1
|
Mei X, Zou J, Shi B, Qian Z, Yi Z. High-Resolution Genomic Profiling of a Genotype 3b Hepatitis C Virus from a Flare of an Occult Hepatitis Patient with Acute-on-Chronic Liver Failure. Viruses 2023; 15:v15030634. [PMID: 36992343 PMCID: PMC10059314 DOI: 10.3390/v15030634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
Acute-on-chronic liver failure (ACLF) is defined as a syndrome of acutely decompensated cirrhosis in patients with chronic liver disease (CLD). Here we report an ACLF case caused by a flare of occult hepatitis C infection. This patient was infected with hepatitis C virus (HCV) more than a decade ago and hospitalized due to alcohol-associated CLD. Upon admission, the HCV RNA in the serum was negative and the anti-HCV antibody was positive, whereas the viral RNA in the plasma dramatically increased during hospitalization, which suggests an occult hepatitis C infection. Overlapped fragments encompassing the nearly whole HCV viral genome were amplified, cloned, and sequenced. Phylogenetic analysis indicated an HCV genotype 3b strain. Sanger sequencing to 10-fold coverage of the 9.4-kb nearly whole genome reveals high diversity of viral quasispecies, an indicator of chronic infection. Inherent resistance-associated substitutions (RASs) in the NS3 and NS5A but not in the NS5B regions were identified. The patient developed liver failure and accepted liver transplantation, followed by direct-acting antiviral (DAA) treatment. The hepatitis C was cured by the DAA treatment despite the existence of RASs. Thus, care should be taken for occult hepatitis C in patients with alcoholic cirrhosis. The analysis of viral genetic diversity may help to identify an occult hepatitis C virus infection and predict the efficacy of anti-viral treatment.
Collapse
Affiliation(s)
- Xue Mei
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jingyi Zou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Bisheng Shi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhiping Qian
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhigang Yi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
- Correspondence:
| |
Collapse
|
2
|
Mane A, Kasibhatla SM, Vidhate P, Saxena V, Patil S, Rao A, Nirmalkar A, Kulkarni-Kale U, Panda S. Phylogenetic Analysis of Spread of Hepatitis C Virus Identified during HIV Outbreak Investigation, Unnao, India. Emerg Infect Dis 2022; 28:725-733. [PMID: 35318918 PMCID: PMC8962895 DOI: 10.3201/eid2804.211845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
An HIV outbreak investigation during 2017–2018 in Unnao District, Uttar Pradesh, India, unearthed high prevalence of hepatitis C virus (HCV) antibodies among the study participants. We investigated these HCV infections by analyzing NS5B and core regions. We observed no correlation between HIV–HCV viral loads and clustering of HCV sequences, regardless of HIV serostatus. All HCV isolates belonged to genotype 3a. Monophyletic clustering of isolates in NS5B phylogeny indicates emergence of the outbreak from a single isolate or its closely related descendants. The nucleotide substitution rate for NS5B was 6 × 10−3 and for core was 2 × 10−3 substitutions/site/year. Estimated time to most recent common ancestor of these isolates was 2012, aligning with the timeline of this outbreak, which might be attributable to unsafe injection practices while seeking healthcare. HIV–HCV co-infection underlines the need for integrated testing, surveillance, strengthening of healthcare systems, community empowerment, and molecular analyses as pragmatic public health tools.
Collapse
|
3
|
Chatterjee K, Kalita D, Omar BJ, Gupta R, Jha MK, Gupta P. Hepatitis C virus subtyping in Uttarakhand, India: a comparative study. Virusdisease 2021; 32:576-581. [PMID: 34631982 DOI: 10.1007/s13337-021-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
The objective of this study was to compare Reverse Hybridisation Assay with conventional sequencing for determination of Hepatitis C Virus Genotype and Subtypes. Anti-HCV antibody was determined followed by HCV RNA extraction which was used for (1) viral load determination (2) qualitative real-time PCR RHA for genotyping and (3) conventional sequencing. Compared to conventional sequencing, accuracy of RHA results was 96.55% for determination of genotype (κ = 0.93) and 89.66% for subtype (κ = 0.85). Sensitivity, specificity, negative predictive value (NPV) and positive predictive value (PPV) of the qualitative PCR were 82.29%, 100%, 44.44% and 100% respectively with an accuracy of 86.84%. RHA is a less time consuming and cheaper method for determination of HCV genotype and subtype yet results must be interpreted with caution and quality control monitoring should be strictly followed to ensure validity. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-021-00729-9.
Collapse
Affiliation(s)
- Kuhu Chatterjee
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India
| | - Deepjyoti Kalita
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India
| | - Rohit Gupta
- Department of Gastroenterology, All India Institute of Medical Sciences, Rishikesh, India
| | - Mithilesh Kumar Jha
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India.,Department of Microbiology, All India Institute of Medical Sciences, Patna, India
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203 Uttarakhand India
| |
Collapse
|
4
|
Chatterjee K, Gupta R, Omar BJ, Gupta P, Kalita D. Genotypic distribution of hepatitis C virus in Uttarakhand. Indian J Med Microbiol 2021; 39:479-483. [PMID: 34210508 DOI: 10.1016/j.ijmmb.2021.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/26/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE Hepatitis C virus is a major cause of chronic hepatitis with seven known genotypes. Uttarakhand is a north Indian state in the Sub-Himalayan region where the genotypic distribution of HCV is largely unknown. This study was undertaken in order to assess the pattern of genotype and subtype and understand the risk factors leading to transmission of Hepatitis C virus in this understudied region. METHODS Anti-HCV reactive cases were selected for determination of the circulating genotypes. Viral RNA was confirmed by real-time PCR. Strains were amplified and sequenced using Sanger's methods. Phylogenetic tree was constructed to determine the genotype. RESULTS Genotype 3 was found to be the predominant genotype majority being subtype 3a and 3b followed by genotype 1. Subtypes 3g and genotype 4a were also observed. Major risk factor found was parenteral injection therapy from unregistered medical practitioners for minor ailments. CONCLUSIONS Findings of our study will help in tailoring management and prevention protocols for HCV for the people of this region.
Collapse
Affiliation(s)
- Kuhu Chatterjee
- Dept. of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Rohit Gupta
- Dept. of Gastroenterology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Balram Ji Omar
- Dept. of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Pratima Gupta
- Dept. of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Deepjyoti Kalita
- Dept. of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India.
| |
Collapse
|
5
|
Solomon SS, Boon D, Saravanan S, Srikrishnan AK, Vasudevan CK, Balakrishnan P, Persaud D, Ray SC, Mehta S, Mehta SH. Diversity of hepatitis C virus infection among HIV-infected people who inject drugs in India. Virusdisease 2019; 30:490-497. [PMID: 31897414 PMCID: PMC6917681 DOI: 10.1007/s13337-019-00553-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/11/2019] [Indexed: 12/14/2022] Open
Abstract
The availability of generic direct acting antivirals (DAAs) for hepatitis C virus (HCV) treatment has prompted many low-and-middle-income countries to launch HCV elimination programs. Because the efficacy of some of these generic DAAs varies by HCV viral subtype, information on subtype distribution can contribute important information to these elimination programs. We conducted a cross-sectional serosurvey to characterize HCV subtype diversity among HIV positive people who inject drugs (PWID) across 14 cities in India. Of 801 HIV positive PWID sampled, 639 tested HCV antibody positive (78.9%). Among 105 samples sequenced, genotype 3 (58.1%) was the most commonly observed followed by genotype 1 (36.2%) and genotype 6 (5.7%). Of the genotype 3 infections, 65% were subtype 3a and 35% were subtype 3b. Of the genotype 1 infections, 94% were subtype 1a and 6% were subtype 1b. All genotype 6 samples were subtype 6n. There was some variability in genotype diversity depending on geographic region and PWID epidemic stage with greater diversity observed in older PWID epidemics. One sequence, HY018, did not cluster with any known reference sequences in phylogenetic analysis. Nearly 80% of HIV infected PWID across India are co-infected with HCV, and subtype prevalence and genetic diversity varied by region and PWID epidemic stage. HCV elimination programs in India will need to consider HCV subtype.
Collapse
Affiliation(s)
- S. S. Solomon
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- YR Gaitonde Centre for AIDS Research and Education, Chennai, India
| | - D. Boon
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - S. Saravanan
- YR Gaitonde Centre for AIDS Research and Education, Chennai, India
| | | | - C. K. Vasudevan
- YR Gaitonde Centre for AIDS Research and Education, Chennai, India
| | - P. Balakrishnan
- YR Gaitonde Centre for AIDS Research and Education, Chennai, India
| | - D. Persaud
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - S. C. Ray
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - S. Mehta
- Department of Medicine, University of California at San Diego School of Medicine, La Jolla, CA USA
| | - S. H. Mehta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| |
Collapse
|
6
|
Kar SK, Sabat J, Ho LM, Arora R, Dwibedi B. High Prevalence of Hepatitis C Virus Infection in Primitive Tribes of Eastern India and Associated Sociobehavioral Risks for Transmission: A Retrospective Analysis. Health Equity 2019; 3:567-572. [PMID: 31701081 PMCID: PMC6830531 DOI: 10.1089/heq.2019.0005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Purpose: The primitive tribal groups (PTGs) need special attention because of their low population growth: declining population size with high mortality rates. Scanty reports are available on the prevalence of hepatitis C virus (HCV) infection in primitive tribes of the country emphasizing their cultural and social practices associated with transmission of the disease. Methods: The study was conducted on 1765 tribal individuals covering 5 PTGs, namely Lodha, Saora, Khadia, Juanga, and Mankidia, from 6 districts of Odisha. Serum samples were tested for the anti-HCV antibody using commercially available enzyme immunoassays. HCV RNA was detected based on the 5′ NCR region and genotyping was done by direct sequencing of the core region. Potential risk factors for HCV transmission were collected using a questionnaire and subjected to regression analysis through SPSS, version 17.0. Results: Antibody to HCV was detected in 0%, 3.3%, 5.7%, 8.5%, and 13.4% in Saora, Lodha, Khadia, Juanga, and Mankidia tribes, respectively. HCV RNA was detected in 8.6% (11/127) of the samples tested. Genotyping of HCV isolates in all HCV RNA-positive samples revealed genotype 1b. Sharing of razors and shaving by the village barber were found to be significantly (p<0.05) associated with HCV transmission in males, whereas tattooing and multiple injections were found to be significant risk factors for females. Conclusion: This study indicated a high prevalence of HCV infection in Mankidia and Juanga tribes in comparison with the national scenario, which needs public health attention.
