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Ullah S, Naveed M, Ali A, Bibi S, Idrees W, Rafique S, Idrees M, Waqas M, Uddin J, Jan A, Khan A, Al-Harrasi A. Assessment of ubiquitin specific Peptidase-18 gene in peripheral blood of chronic hepatitis C patients treated with direct-acting antiviral drugs. Heliyon 2024; 10:e24581. [PMID: 38298711 PMCID: PMC10828700 DOI: 10.1016/j.heliyon.2024.e24581] [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: 10/23/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Hepatitis C virus (HCV) infection remains one of the leading causes of liver complications globally. Ubiquitin Specific Peptidase-18 (USP18) is a ubiquitin-specific protease that cleaves interferon-stimulated gene 15 (ISG15) from ISGylated protein complexes and is involved in regulating interferon responsiveness. To study the effect of direct-acting antivirals (DAAs) on the USP18 gene using qPCR, 132 participants were recruited and classified into different groups based on treatment duration. USP18 expression was raised compared to rapid virologic response (RVR) and early virologic response (EVR) groups with P = 0.0026 and P = 0.0016, respectively. USP18 was found to be 7.36 folds higher in naïve patients than those with RVR and sustained viral response (SVR). In RVR and SVR groups where patients had cleared HCV RNA after treatment with direct-acting antiviral agents (DAA) therapy, the expression of USP18 was found to be low, with a fold change of 1.3 and 1.4 folds, respectively. Expression of USP18 was significantly higher in the non-RVR group than in the RVR group. In the No EVR group, gene expression was significantly higher than in the EVR group. It is concluded that targeting HCV proteins using DAAs can cause USP18 expression to be normalized more effectively. Moreover, USP18 is a vital marker indicating treatment resistance and distinguishing responders from non-responders during DAA therapy.
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Affiliation(s)
- Sami Ullah
- Molecular Virology laboratory Centre for Applied Molecular Biology (CAMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Mariam Naveed
- Molecular Virology laboratory Centre for Applied Molecular Biology (CAMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Amjad Ali
- Molecular Virology laboratory Centre for Applied Molecular Biology (CAMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Sadia Bibi
- Department of Botany, University of Malakand Chakdara, Dir lower, Khyber Pakhtunkhwa, Pakistan
| | - Wafa Idrees
- Khyber Medical College, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Shazia Rafique
- Division of Molecular Virology, Centre of Excellence in Molecular Biology (CEMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Division of Molecular Virology, Centre of Excellence in Molecular Biology (CEMB), 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
- Vice Chancellor, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Khyber Pakhtunkhwa, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Jalal Uddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 62529, Kingdom of Saudi Arabia
| | - Afnan Jan
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
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Barik S. Suppression of Innate Immunity by the Hepatitis C Virus (HCV): Revisiting the Specificity of Host-Virus Interactive Pathways. Int J Mol Sci 2023; 24:16100. [PMID: 38003289 PMCID: PMC10671098 DOI: 10.3390/ijms242216100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The hepatitis C virus (HCV) is a major causative agent of hepatitis that may also lead to liver cancer and lymphomas. Chronic hepatitis C affects an estimated 2.4 million people in the USA alone. As the sole member of the genus Hepacivirus within the Flaviviridae family, HCV encodes a single-stranded positive-sense RNA genome that is translated into a single large polypeptide, which is then proteolytically processed to yield the individual viral proteins, all of which are necessary for optimal viral infection. However, cellular innate immunity, such as type-I interferon (IFN), promptly thwarts the replication of viruses and other pathogens, which forms the basis of the use of conjugated IFN-alpha in chronic hepatitis C management. As a countermeasure, HCV suppresses this form of immunity by enlisting diverse gene products, such as HCV protease(s), whose primary role is to process the large viral polyprotein into individual proteins of specific function. The exact number of HCV immune suppressors and the specificity and molecular mechanism of their action have remained unclear. Nonetheless, the evasion of host immunity promotes HCV pathogenesis, chronic infection, and carcinogenesis. Here, the known and putative HCV-encoded suppressors of innate immunity have been reviewed and analyzed, with a predominant emphasis on the molecular mechanisms. Clinically, the knowledge should aid in rational interventions and the management of HCV infection, particularly in chronic hepatitis.
