605 DOI: 10.1128/jcm.02034-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We evaluated two genotyping methodologies that characterize the 5' untranslated region (5' UTR) of the hepatitis C virus (HCV) genome. The limitations of these genotype assays need to be thoroughly evaluated, and sequencing-based approaches may be needed to complement these methods in clinical settings.
Collapse
|
|
14
|
Ho YP, Reddy PM. Advances in mass spectrometry for the identification of pathogens. MASS SPECTROMETRY REVIEWS 2011; 30:1203-24. [PMID: 21557290 PMCID: PMC7168406 DOI: 10.1002/mas.20320] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 08/06/2010] [Accepted: 08/06/2010] [Indexed: 05/25/2023]
Abstract
Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.
Collapse
Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan.
| | | |
Collapse
|
|
15
|
Zhou YQ, Wang XH, Hong GH, Zhu Y, Zhang XQ, Hu YJ, Mao Q. Twenty-four weeks of pegylated interferon plus ribavirin effectively treat patients with HCV genotype 6a. J Viral Hepat 2011; 18:595-600. [PMID: 21105968 DOI: 10.1111/j.1365-2893.2010.01373.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The optimal duration of treatment and expected response rate for hepatitis C virus genotype (HCV-6)-infected patients have not been determined. Our aims were to determine the treatment outcome with pegylated interferon (PEG-IFN) plus ribavirin for HCV-6a-infected patients at Southwest Hospital and assess the association of the on-treatment virological response with the sustained virological response (SVR). Medical records were reviewed retrospectively. Twenty-two HCV-6a-infected patients were treated for 24 weeks, and 21 (95.5%) achieved an early virological response (EVR), 20 (90.9%) an end-of-treatment response (ETR) and 18 (81.8%) a SVR. However, only 18 of the 22 HCV-6a-infected patients were tested for serum HCV RNA level at week 4 of treatment and 15 (83.3%) achieved a rapid virological response (RVR). The rates of SVR, RVR, EVR and ETR in these patients were all similar to those in HCV-2/3 treated for 24 weeks and higher than those in HCV-1b-infected patients treated for 48 weeks. A lower relapse rate (10.0%) was seen in HCV-6a compared with HCV-2/3 (12.5%) or HCV-1b-infected patients (23.3%). The positive predictive values of RVR and EVR for HCV-6a were comparable with those for HCV-2/3-infected patients (86.7%vs 90.9%, P = 0.683 and 85.7%vs 86.8%, P = 0.904, respectively). Of the 3 HCV-6a-infected patients who did not achieve a RVR, 2 achieved an EVR and went on to achieve a SVR. The patient who did not achieve an EVR did not achieve a SVR. In summary, our results indicate that 24 weeks of PEG-IFN plus ribavirin can effectively treat patients with HCV-6a chronic infection.
Collapse
Affiliation(s)
- Y Q Zhou
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University of Chinese People's Liberation Army, Chongqing, China
| | | | | | | | | | | | | |
Collapse
|
|
16
|
Han KH, Hong SP, Choi SH, Shin SK, Cho SW, Ahn SH, Hahn JS, Kim SO. Comparison of multiplex restriction fragment mass polymorphism and sequencing analyses for detecting entecavir resistance in chronic hepatitis B. Antivir Ther 2011; 16:77-87. [PMID: 21311111 DOI: 10.3851/imp1702] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Drug resistance is a major limitation to the long-term efficacy of controlling chronic hepatitis B (CHB). There is a growing need to analyse multiple mutations associated with drug resistance because sequential or combinational use of antivirals is increasingly being used in treatment. In this study, we introduced a multiplex restriction fragment mass polymorphism (RFMP) assay for detecting mutations conferring entecavir and lamivudine resistance, and compared its performance with direct or clonal sequencing assays. METHODS Multiplex PCR was performed with mixed primers designed to interrogate rt184, rt202, rt204 and rt250. The PCR products were digested with restriction enzymes and the resulting fragments were analysed by mass spectrometry. A total of 251 serum samples, taken serially from 45 patients who received entecavir treatment after confirmed diagnosis of lamivudine resistance and inadequate adefovir dipivoxil response, were analysed by the multiplex RFMP assay. RESULTS The multiplex RFMP assay correctly identified known viral sequences with sufficient analytical sensitivity to detect as few as 100 IU/ml of HBV and with superior ability to determine haplotypes composed of neighbouring variations. Complex mutational patterns and relative abundances determined by multiplex RFMP assay were in good concordance with results obtained by direct or clonal sequencing analyses. Defined mixtures were successfully and consistently identified at 2% relative concentration of mutant versus wild-type virus by the assay. CONCLUSIONS The multiplex RFMP assay is an accurate and sensitive means to detect entecavir and lamivudine resistance mutations, simultaneously. The method is expected to enable early and efficient diagnosis of multiple drug resistance mutations for optimal management of CHB.