Collapse
Affiliation(s)
- Shantanu Kumar Kar
- Directorate of Medical Research, IMS and SUM Hospital, S "O" A University, BBSR, Bhubaneswar, India
| | - Jyotsnamayee Sabat
- Virus Research and Diagnostic Laboratory, Regional Medical Research Centre (ICMR), Bhubaneswar, India
| | - Lal M Ho
- Virus Research and Diagnostic Laboratory, Regional Medical Research Centre (ICMR), Bhubaneswar, India
| | - Rasmi Arora
- Division of Enteric and Communicable Disease, Indian Council of Medical Research, New Delhi, India
| | | |
Collapse
|
7
|
Bhebhe L, Anderson M, Souda S, Choga WT, Zumbika E, Shaver ZM, Mbangiwa T, Phinius BB, Banda CC, Melamu P, Musonda RM, Essex M, Blackard JT, Moyo S, Gaseitsiwe S. Molecular characterization of hepatitis C virus in liver disease patients in Botswana: a retrospective cross-sectional study. BMC Infect Dis 2019; 19:875. [PMID: 31640596 PMCID: PMC6805647 DOI: 10.1186/s12879-019-4514-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background Hepatitis C virus (HCV) infection is a major cause of chronic liver disease globally. Direct acting antivirals (DAAs) have proven effective in curing HCV. However, the current standard of care (SOC) in Botswana remains PEGylated interferon-α (IFN-α) with ribavirin. Several mutations have been reported to confer resistance to interferon-based treatments. Therefore, there is a need to determine HCV genotypes in Botswana, as these data will guide new treatment guidelines and understanding of HCV epidemiology in Botswana. Methods This was a retrospective cross-sectional pilot study utilizing plasma obtained from 55 participants from Princess Marina Hospital in Gaborone, Botswana. The partial core region of HCV was amplified, and genotypes were determined using phylogenetic analysis. Results Four genotype 5a and two genotype 4v sequences were identified. Two significant mutations – K10Q and R70Q – were observed in genotype 5a sequences and have been associated with increased risk of hepatocellular carcinoma (HCC), while R70Q confers resistance to interferon-based treatments. Conclusion Genotypes 5a and 4v are circulating in Botswana. The presence of mutations in genotype 5 suggests that some patients may not respond to IFN-based regimens. The information obtained in this study, in addition to the World health organization (WHO) recommendations, can be utilized by policy makers to implement DAAs as the new SOC for HCV treatment in Botswana.
Collapse
Affiliation(s)
- Lynnette Bhebhe
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Motswedi Anderson
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Sajini Souda
- Department of Pathology, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Edward Zumbika
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Zachary M Shaver
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Tshepiso Mbangiwa
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Bonolo B Phinius
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Chabeni C Banda
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Pinkie Melamu
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Rosemary M Musonda
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jason T Blackard
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana. .,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| |
Collapse
|
8
|
Subgenotyping and genetic variability of hepatitis C virus in Palestine. PLoS One 2019; 14:e0222799. [PMID: 31589628 PMCID: PMC6779298 DOI: 10.1371/journal.pone.0222799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) is a major cause of liver cirrhosis and hepatocellular carcinoma. Genotyping of HCV is crucial for successful therapy. To determine the HCV subgenotypes circulating in Palestine and to study the genetic variability of their core, we collected 84 serum samples which had tested positive for anti-HCV antibodies. Thirty-seven of these samples came from hemodialysis patients. Serum samples were subjected to viral RNA isolation and amplification of the HCV core gene. Thirty-three of the samples (39%) tested positive for HCV RNA. The HCV subgenotypes circulating in Palestine included 1a, 3a, and 4a, detected in 38%, 25%, and 22% of the samples, respectively. Furthermore, subgenotype 1b was present in three samples (9%), while the rare subgenotype 4v was present in two samples (6%). We identified a number of substitutions in the retrieved HCV core sequences, such as HCV 1b substitutions R70Q and M91L, which some studies have associated with hepatocellular carcinoma risk and poor virological response. In contrast to two previous studies reporting that HCV genotype 4 was predominant in the Gaza strip (present in just over 70% of samples), genotype 4 was detected in only 31% of the samples in our current study, whereas genotype 1 and 3 were present in 69% of samples. These differences may relate to the fact that many of our samples came from the West Bank and East Jerusalem. The co-circulation of different HCV genotypes and subgenotypes in Palestine suggests that subgenotyping prior to treatment is crucial in Palestinian patients.
Collapse
|
9
|
Tagnouokam-Ngoupo PA, Ngoufack MN, Kenmoe S, Lissock SF, Amougou-Atsama M, Banai R, Ngono L, Njouom R. Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients. Virol J 2019; 16:101. [PMID: 31399103 PMCID: PMC6688274 DOI: 10.1186/s12985-019-1214-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
Background Current HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients. Methods All plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences. Results A total of 369 samples were received during the study period with high viral load values (median: 930,952 IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p = 0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region. Conclusions We found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1–4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.
Collapse
Affiliation(s)
| | - Marie Nicole Ngoufack
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Sebastien Kenmoe
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Simon Frédéric Lissock
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Marie Amougou-Atsama
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Robert Banai
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Laure Ngono
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Richard Njouom
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon.
| |
Collapse
|
10
|
Nii-Trebi NI, Brown CA, Osei YD, Ampofo WK, Nyarko AK. Core encoding sequences of Hepatitis C virus in Ghanaian blood donors are predominantly mosaics of different genotype 2 strains and cannot distinguish subtypes. BMC Infect Dis 2019; 19:533. [PMID: 31208352 PMCID: PMC6580569 DOI: 10.1186/s12879-019-4155-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/31/2019] [Indexed: 11/10/2022] Open
Abstract
Background Distribution of Hepatitis C virus (HCV) genotypes varies significantly worldwide. Genomic diversity between genotypes has implications for treatment, vaccine development and optimal design of HCV diagnostic assays. Molecular characterization of HCV in different geographical areas is therefore very essential for management and public health control of HCV infection. This study investigated the molecular epidemiology and characteristics of HCV genotypes in healthy individuals in Accra, Ghana. Methods An experimental study was carried out on blood samples obtained from voluntary blood donors. Two hundred samples were initially screened for HCV antibodies and infection was confirmed by RNA detection through RT-PCR of the 5′-untranslated region (5’UTR). The core gene sequences were analysed for HCV genotype determination by genotype-specific PCR; and then by cloning and direct sequencing followed by phylogenetic analysis. The sequences were further analysed in detail by similarity plotting. Results Molecular diagnosis confirmed the presence of HCV RNA in 2 out of 200 (1%) blood donors. Initial genotyping by genotype-specific PCR identified all two infections as subtypes 2a and 2b of genotype 2. Extensive evolutionary and genetic analyses indicated two epidemiological profiles. First, phylogenetic tree topologies clearly showed that, collectively, the core sequences of the Ghanaian HCV isolates belong to a single, distinct genetic group within HCV genotype 2 cluster, with high genetic similarity and rapid sequence variation in a single individual. Second, the sequences are mosaics comprising 2e and other genotype 2 subtype fragments. The analyses underscore a unique and complex HCV genotype 2 core sequence profile of the Ghanaian isolates. Conclusions Analysis of HCV core encoding sequences from Ghanaian blood donors in Accra confirmed predominance of genotype 2 HCV among healthy individuals. However, the isolates could not be classified into subtypes, possibly due to their complex sequence pattern that might suggest high mutability of the prevailing genotype. The core region of Ghanaian HCV therefore may not be suitable for distinguishing subtypes. These findings extend those from previous studies and thus underscore the need to search for subtype-informative region of Ghanaian HCV to elucidate the genetic diversity and factors determining outcome of HCV infections in Ghana.
Collapse
Affiliation(s)
- Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana.
| | - Charles Addoquaye Brown
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Yaa Difie Osei
- Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - William Kwabena Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Alexander Kwadwo Nyarko
- Department of Clinical Pathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.
| |
Collapse
|
11
|
Nikitha S, Sabeena S, Robin S, Hiren D, Prasad V, Aswathyraj S, Devadiga S, Anup J, Arunkumar G. The prevalence of anti-hepatitis C antibody among acute febrile illness cases in Idar Taluk, Gujarat, West India. Indian J Med Microbiol 2019; 37:225-229. [PMID: 31745023 DOI: 10.4103/ijmm.ijmm_19_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Purpose The major cause of chronic hepatitis is infections with hepatitis B virus and hepatitis C virus (HCV) globally. However, there exists sparse epidemiological data regarding the prevalence of HCV infection from India. Methodology We carried out a cross-sectional study to estimate the prevalence of anti-HCV antibody among acute febrile illness cases aged between 1 and 65 years in Idar Taluk, Sabarkantha district, Gujarat state located in West India. A total of 702 serum samples collected from the study area during the year 2017, were screened for anti-hepatitis C IgG by enzyme-linked immunosorbent assay. The serum samples screened positive were then subjected to molecular testing for confirmation. Results Among the 702 study participants screened, 16 cases were reported to be anti-HCV IgG positive with an estimated seroprevalence rate of 2.3% (95% confidence interval: 1.4%-3.7%). Out of the 16 cases, two samples were confirmed positive by molecular testing indicating active infection. When analysed phylogenetically, one strain was genotyped as HCV1b genotype, and the other one was clustered along with HCV3a genotype. Both the patients with hepatitis C infection were observed to be having a probable 1-year survival rate of 100% and a 2-year survival rate of 85% when the Child-Turcotte-Pugh classification was applied. Conclusion The estimated seroprevalence of hepatitis C in Idar Taluk, Sabarkantha district, west India was 2.3%. HCV genotypes 1b and 3a were observed to be circulating in the study area.
Collapse
Affiliation(s)
- Shekara Nikitha
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | - Sudandiradas Robin
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Dodia Hiren
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Varamballi Prasad
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sushama Aswathyraj
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Santhosha Devadiga
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Jayaram Anup
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | |
Collapse
|
12
|
Roy P, Patel A, Lole K, Gupta RM, Kumar A, Hazra S. Prevalence and genotyping pattern of hepatitis C virus among patients on maintenance hemodialysis at five centers in Pune, India. Med J Armed Forces India 2018; 75:74-80. [PMID: 30705482 DOI: 10.1016/j.mjafi.2018.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 08/07/2018] [Indexed: 01/05/2023] Open
Abstract
Background Worldwide prevalence of Hepatitis C virus (HCV) infection hemodialysis (HD) ranges from 1 to 84.6% with serious complications. Assessment of prevalence, risk factors, and genotyping of HCV infection in patient on HD was carried out at Pune, India. Methods A total of 250 patients on HD from five HD centers were recruited and tested for anti-HCV antibody using third-generation enzyme-linked immunosorbent assay (ELISA). Qualitative HCV RNA detection was carried out by nested reverse transcriptase polymerase chain reaction (RT-PCR). Genotyping and sequencing were carried out using the BigDye Terminator cycle sequencing ready reaction kit. Results Mean age of patients was 47.3 years. Forty-seven cases out of a total of 250 were reactor for HCV antibody. Overall prevalence rate was 18.8% ranging from 6.7% to 35.6% in the five centers. Of total, 44.1% of females and 13.5% of males were HCV infected. The mean duration of HD in HCV-infected patients was 6.03 years. Prevalence was higher in patients aged > 5 years on HD with higher number of blood transfusions. Thirty-six cases were positive for HCV RNA. Only one HCV RNA was detected among the 203 anti-HCV negative samples. Discordance between antibody and HCV RNA positivity was noted. Seventeen infected cases had changed dialysis centers four times. Thirteen cases were HBsAg positive, of which six cases were coinfected with HCV. Thirty-seven samples were genotyped. Conclusion The predominant genotype was 1a (54.1%) followed by 1b (43.2%) and 3a (2.7%). Highest prevalence of HCV (35.6%) and intracenter PNI of 99.3% of genotype 1b (84.6%) in center 3 indicates a possible nosocomial transmission.