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Affiliation(s)
- Sailen Barik
- EonBio, 3780 Pelham Drive, Mobile, AL 36619, USA
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Adugna A. Therapeutic strategies and promising vaccine for hepatitis C virus infection. Immun Inflamm Dis 2023; 11:e977. [PMID: 37647422 PMCID: PMC10461427 DOI: 10.1002/iid3.977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/22/2023] [Accepted: 07/30/2023] [Indexed: 09/01/2023] Open
Abstract
Hepatitis C virus (HCV) infection is still a significant global health problem despite therapeutic advancements. Ribavirin and interferon therapy have been the sole available treatments for HCV infection for a number of years with low efficacy. Thus, currently, a number of therapeutic strategies are being used, including nanoparticles (NPs), micro-RNAs such as small interfering RNA (siRNA), RNAi-based gene silencing and antisense oligonucleotide-based microRNA-122, microRNA-155, and short hairpin RNAs (shRNAs), and immunotherapeutic approaches such as anti-programmed cell death 1(PD-1), monoclonal antibodies (mAb or moAb), and monocyte-derived dendritic cells (Mo-DCs). Furthermore, direct-acting antivirals (DAAs) and host-targeting agents (HTA) were also the current therapeutic approaches with great efficacy. In spite of different clinical trials on HCV vaccine developments, nowadays there is no effective HCV vaccine in opposition to virus due to various challenges including genetic diversity, lack of immunocompetent small animal models, shortage of HCV vaccination testing alternatives, lack of an effective tissue culture method for replicating HCV, and inadequate knowledge regarding to immune responses against HCV infection. Nowadays, mRNA vaccine, recombinant viral vector, peptides vaccine, virus-like particles, DNA vaccine, rational designed vaccine, and recombinant polyantigenic T-cell-based vaccine are novel promising candidates for HCV vaccine based on various clinical trials. This review summarizes the different therapeutic approaches and the advancements of vaccine candidates for HCV infection.
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Affiliation(s)
- Adane Adugna
- Medical Microbiology, Medical Laboratory Sciences, College of Health SciencesDebre Markos UniversityDebre MarkosEthiopia
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Abdullah MAF, McWhirter SM, Suo Z. Modulation of Kinase Activities In Vitro by Hepatitis C Virus Protease NS3/NS4A Mediated-Cleavage of Key Immune Modulator Kinases. Cells 2023; 12:406. [PMID: 36766748 PMCID: PMC9913602 DOI: 10.3390/cells12030406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/09/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023] Open
Abstract
Hepatitis C Virus NS3/NS4A, a serine protease complex, has been found to interact with many host proteins and cause various adverse effects on cellular function and immune response. For example, the cleavage of important immune factors by NS3/NS4A has been suggested as a mechanism for the hepatitis C virus to evade innate immunity. The spectrum of susceptible substrates for NS3/NS4A cleavage certainly includes important immune modulator kinases such as IKKα, IKKβ, IKKε, and TBK1, as demonstrated in this paper. We show that the kinase activities of these four host kinases were transformed in unexpected ways by NS3/NS4A. Treatment with NS3/NS4A caused a significant reduction in the kinase activities of both IKKα and IKKβ, suggesting that HCV might use its NS3/NS4A protease activity to deactivate the NF-κB-associated innate immune responses. In contrast, the kinase activities of both IKKε and TBK1 were enhanced after NS3/NS4A treatment, and more strikingly, the enhancement was more than 10-fold within 20 min of treatment. Our mass spectroscopic results suggested that the cleavage after Cys89 in the kinase domain of IKKε by NS3/NS4A led to their higher kinase activities, and three potential mechanisms were discussed. The observed kinase activity enhancement might facilitate the activation of both IKKε- and TBK1-dependent cellular antiviral pathways, likely contributing to spontaneous clearance of the virus and observed acute HCV infection. After longer than 20 min cleavage, both IKKε- and TBK1 gradually lost their kinase activities and the relevant antiviral pathways were expected to be inactivated, facilitating the establishment of chronic HCV infection.