Collapse
Affiliation(s)
- Kyung Ho Han
- National Institute of Food and Drug Safety Evaluation, Korea Food and Drug Administration, Seoul, South Korea
| | | | | | | | | | | | | | | |
Collapse
|
|
17
|
Meyer K, Ueland PM. Use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for multiplex genotyping. Adv Clin Chem 2011; 53:1-29. [PMID: 21404912 DOI: 10.1016/b978-0-12-385855-9.00001-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
After completion of the human genome project, the focus of geneticists has shifted to elucidation of gene function and genetic diversity to understand the mechanisms of complex diseases or variation of patient response in drug treatment. In the past decade, many different genotyping techniques have been described for the detection of single-nucleotide polymorphisms (SNPs) and other common polymorphic variants. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is among the most powerful and widely used genotyping technologies. The method offers great flexibility in assay design and enables highly accurate genotyping at high sample throughput. Different strategies for allele discrimination and quantification have been combined with MALDI (hybridization, ligation, cleavage, and primer extension). Approaches based on primer extension have become the most popular applications. This combination enables rapid and reliable multiplexing of SNPs and other common variants, and makes MALDI-TOF-MS well suited for large-scale studies in fine-mapping and verification of genome-wide scans. In contrast to standard genotyping, more demanding approaches have enabled genotyping of DNA pools, molecular haplotyping or the detection of free circulating DNA for prenatal or cancer diagnostics. In addition, MALDI can also be used in novel applications as DNA methylation analysis, expression profiling, and resequencing. This review gives an introduction to multiplex genotyping by MALDI-MS and will focus on the latest developments of this technology.
Collapse
|
|
18
|
Lim YS. Current status of liver disease in Korea: hepatitis C. THE KOREAN JOURNAL OF HEPATOLOGY 2010; 15 Suppl 6:S25-8. [PMID: 20037276 DOI: 10.3350/kjhep.2009.15.s6.s25] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Chronic hepatitis C (CHC) is the third most common cause of chronic liver disease and hepatocellular carcinoma (HCC) in Korea, following hepatitis B virus (HBV) infection and alcohol. HCV prevalence among Koreans older than 40 years of age has been estimated to be 1.29%. The prevalence of CHC increases with age, with the peak prevalence at the age of 60 or older. Blood transfusions have generated no risk of HCV infection since April 1991, when routine screening for anti-HCV in blood donors was adopted in Korea. Although injection drug use seems to be one of the most important risk factors of HCV infection among young adults in urban areas, the majority of CHC patients are not associated with injection drug use. Exposure to acupuncture was identified as a significant risk factor among older adults in rural areas. The mean age of patients with HCV-related cirrhosis and HCC was consistently about 10 years above that of patients associated with HBV. Genotypes 1b and 2a are the two most common types with almost equal proportions, and other genotypes are extremely rare. Korean patients with CHC have a high likelihood of responding to combination therapy with pegylated interferon and ribavirin, with a sustained virological response rate of 60-70% in patients with genotype 1 and 85-90% in those with genotype 2.