Collapse
Affiliation(s)
- Partha Roy
- Senior Consultant (Microbiology and Virology), Oncquest Laboratories Ltd, New Delhi 110029, India
| | - Anubha Patel
- Resident, Department of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - Kavita Lole
- Scientist E, National Institute of Virology, Pune 411001, India
| | - R M Gupta
- Commandant, Command Hospital (Northern Command), C/o 56 APO, India
| | - Arun Kumar
- Senior Advisor (Gastroenterology), Command Hospital (Central Command), Lucknow, India
| | - S Hazra
- Resident, Department of Microbiology, Armed Forces Medical College, Pune 411040, India
| |
Collapse
|
13
|
Prakash S, Shukla S, Ramakrishna V, Jain A. Distribution of hepatitis C genotypes in Uttar Pradesh, India; rare genotype 4 detected. J Med Virol 2018; 90:1875-1881. [PMID: 30085356 DOI: 10.1002/jmv.25277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/07/2018] [Indexed: 12/29/2022]
Abstract
AIM The worldwide prevalence of hepatitis C virus infection (HCV) is nearly 150 to 170 million cases. The prevalence of HCV infection in India is estimated to be around 1%. In India HCV genotype (GT)3 is the predominant GT followed by GT1. Our study aims to establish the prevalent GTs/subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. METHODS The study was a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital from September 2014 to April 2017, and was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried out on a stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger's sequencing of the core region. The phylogenetic analysis of 179 HCV strains with a high-quality sequencing data was performed. RESULTS The distributions of prevalent GTs/subtypes as noted in the current study were ( n [%]): GT1a, 101 (25%); GT1b, 12 (2.9%); GT1c, 1 (0.25%); GT3a, 275 (68.07%); GT3b, 9 (2.2%); GT3g, 2 (0.49%); GT3i, 3 (0.74%); and GT4a, 1 (0.24%). HCV GTs GT2, GT5, and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. CONCLUSIONS HCV GTs 3a and 1a are the commonest circulating GTs in Uttar Pradesh, India.
Collapse
Affiliation(s)
- Shantanu Prakash
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Suruchi Shukla
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Vangala Ramakrishna
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| | - Amita Jain
- Virology Research and Diagnostic Laboratory, Department of Microbiology, King George's Medical University, Lucknow, India
| |
Collapse
|
14
|
Patil SR, Datkhile KD, Ghorpade MV, Patil SS, Kakade SV. Seroprevalence, risk factors and genotype distribution for Hepatitis C infection: A study from rural hospital in Maharashtra. Indian J Med Microbiol 2018; 35:563-567. [PMID: 29405150 DOI: 10.4103/ijmm.ijmm_16_96] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND OBJECTIVES Hepatitis C is global health problem affecting a significant portion of the world's population. Available data in Western Maharashtra on seroprevalence, risk factors and genotype distribution are very limited. OBJECTIVES The present study was carried out to estimate the seroprevalence, factors influencing transmission and distribution of genotype of hepatitis C virus (HCV) in a hospital-based population. MATERIALS AND METHODS This was a cross-sectional, hospital-based study. A total of 25193 serum samples were tested for HCV and HBV infection. All samples from HCV antibody-positive patients were subjected for HCV RNA detection and genotype. Chi-square, unpaired t-test, logistic regression analysis was used for statistical analysis. RESULTS The seroprevalence for anti-HCV-Ab was 0.46%. Backward multivariate logistic regression analysis revealed increasing age; alcoholic, blood transfusion and dialysis were significant risk factors. Of 116 patients with HCV, 8 (6.89%) patients had HCV-HBV co-infection. The most common genotype (61.90%) was 3 followed by Genotype 1 (38.09%). CONCLUSIONS In the present study, significant risk factors were a history of blood transfusion, habit of alcohol, dialysis. The prevention of HCV infection can be achieved by screening of blood and blood products and creating awareness about risk factors. Since the efficacy of current and new therapies differ by genotype, genotype study is essential.
Collapse
Affiliation(s)
| | - Kailash D Datkhile
- Department of Molecular Biology and Genetics, Krishna Institute of Medical Sciences, Karad, Maharashtra, India
| | - M V Ghorpade
- Department of Microbiology, Krishna Institute of Medical Sciences, Karad, Maharashtra, India
| | - Supriya Satish Patil
- Department of Community Medicine, Krishna Institute of Medical Sciences, Karad, Maharashtra, India
| | - Satish V Kakade
- Department of Community Medicine, Krishna Institute of Medical Sciences, Karad, Maharashtra, India
| |
Collapse
|
15
|
Abdallah F, Mohamed G, Ibrahim M, El Tarabily M. Effectiveness of Sofosbuvir, Ribavirin and PEG-IFNα-2a in the Treatment of Naïve Egyptian Patients With Chronic Hepatitis C Virus Genotype 4. Am J Med Sci 2017; 355:456-466. [PMID: 29753376 DOI: 10.1016/j.amjms.2017.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 12/23/2017] [Accepted: 12/27/2017] [Indexed: 11/17/2022]
Abstract
BACKGROUND Egypt is one of the largest epidemic areas of hepatitis C virus (HCV) in the world. Its prevalent genotype is 4 with a majority of subtype 4a. In 2013, the Food and Drug Administration approved a new direct-acting antiviral drug (sofosbuvir) to treat patients with chronic HCV infection. In Egypt, the patients are already being treated with sofosbuvir in conjunction with ribavirin and pegylated interferon alfa-2a (PEG-IFNα-2a) for 12 weeks since 2015. The present study was planned to explain the efficacy of this treatment regimen against the HCV genotype 4a in Egyptian patients and its pretreatment predictive factors of virological response. METHODS In this population-based study, serum samples were biochemically analyzed and the HCV RNA levels were quantified. The direct sequencing and bioinformatics analysis were utilized to investigate the mutation of the core protein. RESULTS The sustained virological response (SVR) and non-SVR were 72% and 16% respectively, but the nonvirological response was only 12% following the treatment regimen. The multivariable analysis recognized viral (level of viremia and substitution of aa70) and host-related factors (age, alanine aminotransferase and aspartate aminotransferase levels) affecting the virological response in patients infected with high viral load of HCV 4a. CONCLUSIONS Overall, these results concluded that sofosbuvir with ribavirin and PEG-IFNα-2a are highly efficient in HCV-4a Egyptian patients where a high SVR was achieved (72%). In addition to this, there is a significant association between core protein mutations and treatment outcome predominantly at amino acid position 70 (Arg or Gln).
Collapse
Affiliation(s)
- Fatma Abdallah
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt.
| | - Gehad Mohamed
- Department of Botany (Microbiology), Faculty of Science, Port Said University, Port Said, Egypt
| | - Mohsen Ibrahim
- Department of Botany (Microbiology), Faculty of Science, Port Said University, Port Said, Egypt
| | - Mokhtar El Tarabily
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| |
Collapse
|
16
|
Andre-Garnier E, Besse B, Rodallec A, Ribeyrol O, Ferre V, Luco C, Le Guen L, Bourgeois N, Gournay J, Billaud E, Raffi F, Coste-Burel M, Imbert-Marcille BM. An NS5A single optimized method to determine genotype, subtype and resistance profiles of Hepatitis C strains. PLoS One 2017; 12:e0179562. [PMID: 28727784 PMCID: PMC5519038 DOI: 10.1371/journal.pone.0179562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/30/2017] [Indexed: 02/07/2023] Open
Abstract
The objective was to develop a method of HCV genome sequencing that allowed simultaneous genotyping and NS5A inhibitor resistance profiling. In order to validate the use of a unique RT-PCR for genotypes 1-5, 142 plasma samples from patients infected with HCV were analysed. The NS4B-NS5A partial region was successfully amplified and sequenced in all samples. In parallel, partial NS3 sequences were analyzed obtained for genotyping. Phylogenetic analysis showed concordance of genotypes and subtypes with a bootstrap >95% for each type cluster. NS5A resistance mutations were analyzed using the Geno2pheno [hcv] v0.92 tool and compared to the list of known Resistant Associated Substitutions recently published. In conclusion, this tool allows determination of HCV genotypes, subtypes and identification of NS5A resistance mutations. This single method can be used to detect pre-existing resistance mutations in NS5A before treatment and to check the emergence of resistant viruses while undergoing treatment in major HCV genotypes (G1-5) in the EU and the US.
Collapse
Affiliation(s)
- Elisabeth Andre-Garnier
- Service de Virologie, CHU Nantes, Nantes, France
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France
| | | | | | | | | | | | | | | | - Jérôme Gournay
- Service d’Hépato-gastroentérologie, CHU Nantes, Nantes, France
| | - Eric Billaud
- Service des Maladies Infectieuses et Tropicales, CHU Nantes, Nantes, France
| | - François Raffi
- Service des Maladies Infectieuses et Tropicales, CHU Nantes, Nantes, France
| | | | - Berthe-Marie Imbert-Marcille
- Service de Virologie, CHU Nantes, Nantes, France
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France
| |
Collapse
|
17
|
Mehta R, Kabrawala M, Nandwani S, Tekriwal R, Nandania P. Early Experience of Sofosbuvir based Combination Therapy in "Real-Life" Cohort with Chronic Hepatitis-C Infection. J Clin Diagn Res 2017; 11:OC05-OC08. [PMID: 28511425 DOI: 10.7860/jcdr/2017/23184.9335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 10/21/2016] [Indexed: 12/18/2022]
Abstract
INTRODUCTION There is scarcity of data in literature regarding the treatment response with Sofosbuvir (SOF) based therapy in Indian patients with chronic Hepatitis-C Virus (HCV) infection. AIM This study was designed to observe initial treatment response to SOF based therapy in a "real-life" cohort of Indian patients with HCV infection. MATERIALS AND METHODS This is a prospective, observational and single center study. A total of 107 patients who were diagnosed with chronic HCV infection and received SOF based treatment between March 2015 and December 2015 were included. The patients were treated with either triple drug regimen [SOF, Ribavirin (RBV) and Pegylated Interferon-α (Peg IFN-α)] or dual drug regimen (SOF and RBV) for either 12 or 24 weeks. The virological responses were obtained at baseline and thereafter weekly (up to four weeks) till viral load became undetected during treatment. RESULTS A total of 107 patients who received SOF based therapy for chronic HCV infection were included in the study. Mean age of the patients was 48.7±10.7 years. Among included patients, 24 (22.4%) patients were treatment-experienced. Majority of the patients (n=69; 64.5%) were infected with HCV genotype-3. Except one patient, all the included patients achieved virological response up to week-4 of the treatment. There was statistically insignificant association between virological response (up to four week of the treatment) and severity of the disease (cirrhosis and non-cirrhosis) or treatment status (treatment-naïve and treatment-experienced), or HCV genotype (genotype-1 and 3). CONCLUSION The results of this observational study demonstrated rapid initial virological response of SOF based therapy in "real-life" cohort of Indian patients with chronic HCV infection. However, long-term follow-up data are needed to ensure the sustained antiviral efficacy of SOF based therapy.