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Affiliation(s)
| | - Sarah M. McWhirter
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Zucai Suo
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA
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Kiattanaphon A, Vipsoongnern Y, Kunthalert D, Sistayanarain A. Partial nonstructural 3 region analysis of hepatitis C virus genotype 3a. Mol Biol Rep 2022; 49:9437-9443. [PMID: 36002650 DOI: 10.1007/s11033-022-07803-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND The hepatitis C virus (HCV) is a major cause of illness around the world. HCV genotype 3a is the most prevalent genotype in Thailand. Direct-acting antiviral (DAA) drugs are available for treatment, and these drugs target the NS3, NS5A, and NS5b proteins of HCV. However, HCV variants that are resistant to NS3 protease inhibitors have been found during treatment. This resistance can be naturally occurring or in response to treatment. The purpose of this study is to analyze the codon positions of the main mutation of the partial NS3 gene region of HCV genotype 3a. METHODS In order to detect mutations and confirm the genotype of HCV genotype 3a, the nucleotide sequencing and amino acid portion of NS3 were analyzed. RESULTS Twenty-six samples were successfully sequenced and clustered within two sub-clades defined as 3a-1 and 3a-2. Through amino acid mutation analysis, the variations were detected at codon positions 122 (3.8%), 132 (84.6%), 168 (100%), 170 (92.3%), 174 (100%), and 175 (100%). CONCLUSIONS In conclusion, mutations at positions 168, 170, 174, and 175 of the NS3 region are common within the HCV genotype 3a. This information should be useful in the development of effective anti-viral drugs that can successfully treat HCV infection.
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Affiliation(s)
- Anusorn Kiattanaphon
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | | | - Duangkamol Kunthalert
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Anchalee Sistayanarain
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
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Redwan EM, Aljadawi AA, Uversky VN. Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors. BIOLOGY 2022; 11:1091. [PMID: 36101469 PMCID: PMC9312352 DOI: 10.3390/biology11071091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
In this study, we examined the interplay between protein intrinsic disorder, hepatitis C virus (HCV) infection, and signaling pathways induced by Toll-like receptors (TLRs). To this end, 10 HCV proteins, 10 human TLRs, and 41 proteins from the TLR-induced downstream pathways were considered from the prevalence of intrinsic disorder. Mapping of the intrinsic disorder to the HCV-TLR interactome and to the TLR-based pathways of human innate immune response to the HCV infection demonstrates that substantial levels of intrinsic disorder are characteristic for proteins involved in the regulation and execution of these innate immunity pathways and in HCV-TLR interaction. Disordered regions, being commonly enriched in sites of various posttranslational modifications, may play important functional roles by promoting protein-protein interactions and support the binding of the analyzed proteins to other partners such as nucleic acids. It seems that this system represents an important illustration of the role of intrinsic disorder in virus-host warfare.
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Affiliation(s)
- Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria 21934, Egypt
| | - Abdullah A. Aljadawi
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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Recent advancement in small molecules as HCV inhibitors. Bioorg Med Chem 2022; 60:116699. [PMID: 35278819 DOI: 10.1016/j.bmc.2022.116699] [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: 09/21/2021] [Revised: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]
Abstract
Hepatitis C virus (HCV) has caused a considerable threat to human health. To date, no treatments are without side effects. The proteins and RNA associated with HCV have specific functions during the viral life cycle. The vulnerabilities to virus are associated with those proteins or RNA. Thus, targeting these proteins and RNA is an efficient strategy to develop anti-HCV therapeutics. The treatment for HCV-infected patients has been greatly improved after the approval of direct-acting antivirals (DAAs). However, the cost of DAAs is unusually high, which adds to the economic burden on patients with chronic liver diseases. So far, many efforts have been devoted to the development of small molecules as novel HCV inhibitors. Investigations on the inhibitory activities of these small molecules have involved the target identification and the mechanism of action. In this mini-review, these small molecules divided into four kinds were elaborated, which focused on their targets and structural features. Furthermore, we raised the current challenges and promising prospects. This mini-review may facilitate the development of small molecules with improved activities targeting HCV based on the chemical scaffolds of HCV inhibitors.