Collapse
Affiliation(s)
- Young Suk Lim
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| |
Collapse
|
|
19
|
Abstract
BACKGROUND Mass spectrometry (MS) is a suitable technology for microorganism identification and characterization. CONTENT This review summarizes the MS-based methods currently used for the analyses of pathogens. Direct analysis of whole pathogenic microbial cells using MS without sample fractionation reveals specific biomarkers for taxonomy and provides rapid and high-throughput capabilities. MS coupled with various chromatography- and affinity-based techniques simplifies the complexity of the signals of the microbial biomarkers and provides more accurate results. Affinity-based methods, including those employing nanotechnology, can be used to concentrate traces of target microorganisms from sample solutions and, thereby, improve detection limits. Approaches combining amplification of nucleic acid targets from pathogens with MS-based detection are alternatives to biomarker analyses. Many data analysis methods, including multivariate analysis and bioinformatics approaches, have been developed for microbial identification. The review concludes with some current clinical applications of MS in the identification and typing of infectious microorganisms, as well as some perspectives. SUMMARY Advances in instrumentation (separation and mass analysis), ionization techniques, and biological methodologies will all enhance the capabilities of MS for the analysis of pathogens.
Collapse
Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan.
| | | |
Collapse
|
|
20
|
CS-SELEX generates high-affinity ssDNA aptamers as molecular probes for hepatitis C virus envelope glycoprotein E2. PLoS One 2009; 4:e8142. [PMID: 19997645 PMCID: PMC2780912 DOI: 10.1371/journal.pone.0008142] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2009] [Accepted: 10/29/2009] [Indexed: 01/03/2023] Open
Abstract
Currently, the development of effective diagnostic reagents as well as treatments against Hepatitis C virus (HCV) remains a high priority. In this study, we have described the development of an alive cell surface -Systematic Evolution of Ligands by Exponential Enrichment (CS-SELEX) technique and screened the functional ssDNA aptamers that specifically bound to HCV envelope surface glycoprotein E2. Through 13 rounds of selection, the CS-SELEX generated high-affinity ssDNA aptamers, and the selected ssDNA aptamer ZE2 demonstrated the highest specificity and affinity to E2-positive cells. HCV particles could be specifically captured and diagnosed using the aptamer ZE2. A good correlation was observed in HCV patients between HCV E2 antigen-aptamer assay and assays for HCV RNA quantities or HCV antibody detection. Moreover, the selected aptamers, especially ZE2, could competitively inhibit E2 protein binding to CD81, an important HCV receptor, and significantly block HCV cell culture (HCVcc) infection of human hepatocytes (Huh7.5.1) in vitro. Our data demonstrate that the newly selected ssDNA aptamers, especially aptamer ZE2, hold great promise for developing new molecular probes, as an early diagnostic reagent for HCV surface antigen, or a therapeutic drug specifically for HCV.
Collapse
|
|
21
|
Molecular and Contextual Markers of Hepatitis C Virus and Drug Abuse. Mol Diagn Ther 2009. [DOI: 10.1007/bf03256323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
|
22
|
Shapshak P, Somboonwit C, Drumright LN, Frost SDW, Commins D, Tellinghuisen TL, Scott WK, Duncan R, McCoy C, Page JB, Giunta B, Fernandez F, Singer E, Levine A, Minagar A, Oluwadara O, Kotila T, Chiappelli F, Sinnott JT. Molecular and contextual markers of hepatitis C virus and drug abuse. Mol Diagn Ther 2009; 13:153-79. [PMID: 19650670 PMCID: PMC4447498 DOI: 10.2165/01250444-200913030-00002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The spread of hepatitis C virus (HCV) infection involves a complex interplay of social risks, and molecular factors of both virus and host. Injection drug abuse is the most powerful risk factor for HCV infection, followed by sexual transmission and additional non-injection drug abuse factors such as co-infection with other viruses and barriers to treatment. It is clearly important to understand the wider context in which the factors related to HCV infection occur. This understanding is required for a comprehensive approach leading to the successful prevention, diagnosis, and treatment of HCV. An additional consideration is that current treatments and advanced molecular methods are generally unavailable to socially disadvantaged patients. Thus, the recognition of behavioral/social, viral, and host factors as components of an integrated approach to HCV is important to help this vulnerable group. Equally important, this approach is key to the development of personalized patient treatment - a significant goal in global healthcare. In this review, we discuss recent findings concerning the impact of drug abuse, epidemiology, social behavior, virology, immunopathology, and genetics on HCV infection and the course of disease.
Collapse
Affiliation(s)
- Paul Shapshak
- Division of Infectious Disease and International Medicine, Department of Internal Medicine, Tampa General Hospital, University of South Florida, College of Medicine, Tampa, Florida, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|