Collapse
Affiliation(s)
- Rajiv Mehta
- Consultant Gastroenterologist, Department of Gastroenterology, Surat Institute of Digestive Sciences (SIDS), Surat, Gujarat, India
| | - Mayank Kabrawala
- Consultant Gastroenterologist, Department of Gastroenterology, Surat Institute of Digestive Sciences (SIDS), Surat, Gujarat, India
| | - Subhash Nandwani
- Consultant Gastroenterologist, Department of Gastroenterology, Surat Institute of Digestive Sciences (SIDS), Surat, Gujarat, India
| | - Rini Tekriwal
- Research Scholar, Department of Physiology, Government College, Surat, Gujarat, India
| | - Payal Nandania
- Research Scholar, Department of Physiology, Government College, Surat, Gujarat, India
| |
Collapse
|
18
|
Ashraf A, Chakravarti A, Roy P, Kar P, Siddiqui O. Frequency of nucleotide sequence variations in the internal ribosome entry site region of hepatitis C virus RNA isolated from responding and non-responding patients with hepatitis C virus genotype 3 infection. Virusdisease 2016; 27:251-259. [PMID: 28466036 PMCID: PMC5394696 DOI: 10.1007/s13337-016-0335-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/27/2016] [Indexed: 01/18/2023] Open
Abstract
Located within 5' untranslated region of HCV RNA is internal ribosome entry site (IRES) which directs cap-independent translation of viral polyprotein. Mutations in IRES sequence have been shown to cause changes in efficiency of protein translation in vitro in few instances. No study has been done to investigate association between frequency of nucleotide sequence variations in IRES region of HCV-3 RNA and response to pegylated interferon-α plus ribavirin therapy. Hence, this study was planned to analyze relationship between frequency of nucleotide sequence variations of HCV-3 IRES region and response to therapy. Twenty-seven HCV-3 patients were studied, of whom 19 responded to therapy and 8 did not. Alanine aminotransferase and aspartate aminotransferase levels were significantly lower in responders compared to non-responders. HCV RNA detection and genotyping was performed by nested-PCR and RFLP respectively. Viral load quantification in pre and post therapy samples was done by real time PCR. The viral load was significantly lower in the patients after treatment as compared to before treatment. HCV IRES region from pre-treatment sera of 27 HCV-3 infected patients was amplified by nested PCR and sequenced. Secondary structure of IRES region of HCV-3 was predicted using the M fold Web Server. Mutational analysis revealed hot spot of mutations in HCV-3 IRES region from 40-80 and 210-280 nucleotides. Though more mutations were found in non-responders as compared to responders, this difference was statistically insignificant. Therefore, in addition to IRES region of HCV-3, some other host and viral factors may contribute to therapy outcome.
Collapse
Affiliation(s)
- Anzar Ashraf
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
| | - Anita Chakravarti
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
- 79, South Park Apartment, Kalkaji, New Delhi, Delhi 110019 India
| | - Priyamvada Roy
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
| | - Premashish Kar
- Department of Medicine, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, Delhi 110002 India
| | - Oves Siddiqui
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
| |
Collapse
|
19
|
Souii A, Elargoubi A, Fallecker C, Mastouri M, Drouet E. Hepatitis C Genotype Prevalence in Monastir Region, Tunisia: Correlation between 5' Untranslated Region (5'UTR), Non-structural 5B (NS5B), and Core Sequences in HCV Subtyping. Curr Microbiol 2016; 73:324-334. [PMID: 27189386 DOI: 10.1007/s00284-016-1064-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/07/2016] [Indexed: 12/23/2022]
Abstract
Hepatitis C virus (HCV) is a causative agent of chronic liver disease, cirrhosis, and hepatocellular carcinoma. It constitutes a major public health around the world. There is no vaccine available against HCV, and current therapies are effective in only small percentage of patients. HCV has wide population-specific genotype variability. Genotype knowledge and viral load assessment are equally important for designing therapeutic strategies. Taking into account that the molecular epidemiology of HCV variants circulating in Tunisia is not yet well elucidated, and that, at present, little is known about the distribution pattern of HCV in Monastir region (Tunisia), we aimed, herein, to evaluate the prevalence of HCV genotypes in Monastir and to identify risk-related factors. For this purpose, 50 anti-HCV antibody-positive cases were diagnosed and subjected to viral RNA extraction, amplification, genotyping, and viral load quantification. Molecular epidemiology was studied by 5' untranslated region (5' UTR) sequencing as compared with the non-structural 5B (NS5B) and core region sequences. Overall concordance between 5' UTR, core, and NS5B sequencing was 100 %. The highest prevalent genotype was 1b (50 %) followed by genotypes 1a (16 %), 4a (12 %), 2a (10 %), 2c (8 %), and 3a (4 %). Interestingly, the subtype 1b had a statistically significant higher viral load than the other genotypes followed by subtype 1a. Based on these data, this study revealed a high prevalence of HCV genotype 1 (subtypes 1b and 1a) compared to other genotypes. A continued monitoring of HCV and knowledge of circulating genotypes could impact on future vaccine formulations.
Collapse
Affiliation(s)
- Amira Souii
- Department of Biotechnology, Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El Manar, 09 Sreet Zouhair Essafi, 1006, Tunis, Tunisia.
| | - Aida Elargoubi
- Laboratory of Microbiology of the University Hospital Center Fattouma Bourguiba of Monastir, Avenue Farhat HACHED, 5000, Monastir, Tunisia
| | - Catherine Fallecker
- Institute of Structural Biology (Ibs), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, Street of Martyrs, 38042, Grenoble, France
| | - Maha Mastouri
- Laboratory of Microbiology of the University Hospital Center Fattouma Bourguiba of Monastir, Avenue Farhat HACHED, 5000, Monastir, Tunisia.,Laboratory of Contagious Diseases and Biologically Active Substances, LR99 - ES27, Faculty of Pharmacy, University of Monastir, Avicenne Street, 5000, Monastir, Tunisia
| | - Emmanuel Drouet
- Institute of Structural Biology (Ibs), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, Street of Martyrs, 38042, Grenoble, France
| |
Collapse
|
20
|
Trimbitas RD, Fayssel N, Serghini FZ, Wakrim L, Khyatti M, Essalhi M, Bellefquih AM, Benani A. Molecular characterization of hepatitis C virus core region in moroccan intravenous drug users. J Med Virol 2016; 88:1376-83. [PMID: 26754854 DOI: 10.1002/jmv.24470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2015] [Indexed: 12/28/2022]
Abstract
Intravenous drug users (IDUs) represent a highly-infected reservoir for Hepatitis C virus (HCV) worldwide, harboring some of the most elevated prevalences and majority of the epidemic in developed nations. Studies aimed at sequencing regions of the viral genome uncovered amino acid mutations, some of which have been implicated in resistance to standard of care pegylated interferon/Ribavirin double therapy. Using the nested PCR method on the Core region of HCV strains in Moroccan IDUs living in the Tangier region this study sought to identify genotype-specific amino acid mutations, followed by Phylogenetic methods in order to compare them with international strains so as to identify sequences of highest homology. Genotyping was confirmed and recombination events excluded by line-probe assay. Italy was found most homologous for genotypes 1a and 3a, Iran for genotype 1a and Egypt for genotype 4a. Amino Acid Mutation analysis revealed the following novel genotype 3a-specific mutations: N16I, L36V, T49A, P71S, T75S, and T110N. The outcome of this work describes the HCV genetic heterogeneity in high-risk intravenous drug users, and it gives clues to the global migratory flow of genotypes as they cross geographical boundaries between various IDU populations and identifies "signature" amino acid mutations traceable to HCV genotype 3a. Identification of key amino acid positions in the HCV Core region with higher rates of mutations paves the way for eventual clinical trials seeking to establish a link between these recurrent mutations and response to standard of care Interferon and Ribavirin antiviral therapy. J. Med. Virol. 88:1376-1383, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
| | - Naouar Fayssel
- Virology Laboratory, Pasteur Institute of Morocco, Casablanca, Morocco
| | | | - Lahcen Wakrim
- Virology Laboratory, Pasteur Institute of Morocco, Casablanca, Morocco
| | - Meriem Khyatti
- Oncovirology Laboratory, Pasteur Institute of Morocco, Casablanca, Morocco
| | | | | | - Abdelouaheb Benani
- Molecular Biology Laboratory, Pasteur Institute of Morocco, Casablanca, Morocco
| |
Collapse
|
21
|
Zhou K, Hu F, Wang C, Xu M, Lan Y, Morano JP, Lemon SM, Tucker JD, Cai W. Genotypic distribution and hepatic fibrosis among HIV/HCV co-infected individuals in Southern China: a retrospective cross-sectional study. BMC Infect Dis 2015; 15:401. [PMID: 26424404 PMCID: PMC4589973 DOI: 10.1186/s12879-015-1135-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 09/21/2015] [Indexed: 02/06/2023] Open
Abstract
Background End-stage liver disease and hepatocellular carcinoma due to hepatitis C virus (HCV) co-infection are increasingly common causes of death among HIV-infected individuals. However, there are few clinical investigations of HIV/HCV co-infected individuals from low and middle-income nations. Here, we compare the epidemiology of HCV-infected and HIV/HCV co-infected individuals in Southern China and examine hepatic fibrosis scores in co-infected individuals. Methods We conducted a retrospective cross-sectional study of treatment-naïve HIV/HCV co-infected and HCV mono-infected subjects. Bivariate and multivariate models were used to examine the association between demographics and HCV genotype. Among co-infected individuals, we also studied the relationship between fibrosis scores derived from non-invasive studies and HCV genotype. Results Data were collected from 175 HCV-infected individuals, including 89 (51 %) HIV/HCV co-infected individuals. HIV/HCV co-infection was correlated with intravenous drug use (AOR 46.25, p < 0.001) and not completing high school (AOR 17.39, p < 0.001) in a multivariate model. HIV/HCV co-infected individuals were more likely to be infected with HCV genotype 6a (p < 0.0001) or 3a (p < 0.023), whereas increased fibrosis (FIB-4 score) was associated with HCV genotype 3a infection (β 2.18, p < 0.001). Discussion Our results suggest that intravenous drug use is driving HIV/HCV co-infection in Southern China. While additional studies are needed, HCV genotype 6a is more common and genotype 3a appears to be associated with more severe hepatic fibrosis in co-infected individuals. Conclusions Future HIV/HCV co-infection research in China should focus on at risk populations, HCV testing uptake, and genotype-specific treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1135-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kali Zhou
- Guangzhou Eighth People's Hospital, Guangzhou, China.
| | - Fengyu Hu
- Guangzhou Eighth People's Hospital, Guangzhou, China.
| | - Charles Wang
- UNC-Project - China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA. .,Department of Medicine, Division of Gastroenterology Providence, Brown University School of Medicine, Rhode Island, USA.
| | - Min Xu
- Guangzhou Eighth People's Hospital, Guangzhou, China.
| | - Yun Lan
- Guangzhou Eighth People's Hospital, Guangzhou, China.
| | - Jamie P Morano
- University of South Florida, Morsani College of Medicine, USF International, Tampa, FL, USA.
| | - Stanley M Lemon
- UNC-Project - China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA. .,Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Joseph D Tucker
- Guangzhou Eighth People's Hospital, Guangzhou, China. .,UNC-Project - China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Weiping Cai
- Guangzhou Eighth People's Hospital, Guangzhou, China.
| |
Collapse
|
22
|
Barusrux S, Sengthong C, Urwijitaroon Y. Epidemiology of hepatitis C virus genotypes in northeastern Thai blood samples. Asian Pac J Cancer Prev 2015; 15:8837-42. [PMID: 25374216 DOI: 10.7314/apjcp.2014.15.20.8837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is an important cause of liver cancer in Thailand. The highest prevalence of anti-HCV positive among Thai blood donors is found in the northeastern region. The present analysis of the genotype distribution among anti-HCV positive northeastern-Thai blood donors was conducted to provide a base for the epidemiological pattern of HCV infection in this region. MATERIALS AND METHODS A total of 112 HCV seropositive healthy blood donors were randomly selected and tested for the presence of HCV-RNA by RT-PCR. HCV-RNA positive samples were genotyped by direct sequencing at core region genomes and confirmed by phylogenetic analysis. RESULTS HCV viremia was found in 94.6% (106/112) of HCV seropositive blood donors. There were 3 major genotypes distributed among this population. HCV genotype 3a was the most prevalent (71.7%) followed by genotypes 1a (7.5%), 1b (7.5%), 6i (3.8%), 6f (2.8%) and 6n (1.9%). CONCLUSIONS HCV genotype 3a in asymptomatic infections in northeastern Thailand is significantly higher than other previous reports. Subgenotype 6 prevalence is less than in neighboring countries and distribution patterns differ. The findings are relevant as predictors for using interferon therapy in this population.