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8
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Ko K, Akita T, Satake M, Tanaka J. Epidemiology of viral hepatitis C: Road to elimination in Japan. Glob Health Med 2021; 3:262-269. [PMID: 34782867 DOI: 10.35772/ghm.2021.01069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/26/2021] [Accepted: 07/26/2021] [Indexed: 12/30/2022]
Abstract
Although HCV infection was the main cause of HCC in Japan contributing 70% over two decades after its first cloning in 1989, it was markedly decreased to 49% in 2013 and expected to decrease continuously. Based on blood donor national database, the new incident cases were 0.4/100,000 person-years, the prevalence was 0.13% and the total number was 890,902-1,302,179 in 2015. Establishment of blood donor screening with anti-HCV measurement and nucleic acid test introduced by Japanese Red Cross as pioneer, high-level medical and surgical care, and the government's policy under the Basic Act on Hepatitis Control have changed its epidemiology and outbreak trend and also enforced the disruption of potential transmission cascades. HCV prevalence among the younger generation was extremely low in all regions, and the predominant age for HCC has shifted to over 60 years old population. Considering such changes, HCV induced HCC occurrence is supposed to be ultimately suppressed in the near future. However, taking into account society changes, regulating intravenous drugs users and monitoring high-risk groups such as tattoos, and men who have sex with men are indeed required in Japan. Understanding the epidemiological changes in HCV is important in assigning, modifying, and designating effective response systems. Selective or national action plans, strategic approaches, and cooperation between government sectors have a positive impact on HCV prevention and control. A dramatic decrease in total number of HCV carriers, increase in number of people treated with highly effective DAA, and subsequent high SVR indicates Japan might achieve WHO's target of HCV elimination by 2030.
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Affiliation(s)
- Ko Ko
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoyuki Akita
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masahiro Satake
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Junko Tanaka
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Rahimi P, Sharafi H, Bahramali G, SajadianFard F, Asadi NS, Alavian SM, Iranpur Mobarakeh V, Moravej SZ. Prevalence of Naturally-Occurring NS5A and NS5B Resistance-Associated Substitutions in Iranian Patients With Chronic Hepatitis C Infection. Front Microbiol 2021; 11:617375. [PMID: 33584581 PMCID: PMC7876467 DOI: 10.3389/fmicb.2020.617375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV), non-structural 5A (NS5A), and non-structural 5B (NS5B) resistance-associated substitutions (RASs) are the main causes of failure to direct-acting antiviral agents (DAAs). NS5A and NS5B RASs can occur in patients with HCV infection naturally and before exposure to DAAs. OBJECTIVES This study aimed to evaluate naturally-occurring NS5A and NS5B RASs in Iranian patients with HCV genotype 1a (HCV-1a) and -3a infections. METHODS In this cross-sectional study, viral RNA was extracted from serum specimens. NS5A and NS5B regions were amplified using RT-PCR followed by DNA sequencing. The results of nucleotide sequences were aligned against reference sequences of HCV-1a and -3a and the amino acid substitutions were analyzed using geno2pheno [hcv] web application. RESULTS Among 135 patients with hepatitis C, NS5A amino acid substitutions/RASs were identified in 26.4% and 15.9% of patients with HCV-1a and -3a infections, respectively. The identified amino acid substitutions/RASs in the NS5A region of patients with HCV-1a infection were M28T/V/I 11.1%, Q30R/H 4.2%, L31M 1.4%, and H58Y/P/C/D/Q/S/T 16.7%. Y93H substitution was not found in HCV-1a sequences. In patients with HCV-3a infection, NS5A amino acid substitutions/RASs were A30T/K 9.5%, L31F 1.6%, P58S/T/C 3.2%, Y93H 3.2%, and Y93N 3.2%. No resistance substitutions were identified in NS5B sequences from patients with HCV-1a and -3a infections. CONCLUSION In this study, baseline amino acid substitutions/RASs were only identified in the NS5A region in Iranian patients with HCV-1a and -3a infections, and the prevalence of these amino acid substitutions/RASs were in accordance with similar studies. There were no RASs in the HCV-1a and -3a NS5B region.