Collapse
Affiliation(s)
- Sahapat Barusrux
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand E-mail :
| | | | | |
Collapse
|
23
|
Athar MA, Xu Y, Xie X, Xu Z, Ahmad V, Hayder Z, Hussain SS, Liao Y, Li Q. Rapid detection of HCV genotyping 1a, 1b, 2a, 3a, 3b and 6a in a single reaction using two-melting temperature codes by a real-time PCR-based assay. J Virol Methods 2015; 222:85-90. [PMID: 26068393 DOI: 10.1016/j.jviromet.2015.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 05/26/2015] [Accepted: 05/26/2015] [Indexed: 12/18/2022]
Abstract
The genotype of the hepatitis C virus (HCV) is an important indicator for antiviral therapeutic response. We hereby described development of a rapid HCV genotyping approach that enabled the identification of the six most common HCV subtypes of Asia, i.e., 1a, 1b, 2a, 3a, 3b, and 6a, in a single reaction. Using two dual-labeled, self-quenched probes that target the core region of the HCV genome, the exact subtype could be accurately identified by two-melting temperature codes determined from the two respective probes in a real-time PCR assay. Analytical sensitivity studies using armored RNA samples representing each of the six HCV subtypes showed that 5 copies/reaction of HCV RNA could be detected. The assay was evaluated using 244 HCV-positive serum samples and the results were compared with sequencing analysis. Of the 224 samples, subtype 3a (127, 52.3%) was the dominant, followed by 1b (51, 20.9%), 3b (47, 19.3%), 2a (8, 3.3%), 6a (4, 1.6%) and the least was subtype 1a (1, 0.4%). Moreover, 6 (2.5%) mixed infection samples were also detected. These results were fully concordant with sequencing analysis. We concluded that this real-time PCR-based assay could provide a rapid and reliable tool for routine HCV genotyping in most Asian countries.
Collapse
Affiliation(s)
- Muhammad Ammar Athar
- The State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Engineering Research Center of Molecular Diagnostics, Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong 518057, China
| | - Ye Xu
- The State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Engineering Research Center of Molecular Diagnostics, Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong 518057, China
| | - Xiaoting Xie
- The State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Engineering Research Center of Molecular Diagnostics, Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhenxing Xu
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen 361005, Fujian, China
| | - Vakil Ahmad
- Division of Health Biotechnology, National Institute for Biotechnology & Genetic Engineering, P.O. Box 577, Faisalabad, Punjab, Pakistan
| | - Zulfiqar Hayder
- Department of Pathology, Quid-e-Azam Medical College, Bahawalpur, Punjab, Pakistan
| | - Syed Sajid Hussain
- Department of Pathology, Quid-e-Azam Medical College, Bahawalpur, Punjab, Pakistan
| | - Yiqun Liao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361005, Fujian, China.
| | - Qingge Li
- The State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Engineering Research Center of Molecular Diagnostics, Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong 518057, China.
| |
Collapse
|
24
|
Caliskan A, Kirisci O, Ozkaya E, Ozden S, Tumer S, Caglar S, Guler SA, Senol H. Distribution and predominance of genotype 3 in hepatitis C virus carriers in the province of kahramanmaras, Turkey. HEPATITIS MONTHLY 2015; 15:e25142. [PMID: 25972903 PMCID: PMC4426333 DOI: 10.5812/hepatmon.15(4)2015.25142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/02/2015] [Accepted: 04/02/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND The hepatitis C virus (HCV) has six major genotypes and more than 100 subtypes, and the determination of the responsible genotype, collection of epidemiological data, tailoring antiviral therapy, and prediction of prognosis have an important place in disease management. OBJECTIVES The aim of the present study was to determine the distribution of HCV genotypes across geographic regions and compare these data with those obtained from other geographic locations. PATIENTS AND METHODS The HCV genotypes were identified in HCV RNA positive blood samples, obtained from different centers. The HCV genotype was determined using molecular methods [Real-Time Polymerase Chain Reaction (RT-PCR)] in 313 patients, who were found to be positive for HCV RNA. The presence of HCV RNA was investigated using the RT-PCR method in serum samples delivered to the Microbiology Laboratory at Kahramanmaras Necip Fazıl City Hospital, Kahramanmaras, Turkey, from the centers located in Kahramanmaras City center and peripheral districts of the province, between March 2010 and August 2014. The HCV genotype analysis was performed in HCV RNA positive samples, using RT-PCR reagents kit. Urine samples from the patients were tested for amphetamine with an Amphetamines II (AMPS2) kit, cocaine was tested with a Cocaine II (COC2) kit, opiates were tested with an Opiates II (OPI2) kit, and cannabinoids were tested with a Cannabinoids II (THC2) kit in Roche/Hitachi Cobas c501 device. RESULTS The blood samples collected from 313 patients were included in the study. Of these patients, 212 (67.7%) were male and 101 (32.3%) were female. The mean age of the patients was 41.29 ± 20.32 years. In terms of HCV genotype distribution, 162 patients (51.7%) had genotype 1, 144 patients (46%) had genotype 3, four patients (1.3%) had genotype 2, and three patients (1%) had genotype 4. The results of urine drug tests were available in only 65 patients (20.2%). Of these, 61 (93.8%) patients had HCV genotype 3. CONCLUSIONS In conclusion, the prevalence of HCV genotype 1 was 51.7%, which was lower than the rates reported in other studies in Turkey, while the prevalence of HCV genotype 3 was 46%, which was remarkably higher than the reported Turkish data. In addition, the prevalence rate for genotype 3 reported in the present study is the highest that has ever been reported in the literature.
Collapse
Affiliation(s)
- Ahmet Caliskan
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Ozlem Kirisci
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Esra Ozkaya
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Sevinc Ozden
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Seray Tumer
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Serkan Caglar
- Department of Medical Biohemistry, Necip Fazıl City Hospital, Kahramanmaras, Turkey
| | - Selma Ates Guler
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sutcu Imam University, Kahramanmaras, Turkey
| | - Hande Senol
- Department of Biostatistics, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| |
Collapse
|
25
|
Maksyutov RA, Gavrilova EV, Maksyutov AZ, Kanev AN. Genotyping of hepatitis B and C virus Russian isolates for reference serum panel construction. J Med Virol 2015; 87:1192-8. [PMID: 25758235 DOI: 10.1002/jmv.24170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 12/18/2022]
Abstract
Approximately 2% and 5% of the world human population is estimated to be infected with HCV and HBV, respectively. Reference panels of HCV and HBV serum samples with defined genotypes and serotypes is necessary for monitoring of the specificity and sensitivity of diagnostic test kits. The aim of this study was to determine genotypes/serotypes of HBV and HCV circulating in Russia in order to construct a panel of reference sera containing these HCV genotypes and HBV serotypes. A total of 343 HBsAg-positive and 207 anti-HCV positive serum samples were collected from patients with HBV and HCV infection from different cities between years 2002 and 2010 in St. Petersburg, Krasnodar, Nizhny Novgorod, Novosibirsk, Barnaul, Gorno-Altaisk, and Khabarovsk. HBV DNA was found in 76.4% of HBsAg positive samples by PCR for the S gene and HCV RNA was found in 71.5, 70.0, and 64.7% of anti-HCV positive samples in the 5'UTR, Core, and NS5B regions, respectively. The prevalence and proportion of HBV genotype/serotype associations were as follows: A/adw2, 2.1%; D/ayw2, 54.0%; D/ayw3, 43.1%; D/adw2, 0.7%. A new combination of genotype D and adw2 serotype was discovered. The distribution of HCV genotypes was the following: 43.6%, b; 3.8%, 2a; and 52.6%, 3a. Russian National reference panels of HBV and HCV lyophilized sera were developed to monitor specificity and sensitivity of approved kits and for the certification of newly developed assays.
Collapse
Affiliation(s)
- Rinat A Maksyutov
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | | | | | | |
Collapse
|
26
|
Esmaeilzadeh A, Erfanmanesh M, Ghasemi S, Mohammadi F. Serological assay and genotyping of hepatitis C virus in infected patients in zanjan province. HEPATITIS MONTHLY 2014; 14:e17323. [PMID: 25368655 PMCID: PMC4214121 DOI: 10.5812/hepatmon.17323] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 02/22/2014] [Accepted: 05/23/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis C Virus (HCV), a public health problem, is an enveloped, single-stranded RNA virus and a member of the Hepacivirus genus of the Flaviviridae family. Liver cancer, cirrhosis, and end-stage liver are the outcomes of chronic infection with HCV. HCV isolates show significant heterogeneity in genetics around the world. Therefore, determining HCV genotypes is a vital step in determining prognosis and planning therapeutic strategies. OBJECTIVES As distribution of HCV genotypes is different in various geographical regions and HCV genotyping of patients has not been investigated in Zanjan City, this study was designed for the first time, to determine HCV genotypes in the region and to promote the impact of the treatment. MATERIALS AND METHODS Serum samples of 136 patients were collected and analyzed for anti-HCV antibodies using ELISA (The enzyme-linked immunosorbent assay) method. Then, positive samples were exposed to RT-PCR, which was performed under standard condition. Afterwards, they investigated for genotyping using allele-specific PCR (AS-PCR), and HCV genotype 2.0 line probe assay (LiPA). RESULTS Samples indicated 216 bp bands on 2% agarose gel. Analyses of the results demonstrated that the most dominant subtype was 3a with frequency of 38.26% in Zanjan Province followed by subtypes of 1b, 1a, 2, and 4 with frequencies of 25.73%, 22.05%, 5.14%, and 4.41%, respectively. The frequency of unknown HCV genotypes was 4.41%. CONCLUSIONS According to the results, it was found that HCV high prevalent genotype in Zanjan is subtype 3a. Analysis of the results provides identification of certain HCV genotypes, and these valuable findings could affect the type and duration of the treatment.
Collapse
Affiliation(s)
- Abdolreza Esmaeilzadeh
- Department of Immunolory, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, IR Iran
- Cancer Gene Therapy Research Center, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, IR Iran
- Corresponding Author: Abdolreza Esmaeilzadeh, Department of Immunology, Zanjan University of Medical Sciences, Mahdavi Blvd., Zanjan, IR Iran. Tel: +98-2433440301, Fax: +98-2433449553, E-mail:
| | - Maryam Erfanmanesh
- Young Researchers Club, Zanjan Branch, Islamic Azad University, Zanjan, IR Iran
| | - Sousan Ghasemi
- Medical Laboratory, Shaheed Beheshti General Hospital, Zanjan University of Medical Sciences, Zanjan, IR Iran
| | - Farzaneh Mohammadi
- Department of Immunolory, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, IR Iran
| |
Collapse
|
27
|
Characterization of hepatitis C virus genotypes by direct sequencing of HCV 5'UTR region of isolates from Saudi Arabia. PLoS One 2014; 9:e103160. [PMID: 25099694 PMCID: PMC4123900 DOI: 10.1371/journal.pone.0103160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 06/26/2014] [Indexed: 01/18/2023] Open
Abstract
The current study was designed to determine the Hepatitis C Virus (HCV) genotypes in a representative sample of HCV chronically infected patients in Saudi Arabia. All HCV isolates were genotyped by sequencing of the 5′UTR region and newly identified HCV isolates were identified. Specific universal primers targeting 5′UTR region were used for both amplification and sequencing of all isolates that resulted in 244 bp fragment which represent about 80% of 5′UTR region. Most of HCV isolates in this study were genotype 4 (76.4%) where only few isolates were recognized as genotype 1 (19.6%). All results were compared to HCV reference sequences from LOS ALAMOS HCV database, considering only the complete full genomes for the main phylogenetic analysis. Sequences that showed maximum identity (98% –100%) were selected. Most isolates were identical with HCV genotype 4 references. Some isolates were similar to different subtypes of HCV genotypes 4, 1 and 6. Phylogenetic analysis showed resemblance of most isolates to similar ones from the Far East, North America and Egypt. Using sequence Weblogo, Alignment analysis of isolated HCV genotypes 4 and 1 showed 92% and 95.5% nucleotide conservation, respectively. There was no predominant nucleotide in the varied sites, in both genotypes. All isolated sequences were submitted to GenBank database.
Collapse
|
28
|
Li C, Lu L, Murphy DG, Negro F, Okamoto H. Origin of hepatitis C virus genotype 3 in Africa as estimated through an evolutionary analysis of the full-length genomes of nine subtypes, including the newly sequenced 3d and 3e. J Gen Virol 2014; 95:1677-1688. [PMID: 24795446 DOI: 10.1099/vir.0.065128-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We characterized the full-length genomes of nine hepatitis C virus genotype 3 (HCV-3) isolates: QC7, QC8, QC9, QC10, QC34, QC88, NE145, NE274 and 811. To the best of our knowledge, NE274 and NE145 were the first full-length genomes for confirming the provisionally assigned subtypes 3d and 3e, respectively, whereas 811 represented the first HCV-3 isolate that had its extreme 3' UTR terminus sequenced. Based on these full-length genomes, together with 42 references representing eight assigned subtypes and an unclassified variant of HCV-3, and 10 sequences of six other genotypes, a timescaled phylogenetic tree was reconstructed after an evolutionary analysis using a coalescent Bayesian procedure. The results indicated that subtypes 3a, 3d and 3e formed a subset with a common ancestor dated to ~202.89 [95% highest posterior density (HPD): 160.11, 264.6] years ago. The analysis of all of the HCV-3 sequences as a single lineage resulted in the dating of the divergence time to ~457.81 (95% HPD: 350.62, 587.53) years ago, whereas the common ancestor of all of the seven HCV genotypes dated to ~780.86 (95% HPD: 592.15, 1021.34) years ago. As subtype 3h and the unclassified variant were relatives, and represented the oldest HCV-3 lineages with origins in Africa and the Middle East, these findings may indicate the ancestral origin of HCV-3 in Africa. We speculate that the ancestral HCV-3 strains may have been brought to South Asia from Africa by land and/or across the sea to result in its indigenous circulation in that region. The spread was estimated to have occurred in the era after Vasco da Gama had completed his expeditions by sailing along the eastern coast of Africa to India. However, before this era, Arabians had practised slave trading from Africa to the Middle East and South Asia for centuries, which may have mediated the earliest spread of HCV-3.
Collapse
Affiliation(s)
- Chunhua Li
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ling Lu
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Donald G Murphy
- Institut national de santé publique du Québec, Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Francesco Negro
- Divisions of Gastroenterology and Hepatology and of Clinical pathology, University Hospitals, Geneva, Switzerland
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| |
Collapse
|
29
|
Ampuero J, Romero-Gómez M, Reddy KR. Review article: HCV genotype 3 – the new treatment challenge. Aliment Pharmacol Ther 2014; 39:686-98. [PMID: 24612116 DOI: 10.1111/apt.12646] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/27/2013] [Accepted: 01/13/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Over the past several years, hepatitis C therapy has been pegylated interferon and ribavirin based. Although protease inhibitor-based therapy has enhanced response rates in genotype 1, the recent advances in therapy have demonstrated a challenge in genotype 3, a highly prevalent infection globally. AIM To provide a comprehensive summary of the literature evaluating the unique characteristics and evolving therapies in genotype 3. METHODS A structured search in PubMed, the Cochrane Library and EMBASE was performed using defined key words, including only full text papers and abstracts in English. RESULTS HCV genotype 3 is more prevalent in Asia and among intra-venous drug users. Furthermore, it interferes with lipid and glucose metabolism, and the natural history involves a more rapid progression of liver disease and a higher incidence of hepatocellular carcinoma (HCC). New therapies with protease inhibitors have focused on genotype 1 largely and have demonstrated enhanced responses, but have limited activity against genotype 3. Thus far, in clinical trials, NS5B and NS5A inhibitors have performed more poorly in genotype 3, while a cyclophilin inhibitor, alisporivir, has shown promise. CONCLUSIONS As treatments for HCV have evolved, genotype 3 has become the most difficult to treat. Furthermore, genotype 3 has special characteristics, such as insulin resistance and alterations in lipid metabolism, which may partly explain the lower treatment responses. A great deal of emphasis on advancing therapy is needed in this population that appears to have a more rapid progression of liver disease and a higher incidence of HCC.
Collapse
|
30
|
Lin KH, Yu HC, Hsu PI, Tsai WL, Chen WC, Lin CK, Chan HH, Tsay FW, Lai KH. Baseline high viral load and unfavorable patterns of alanine aminotransferase change predict virological relapse in patients with chronic hepatitis C genotype 1 or 2 obtaining rapid virological response during antiviral therapy. HEPATITIS MONTHLY 2013; 13:e11892. [PMID: 24348635 PMCID: PMC3842527 DOI: 10.5812/hepatmon.11892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/27/2013] [Accepted: 09/28/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Rapid virological response (RVR) strongly predicts sustained virological response (SVR) in patients with chronic hepatitis C (CHC), and abbreviates antiviral therapy in some patients. OBJECTIVES To identify factors predicting virological relapse (VR) in CHC patients who attained RVR. PATIENTS AND METHODS Medical records of 133 CHC patients with an RVR after completing 24 weeks of antiviral therapy (a combination of pegylated interferon-α and ribavirin) were analyzed. Baseline characteristics and on-treatment responses were compared between the patients with an SVR and those with VR. Patients with normal alanine aminotransferase (ALT) levels at weeks 4 and 12 and at the end-of-treatment (EoT) and patients with elevated, but constantly decreasing, ALT levels were classified as having favorable patterns of ALT change. A trend of increasing ALT levels either between weeks 4 and 12 or between weeks 12 and EoT was classified as unfavorable. A high viral load (HVL) was defined as a baseline HCV RNA ≥ 600000 IU/mL. RESULTS In total, 116 (87.2%) patients had a SVR and 14 (10.5%) had VR. The VR rates were comparable between patients with genotype-1 (13.1%) and genotype-2 infection (8.7%) (P = 0.572). Multivariate analysis revealed that HVL (P = 0.015; odds ratio [OR] = 14.754; 95% confidence interval (CI) = 1.671-130.240), and unfavorable ALT patterns (P = 0.039; OR = 4.397; 95% CI = 1.078-17.930) independently predicted VR. In subgroup analysis, low viral load (LVL) patients had a minimal VR rate (1.8%). Among the HVL patients, the VR rate of those using peg-IFN-α-2a was relatively low (9.1%). Patients using peg-IFN-α-2b had a slightly higher VR rate (23.8%; P = 0.128), and patients with favorable patterns of ALT changes had a lower VR rate (10.3%) compared to the 53.8% in patients with unfavorable ALT patterns (P = 0.005). CONCLUSIONS In southern Taiwan, 24 weeks of antiviral therapy achieved a high SVR rate in patients with CHC attaining RVR, except in the subgroup of patients treated with peg-IFN-α-2b with HVL and on-treatment unfavorable ALT patterns.
Collapse
Affiliation(s)
- Kung-Hung Lin
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Physical Examination Center, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hsien-Chung Yu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Corresponding author: Hsien-Chung Yu, Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan. Tel: +886-73422121, Fax: +886-73468237, E-mail:
| | - Ping-I Hsu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wei-Lun Tsai
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wen-Chi Chen
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chun-Ku Lin
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hoi-Hung Chan
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Fong-Wei Tsay
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Kwok-Hung Lai
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| |
Collapse
|
31
|
Cai Q, Zhao Z, Liu Y, Shao X, Gao Z. Comparison of three different HCV genotyping methods: core, NS5B sequence analysis and line probe assay. Int J Mol Med 2012; 31:347-52. [PMID: 23241873 DOI: 10.3892/ijmm.2012.1209] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 11/12/2012] [Indexed: 12/14/2022] Open
Abstract
To evaluate the capacity of Versant HCV genotype assay (LiPA) 2.0 to identify hepatitis C virus (HCV) genotypes, 110 serum samples were collected from chronic hepatitis C patients. Three methods were compared: core sequence analysis, NS5B sequence analysis and the INNO-LiPA assay. The result showed that 102 (92.7%) of the samples were amplified in either or both regions, of which 97 were amplified in the core region and 62 were amplified in the NS5B region. Correlation analysis showed that amplification rates of subgenomic regions were associated with viral loads. Basic local alignment search tool (BLAST) and phylogenetic analysis showed that the 102 samples were classified into 5 categories: subtype 1b, 2a, 3a, 3b and 6a at frequencies of 61.8% (63), 9.8% (10), 3.9% (4), 3.9% (4) and 20.6% (21), respectively. Compared with sequencing methods, 66.7% (68) of the 102 samples were identified completely by LiPA 2.0, whereas 19.6% (20) were assigned incompletely (indistinguishable or not identified subtype) and 13.7% (14) were misclassified. Of 21 genotype 6a samples, 11 were mistyped as 1b. In conclusion, LiPA 2.0 was not suitable for identifying HCV genotypes in the samples tested, whereas core sequence analysis remained an ideal method for genotyping HCV.
Collapse
Affiliation(s)
- Qingxian Cai
- Department of Infectious Diseases, The Third Affiliated Hospital, Sun Yat‑sen University, Guangzhou, Guangdong 510630, P.R. China
| | | | | | | | | |
Collapse
|
32
|
Lu L, Li C, Yuan J, Lu T, Okamoto H, Murphy DG. Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant. J Gen Virol 2012; 94:543-548. [PMID: 23152370 DOI: 10.1099/vir.0.049668-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18-25 overlapping fragments. They had lengths of 9579-9660 nt and each contained a single ORF encoding 3020-3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a-3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications.
Collapse
Affiliation(s)
- Ling Lu
- Cancer Research Center, University of Kansas Medical Center, Kansas City, KS 66160, USA.,The Viral Oncology Center, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Chunhua Li
- Cancer Research Center, University of Kansas Medical Center, Kansas City, KS 66160, USA.,The Viral Oncology Center, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Jie Yuan
- Department of Biochemistry of Sun Yat-sen University, Guangzhou 510089, PR China
| | - Teng Lu
- University of Southern California, Los Angeles, CA 90089, USA
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Donald G Murphy
- Institut national de santé publique du Québec, Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| |
Collapse
|
33
|
Amjesh R, Nair AS, Sugunan VS. Diversity of Hepatitis C virus in Southern India Based on 5'UTR Sequence. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:349-53. [PMID: 24293823 DOI: 10.1007/s13337-012-0103-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 08/14/2012] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) exhibits genotype-specific variations in geographical distribution as a consequence of drug and immune induced evolution. Present study was aimed at discerning the distribution and prevalence of the various genotypes and subtypes of HCV in southern India. The HCV positive patient's serum was collected from different hospitals and blood banks from the states of Kerala, Tamil Nadu, Andhra Pradesh and Karnataka. Among 114 HCV positive samples, we could find only 44 isolates that are found both positive in ELISA and RT-PCR. From these samples 5' untranslated region (5'UTR) were amplified, sequenced and sub typed. Analysis of 5'UTR region of the 44 isolates shows that, genotypes 1, 3, 4 and 6 are present with genotype 3 being the most frequent. The present study shows that HCV genotype 3 subtype B was the most prevalent, forming 47.7 % among the population in southern India. The present study urges for discovering novel therapeutic agents that should be specific to genotype 3 subtype B, for the management of HCV in southern India.