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Affiliation(s)
- Pooneh Rahimi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | - Golnaz Bahramali
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
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HCV genotype profile in Brazil of mono-infected and HIV co-infected individuals: A survey representative of an entire country. PLoS One 2020; 15:e0227082. [PMID: 31905224 PMCID: PMC6944355 DOI: 10.1371/journal.pone.0227082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/10/2019] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION To be eligible for government-provided treatment in Brazil, all HCV-infected individuals are required to be genotyped shortly after diagnosis. We describe the HCV genotype (G) profiles by geographic region, gender, age and HIV co-infection. METHODS We assessed 29,071 genotypes collected from HCV-infected individuals from March 2016 to March 2018 (Abbott Real-Time HCV Genotype). We randomly selected 12,336 samples for HIV co-infection testing using an EIA rapid test kit (TR DPP HIV 1/2 Bio-Manguinhos). Descriptive statistical analyses were performed using R. RESULTS Overall, HCV genotype distribution was 40.9% G1A, 30.2% G1B, 23.8% G3, 3.8% G2, 0.7% G4, 0.1% G5 and 0.6% with multiples genotypes. G1A prevalence was 44.4% among males and 35.8% among females. G1B and G2 were more prevalent in older individuals than G1A and G3. G3 was more prevalent in the South region. Of samples tested for HIV co-infection, 15% were HIV+. Median age among HCV/HIV co-infected individuals was 50 years old compared to 57 years old among mono-infected individuals. Distinct HCV genotype prevalence between HCV/HIV co-infected and HCV mono-infected individuals were respectively: G1A 60.6% versus 37.8%, G1B 15.2% versus 32.9%, and G3 18.9% versus 24.7%. G4 was detected among co-infected young men (3.5% versus 0.2% among mono-infected). CONCLUSION The increasing prevalence of G3, as inferred by the younger ages of the HCV-infected individuals, poses an extra challenge with regards to disease progression. Distinct genotypical profiles between HCV mono-infection and HCV/HIV co-infection warrant future research in order to better understand and help mitigate HCV chains of transmission.
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Costa VD, Delvaux N, Brandão-Mello CE, Nunes EP, de Sousa PSF, de Souza Rodrigues LLLX, Lampe E, do Amaral Mello FC. Prevalence of baseline NS3 resistance-associated substitutions (RASs) on treatment with protease inhibitors in patients infected with HCV genotype 1. Clin Res Hepatol Gastroenterol 2019; 43:700-706. [PMID: 30880098 DOI: 10.1016/j.clinre.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Treatment for hepatitis C has evolved significantly with the licensing of direct-acting antiviral drugs (DAAs). However, one of the limiting factors of the effectiveness of antiviral therapy with protease inhibitors (PIs) is the emergence of resistance caused by point mutations. The aim of this study was to determine the prevalence of resistance-associated substitutions (RASs) in HCV NS3 gene in patients infected with genotype 1 before therapy with simeprevir. METHODS A total of 73 serum samples from 15 treatment-experienced patients with boceprevir/telaprevir and 58 DAA-naïve patients were collected before therapy with DAAs simeprevir, daclatasvir and/or sofosbuvir. Presence of baseline resistance-associated substitutions (RAS) in the serine protease domain of HCV NS3 was analyzed by nucleotide sequencing followed by amino acid deduction. RESULTS Overall RAS prevalence in this study was 13.7% (10/73). RAS prevalence for HCV subtype 1b was 17.4% (4/23) while for HCV subtype 1a was 12% (6/50). Primary mutations V36M/L and R155K were observed only in HCV subtype 1a, whereas T54S and Q80K were identified only in HCV subtype 1b. RAS V36M, which is related to reduction of susceptibility to second-generation PIs, was the most frequent in the study (6.9%; 5/73). CONCLUSIONS Our results indicated that Brazilian isolates of HCV present a distinct pattern of RAS depending on the infecting viral subtype. In contrast to data from other countries, RAS Q80K prevalence in Brazil is low in HCV subtype 1a. This study improves the knowledge of genetic barrier for resistance to PIs involving RASs in chronically infected patients and its possible impact on an unsuccessful treatment outcome, information that might be crucial to upcoming decisions of incorporation of new DAAs in Brazilian guidelines of antiviral therapy against HCV infection.