Collapse
Affiliation(s)
- R Amjesh
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India
| | | | | |
Collapse
|
34
|
Alvarado-Mora MV, Moura IM, Botelho-Lima LS, Azevedo RS, Lopes E, Carrilho FJ, Pinho JRR. Distribution and molecular characterization of hepatitis C virus (HCV) genotypes in patients with chronic infection from Pernambuco State, Brazil. Virus Res 2012; 169:8-12. [PMID: 22766449 DOI: 10.1016/j.virusres.2012.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/23/2012] [Accepted: 06/26/2012] [Indexed: 01/06/2023]
Abstract
Hepatitis C virus (HCV) is a public health problem throughout the world and 3% of the world population is infected with this virus. It is estimated that 3-4 millions individuals are being infected every year. It has been estimated that around 1.5% of Brazilian population is anti-HCV positive and the Northeast region showed the highest prevalence in Brazil. The aim of this study was to characterize HCV genotypes circulating in Pernambuco State (PE), Brazil, located in the Northeast region of the country. This study included 85 anti-HCV positive patients followed up between 2004 and 2011. For genotyping, a 380bp fragment of HCV RNA in the NS5B region was amplified by nested PCR. Phylogenetic analysis was conducted using Bayesian Markov chain Monte Carlo simulation (MCMC) using BEAST v.1.5.3. From 85 samples, 63 (74.1%) positive to NS5B fragment were successfully sequenced. Subtype 1b was the most prevalent in this population (42-66.7%), followed by 3a (16-25.4%), 1a (4-6.3%) and 2b (1-1.6%). Twelve (63.1%) and seven (36.9%) patients with HCV and schistosomiasis were infected with subtypes 1b and 3a, respectively. Brazil is a large country with many different population backgrounds; a large variation in the frequencies of HCV genotypes is predictable throughout its territory. This study reports HCV genotypes from Pernambuco State where subtype 1b was found to be the most prevalent. Phylogenetic analysis suggests the presence of the different HCV strains circulating within this population.
Collapse
Affiliation(s)
- Mónica V Alvarado-Mora
- Laboratory of Tropical Gastroenterology and Hepatology, Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.
| | | | | | | | | | | | | |
Collapse
|
35
|
Gupte GM, Arankalle VA. Evaluation of the immunogenicity of liposome encapsulated HVR1 and NS3 regions of genotype 3 HCV, either singly or in combination. Virol J 2012; 9:74. [PMID: 22452828 PMCID: PMC3349533 DOI: 10.1186/1743-422x-9-74] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/27/2012] [Indexed: 01/15/2023] Open
Abstract
Background Hepatitis C virus displays a high rate of mutation and exists as a quasispecies in infected patients. In the absence of an effective universal vaccine, genotype-specific vaccine development represents an alternative. We have attempted to develop a genotype 3 based, liposome encapsulated HCV vaccine with hypervariable region-1 (HVR1) and non-structural region-3 (NS3) components. Results HCV RNA extracted from serum samples of 49 chronically infected patients was PCR amplified to obtain HVR1 region. These amplified products were cloned to obtain 20 clones per sample in order to identify the quasispecies pattern. The HVR1 consensus sequence, along with three variants was reverse transcribed to obtain peptides. The peptides were checked for immunoreactivity individually, as a pool or as a single peptide tetramer interspersed with four glycine residues. Anti-HCV positivity varied from 42.6% (tetramer) to 92.2% (variant-4) when 115 anti-HCV positive sera representing genotypes 1, 3, 4 and 6 were screened. All the 95 anti-HCV negatives were scored negative by all antigens. Mice were immunized with different liposome encapsulated or Al(OH)3 adjuvanted formulations of HVR1 variants and recombinant NS3 protein, and monitored for anti-HVR1 and anti-NS3 antibody titres, IgG isotypes and antigen specific cytokine levels. A balanced Th1/Th2 isotyping response with high antibody titres was observed in most of the liposome encapsulated antigen groups. The effect of liposomes and aluminium hydroxide on the expression of immune response genes was studied using Taqman Low Density Array. Both Th1 (IFN-gamma, Il18) and Th2 (Il4) genes were up regulated in the liposome encapsulated HVR1 variant pool-NS3 combination group. In-vitro binding of the virus to anti-HVR1 antibodies was demonstrated. Conclusion The optimum immunogen was identified to be combination of peptides of HVR1 consensus sequence and its variants along with pNS3 encapsulated in liposomes, which could generate both cellular and humoral immune responses in mice deserving further evaluation in a suitable cell culture system/non-human primate model.
Collapse
Affiliation(s)
- Gouri M Gupte
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune, India 411021
| | | |
Collapse
|
36
|
Ansari MA, Lingaiah R, Irshad M. HCV-Core Region: Its Significance in HCV-Genotyping and Type Dependent Genomic Expression. ACTA ACUST UNITED AC 2012. [DOI: 10.3889/mjms.1857-5773.2011.0208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
|
37
|
Treatment of Chronic Hepatitis due to Hepatitis C Virus (CH-C) in India: A Randomized Controlled Trial Comparing Daily Interferon-alfa-2b and Ribavirin with Daily Interferon-alfa-2b and Glycyrrhizin-A Multicenter Study. J Clin Exp Hepatol 2012; 2:10-8. [PMID: 25755401 PMCID: PMC3940339 DOI: 10.1016/s0973-6883(12)60079-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 02/15/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND AIM Pegylated-interferon-alfa (PEG-IFN-α) with ribavirin is an established treatment in chronic hepatitis due to hepatitis C virus (HCV) (CH-C). Such treatment is expensive and in resource-poor countries such as India, alternative less expensive therapy is needed. METHODS Multicenter randomized controlled trial comparing two treatment regimens (interferon-alfa-2b [IFN-α-2b] 3 million unit/day [MU/day] and ribavirin 1000 mg/day [I+R] vs IFN-α-2b 3 MU/day and glycyrrhizin 250 mg [I+G]) in CH-C. Viral, host characteristics and therapeutic responses were assessed (ICMR-6 months trial for chronic hepatitis-CTRI/2008/091/000105). RESULTS One hundred and thirty-one patients meeting the inclusion criteria were randomized to I + G (n=64) or I+R (n=67) during the period February 2002 to May 2005. About 85% (I+G=53, I+R=58) completed 6 months of treatment and 89% of them (I+G=46, I+R=53) completed 6 months of follow-up after completion of treatment. Hepatitis C virus genotype 3 was the major type detected (71% patients). The mean log10 viral load (copies/mL), histological activity index, and fibrosis stage for all patients were 5.1 ± 0.98, 5 ± 2, and 2± 1.5, respectively. Sustained viral response (SVR) was significantly higher in I + R group than in I + G group (65.7% vs 46.9%, OR=2.2, P = 0.03). Treatment with I + G was associated with significantly lower frequencies of leukopenia (2% vs 17%, P <0.01) and anemia (8% vs 40%, P <0.001) as compared to treatment with I + R. CONCLUSION Genotype 3 HCV infection with low viral load is prevalent in India. Daily IFN with ribavirin showed significantly better responses. Leukopenia and anemia were significantly more in ribavirin group. Responses observed with IFN + ribavirin were similar to the reported response rates with PEG-IFN suggesting that this modality may be considered as a cheaper alternative of treatment for chronic hepatitis C.
Collapse
Key Words
- ALT, alanine aminotransferase
- CHC, chronic hepatitis C
- CLD, chronic liver disease
- ELISA, enzyme-linked immunosorbent assay
- ETVR, end of treatment viral response
- Glycyrrhizin
- HAI, histological activity index
- HCV, hepatitis C virus
- HR, histological response
- PEG-IFN, pegylated-interferon
- RVR, rapid viral response
- SVR, sustained viral response
- hepatitis C virus
- interferon alfa-2b
- ribavirin
- treatment
Collapse
|
38
|
Lin KH, Hsu PI, Yu HC, Lin CK, Tsai WL, Chen WC, Chan HH, Lai KH. Factors linked to severe thrombocytopenia during antiviral therapy in patients with chronic hepatitis c and pretreatment low platelet counts. BMC Gastroenterol 2012; 12:7. [PMID: 22257364 PMCID: PMC3275508 DOI: 10.1186/1471-230x-12-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 01/18/2012] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Baseline low platelet count (< 150,000/μL) increases the risk of on-treatment severe thrombocytopenia (platelet count < 50,000/μL) in patients with chronic hepatitis C (CHC) undergoing antiviral therapy, which may interrupt treatment. The purpose of this study was to identify risk factors for severe thrombocytopenia during treatment for CHC in patients with baseline thrombocytopenia. METHODS Medical records were reviewed for 125 patients with CHC treated with antiviral therapy according to the standard of care, with regular follow-up examinations. Early platelet decline was defined as platelet decrease during the first 2 weeks of therapy. RESULTS Severe thrombocytopenia developed in 12.8% of patients with baseline thrombocytopenia, and predicted a higher therapeutic dropout rate. Multivariate analysis revealed baseline platelet count < 100,000/μL and rapid early platelet decline (> 30% decline in the first 2 weeks) were significantly associated with severe thrombocytopenia (P < 0.001 and 0.003, odds ratios, 179.22 and 45.74, respectively). In these patients, baseline PLT ≥ 100,000/μL and lack of rapid early platelet decline predicted absence of severe thrombocytopenia (negative predictive values were 95.1% and 96.6%, respectively). In contrast, baseline platelet count < 100,000/μL combined with rapid early platelet decline predicted severe thrombocytopenia (positive predictive value was 100%). CONCLUSIONS For patients with CHC on antiviral therapy, baseline platelet counts < 100,000/μL and rapid early platelet decline can identify patients at high risk of developing on-treatment severe thrombocytopenia.
Collapse
Affiliation(s)
- Kung-Hung Lin
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Furui Y, Hoshi Y, Murata K, Ito K, Suzuki K, Uchida S, Satake M, Mizokami M, Tadokoro K. Prevalence of amino acid mutation in hepatitis C virus core region among Japanese volunteer blood donors. J Med Virol 2012; 83:1924-9. [PMID: 21915867 DOI: 10.1002/jmv.22216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
It is not known whether there is a trend of increasing or decreasing incidence of new hepatitis C virus (HCV) infections in Japan. From the treatment point of view, it is important to verify HCV genotypes and the prevalence of treatment-resistant clones of HCV. At the Japanese Red Cross blood centers, all blood samples obtained from blood donation have been screened using serological methods and the minipool nucleic acid amplification testing. One hundred and fourteen donors have been identified over the past 10 years to be HCV RNA-only positive without detectable anti-HCV and were considered to be in the acute phase of HCV infection. There was a trend of decreasing incidence of such new infections among the blood donors. HCV RNA-only-positive samples were examined further for genotyping and HCV RNA quantitation. Genotype 2 (2a plus 2b) was predominant (78.2%) among them followed by genotype 1b (21.2%). Direct sequencing was carried out to detect the possible treatment-resistant mutant clones 70Q and 91M, clones with amino acid substitutions at positions 70 and 91 of the HCV core protein, respectively. 70Q and 91M were found regularly in donors with genotype 1b, but not in those with other genotypes. No particular endemic areas for the mutant clones were identified. There was no significant difference in the mean viral titer between the 70Q mutant type and the non-70Q wild-type. Even in newly infected people, the mutant clone 70Q was detected frequently.
Collapse
Affiliation(s)
- Yasumi Furui
- Central Blood Institute, Japanese Red Cross, Tokyo, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Chan DPC, Lee SS, Lee KCK. The effects of widespread methadone treatment on the molecular epidemiology of hepatitis C virus infection among injection drug users in Hong Kong. J Med Virol 2011; 83:1187-94. [PMID: 21567422 DOI: 10.1002/jmv.22099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The distribution of HCV genotypes among injection drug users in Hong Kong was assessed in context of methadone treatment availability. Three time periods were defined by the year of initiating injection-on or before 1980, 1981-1994, and 1995-2006-with methadone becoming widely available since the second period. Of the 273 HCV RNA-positive cases, the most prevalent subtype was HCV 6a (52.4%), followed by HCV 1b (38.5%). The new variants of HCV subtypes 6e and 6h were detected. Both subtypes 1b and 6a were prevalent among older injectors, while subtype 3a was more common in young injectors and those initiating injection recently during the third time period. Age (P < 0.05) and recent injection frequency (P < 0.01) were independently associated with HCV 6a infection. Subtype 1b was predominant in the first period, whereas 6a was more common in the second and third. Subtype 1b sequences appeared to have originated at two positions on the phylogenetic tree, while 6a showed a more disperse distribution suggestive of multiple introductions. Phylogenetic analysis on the NS5B region did not reveal specific clustering of any subtype/genotype. Overall, there was no suggestion of outbreaks of HCV. The extensive use of methadone may have protected Hong Kong from the emergence of HCV clusters among injection drug users.
Collapse
Affiliation(s)
- Denise P C Chan
- Stanley Ho Centre for Emerging Infectious Diseases, School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, Hong Kong
| | | | | |
Collapse
|
41
|
Justa S, Minz RW, Minz M, Sharma A, Anand S, Das A, Chawla YK, Sakhuja VK. Serial measurements of hepatitis C viral load by real-time polymerase chain reaction among recipients of living-donor renal transplants: a short-term follow-up study from a single center. Transplant Proc 2011; 42:3568-73. [PMID: 21094817 DOI: 10.1016/j.transproceed.2010.07.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Revised: 05/20/2010] [Accepted: 07/08/2010] [Indexed: 12/19/2022]
Abstract
There is a high prevalence of hepatitis C virus (HCV) infection among immunosuppressed patients including renal transplant recipients. The study investigated serum viral loads for up to 6 months posttransplantation among these patients. Serum viral load was serially monitored using real-time polymerase chain reaction (PCR) in 25 HCV-positive renal transplant recipients pretransplantation as well as day 10 and 6 months posttransplantation. A liver biopsy specimen obtained under vision at the time of transplantation was analyzed for viral load as well as for histological changes. There was increased viremia at day 10 followed by a significant (2 log) reduction at 6 months posttransplantation. Pretransplantation serum and intrahepatic viral load showed significant positive correlations (r = 0.727; P = .001), the latter also reflecting liver fibrosis score (r = 0.423; P = .05). The findings suggested that serum viral load reflects intrahepatic viral load, which in turn correlates with liver fibrosis. At 6 months posttransplantation, the modulatory effects of immunosuppressive drugs and of the host immune response may lead to a reduced viral load.
Collapse
Affiliation(s)
- S Justa
- Department of Immunopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Cellular Immune Response and Cytokine Profile Among Hepatitis C Positive Living Donor Renal Transplant Recipients. Transplantation 2010; 90:654-60. [DOI: 10.1097/tp.0b013e3181eac3a7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
43
|
Utama A, Tania NP, Dhenni R, Gani RA, Hasan I, Sanityoso A, Lelosutan SAR, Martamala R, Lesmana LA, Sulaiman A, Tai S. Genotype diversity of hepatitis C virus (HCV) in HCV-associated liver disease patients in Indonesia. Liver Int 2010; 30:1152-60. [PMID: 20492518 DOI: 10.1111/j.1478-3231.2010.02280.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) genotype distribution in Indonesia has been reported. However, the identification of HCV genotype was based on 5'-UTR or NS5B sequence. AIMS This study was aimed to observe HCV core sequence variation among HCV-associated liver disease patients in Jakarta, and to analyse the HCV genotype diversity based on the core sequence. METHODS Sixty-eight chronic hepatitis (CH), 48 liver cirrhosis (LC) and 34 hepatocellular carcinoma (HCC) were included in this study. HCV core variation was analysed by direct sequencing. RESULTS Alignment of HCV core sequences demonstrated that the core sequence was relatively varied among the genotype. Indeed, 237 bases of the core sequence could classify the HCV subtype; however, 236 bases failed to differentiate several subtypes. Based on 237 bases of the core sequences, the HCV strains were classified into genotypes 1 (subtypes 1a, 1b and 1c), 2 (subtypes 2a, 2e and 2f) and 3 (subtypes 3a and 3k). The HCV 1b (47.3%) was the most prevalent, followed by subtypes 1c (18.7%), 3k (10.7%), 2a (10.0%), 1a (6.7%), 2e (5.3%), 2f (0.7%) and 3a (0.7%). HCV 1b was the most common in all patients, and the prevalence increased with the severity of liver disease (36.8% in CH, 54.2% in LC and 58.8% in HCC). These results were similar to a previous report based on NS5B sequence analysis. CONCLUSION Hepatitis C virus core sequence (237 bases) could identify the HCV subtype and the prevalence of HCV subtype based on core sequence was similar to those based on the NS5B region.
Collapse
Affiliation(s)
- Andi Utama
- Molecular Epidemiology Division, Mochtar Riady Institute for Nanotechnology, Lippo Karawaci, Tangerang, Banten, Indonesia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Hepatitis C (HCV) is the disease that has affected around 200 million people globally. HCV is a life threatening human pathogen, not only because of its high prevalence and worldwide burden but also because of the potentially serious complications of persistent HCV infection. Chronicity of the disease leads to cirrhosis, hepatocellular carcinoma and end-stage liver disease. HCV positive hepatocytes vary between less than 5% and up to 100%, indicating the high rate of replication of viral RNA. HCV has a very high mutational rate that enables it to escape the immune system. Viral diversity has two levels; the genotypes and Quasiaspecies. Major HCV genotypes constitute genotype 1, 2, 3, 4, 5 and 6 while more than 50 subtypes are known. All HCV genotypes have their particular patterns of geographical distribution and a slight drift in viral population has been observed in some parts of the globe.
Collapse
Affiliation(s)
- Nazish Bostan
- Department of Biological Sciences, Quaid-i-Azam University, Islamabad-45320, Pakistan
| | | |
Collapse
|
45
|
Gupte GM, Ramdasi AY, Kulkarni AS, Arankalle VA. Complete genome sequences of hepatitis C virus subtype 3i and 3a subtype isolates from India. Indian J Gastroenterol 2010; 29:101-5. [PMID: 20658329 DOI: 10.1007/s12664-010-0030-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 01/07/2010] [Indexed: 02/04/2023]
Abstract
AIM Hepatitis C virus (HCV), a major causative agent of chronic hepatitis, is classified into six major genotypes. Genotype 3 HCV infection is more sensitive to interferon therapy. In India, genotype 3, particularly subtype 3a, HCV infections are common. Three novel HCV subtypes i.e., 3g, 3j, and 3i were identified from India based on partial genomic sequences. This report provides full genome sequences of one isolate each of subtypes 3i and 3a. METHODS Serum samples positive for subtype 3i and 3a HCV RNA based on core region genomic sequences were studied. Complete HCV genomes were amplified as 11 overlapping PCR fragments and sequenced. RESULTS The complete genomic sequence of Indian HCV 3i isolate clustered with other genotype 3 sequences, and was closer to subtypes 3b and 3a (80.5% and 79.1% [SD 0.4%] nucleotide identity). Nucleotide similarities were the highest in the core region (86.1-88.7%), and the least in the E2 region (69.4-70.7%). Phylogenetic tree analysis confirmed the existence of a separate subtype 3i. The Indian HCV 3a isolate's complete genomic sequences clustered with previously known genotype 3a sequences with a nucleotide similarity of 91.1% (SD 0.2%). Neither isolates showed evidence of recombination of different HCV genotypes. CONCLUSION The information on complete genomic sequences of the genotype 3 HCV isolates should be helpful in future studies on HCV evolution and classification, and for development of newer therapeutic and preventive strategies against this infection.
Collapse
|
46
|
Affiliation(s)
- Ashis Mukhopadhyaya
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore 632 004, India.
| |
Collapse
|
47
|
|
48
|
Saravanan S, Velu V, Kumarasamy N, Shankar EM, Nandakumar S, Murugavel KG, Balakrishnan P, Solomon SS, Solomon S, Thyagarajan SP. The prevalence of hepatitis B virus and hepatitis C virus infection among patients with chronic liver disease in South India. Int J Infect Dis 2008; 12:513-8. [DOI: 10.1016/j.ijid.2008.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 01/15/2008] [Accepted: 02/16/2008] [Indexed: 01/26/2023] Open
|
49
|
Xia X, Lu L, Tee KK, Zhao W, Wu J, Yu J, Li X, Lin Y, Mukhtar MM, Hagedorn CH, Takebe Y. The unique HCV genotype distribution and the discovery of a novel subtype 6u among IDUs co-infected with HIV-1 in Yunnan, China. J Med Virol 2008; 80:1142-52. [PMID: 18461611 DOI: 10.1002/jmv.21204] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Yunnan province is the epicenter of HIV-1 epidemics in China and a center for drug trafficking to the other parts of the world. In six prefectures of this province, a total of 132 IDUs were recruited to determine the sero-prevalence of HCV and HIV-1 and the positive rates were 93.94% and 68.18%, respectively (P<0.001). Co-infection with HCV and HIV-1 was found among 89 IDUs, of whom several HCV fragments were amplified and sequenced. Sequences of the HCV 5'NCR-C and NS5B region were determined from 82 IDUs. Phylogenetic analyses showed consistent genotyping among 80 IDUs. Among them HCV genotypes 1a, 1b, 3a, 3b, 6a, 6n, and a tentatively assigned novel 6u subtype were found in 1 (1.25%), 16 (20%), 19 (23.75%), 24 (30%), 4 (5%), 9 (11.25%) and 7 (8.75%) individuals, respectively. In two IDUs, genotyping results were discordant, suggesting mixed HCV infections or recombination. The proportion of patients with HCV 1b tended to decrease from the north to south and from the east to west in this province. Genotype 3 and 6 strains were more frequent in the southern prefectures. The novel subtype 6u strains were only detected in Dehong which borders Myanmar. Our findings showed a unique pattern of HCV genotype distribution, which is similar to that in the southeastern Asian countries but distinct from that among the general population in China. Routes of drug trafficking and the resulting high prevalence of HIV-1 infection may have contributed to this pattern of HCV genotype distribution.
Collapse
Affiliation(s)
- Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Verma V, Chakravarti A, Kar P. Genotypic characterization of hepatitis C virus and its significance in patients with chronic liver disease from Northern India. Diagn Microbiol Infect Dis 2008; 61:408-14. [DOI: 10.1016/j.diagmicrobio.2008.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 03/14/2008] [Accepted: 03/18/2008] [Indexed: 12/14/2022]
|