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Affiliation(s)
- Vanessa Duarte Costa
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil.
| | - Nathália Delvaux
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
| | - Carlos Eduardo Brandão-Mello
- Hospital Universitário Gaffrée & Guinle, UNIRIO, R. Mariz e Barros, 775 - Maracanã, 20270-001, Rio de Janeiro, RJ, Brazil
| | - Estevão Portela Nunes
- Instituto Nacional de Infectologia Evandro Chagas, INI/FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-360, Rio de Janeiro, RJ, Brazil
| | - Paulo Sérgio Fonseca de Sousa
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
| | | | - Elisabeth Lampe
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
| | - Francisco Campello do Amaral Mello
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
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Serdari D, Kostaki EG, Paraskevis D, Stamatakis A, Kapli P. Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV. PeerJ 2019; 7:e7754. [PMID: 31667012 PMCID: PMC6816385 DOI: 10.7717/peerj.7754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022] Open
Abstract
Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
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Affiliation(s)
- Dora Serdari
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics Evolution and Environment, University College London, University of London, London, United Kingdom
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13
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Palanisamy N, Kalaghatgi P, Akaberi D, Lundkvist Å, Chen ZW, Hu P, Lennerstrand J. Worldwide prevalence of baseline resistance-associated polymorphisms and resistance mutations in HCV against current direct-acting antivirals. Antivir Ther 2019; 23:485-493. [PMID: 29745936 DOI: 10.3851/imp3237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 10/16/2022]
Abstract
BACKGROUND HCV infections can now be completely cured, thanks to the currently marketed direct-acting antivirals (DAAs). It is known that HCV patients carry viral populations with baseline polymorphisms and/or mutations that make them resistant against some of these DAAs, which can negatively impact the patient's treatment outcome. Using complete HCV coding sequences isolated from 1,306 treatment-naive patients of genotypes (GTs) 1, 2, 3, 4 and 6 from around the globe, we studied the prevalence of baseline resistance-associated polymorphisms (RAPs) and resistance mutations (RMs) against DAAs that are currently on the market or in clinical trials. METHODS The HCV genome sequences used in this study were retrieved from the NCBI database. RAPs and RMs, with reference to HCV GT1a, were identified using the HCV Geno2pheno web server. RESULTS Nearly 50% of the total amino acid positions (including NS3 protease, NS5A and NS5B) studied are baseline polymorphisms that differentiated one GT from the rest. A proportion of these baseline polymorphisms and baseline non-polymorphic RMs could confer a significant increase in resistance against DAAs. CONCLUSIONS In this study, we show the presence and prevalence of RAPs and RMs in DAA treatment-naive patients against currently used DAAs or DAAs in clinical trials. Our study suggests that RAPs and RMs profiling of HCV patients should be performed before the start of the therapy. Our results should be relevant especially in low- and middle-income countries, where the patients have a large variation of GTs and subtypes, and where the generic HCV treatment is now increasingly available.
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Affiliation(s)
- Navaneethan Palanisamy
- HBIGS, University of Heidelberg, Heidelberg, Germany.,Molecular and Cellular Engineering Group, BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Prabhav Kalaghatgi
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Dario Akaberi
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Åke Lundkvist
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Zhi-Wei Chen
- Department of Infectious Diseases, Institute for Viral Hepatitis, The Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Hu
- Department of Infectious Diseases, Institute for Viral Hepatitis, The Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Johan Lennerstrand
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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14
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Bruno S, Nicole B, Nila J D, Gail M, James N, Peter S M, Christopher S H. Heart Transplantation From Hepatitis C-Positive Donors in the Era of Direct Acting Antiviral Therapy: A Comprehensive Literature Review. Transplant Direct 2019; 5:e486. [PMID: 31579814 PMCID: PMC6739042 DOI: 10.1097/txd.0000000000000928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
While heart transplantation is a highly effective treatment in patients with advanced heart failure, the number of people waiting for a transplant exceeds the number of available donors. With the advent of direct acting antivirals (DAA) for the eradication of Hepatitis C, the heart transplant donor pool has been expanded to include donors with untreated Hepatitis C. To help with the development of future protocols for Hepatitis C-positive heart transplants, we performed a review of the literature on DAA therapy in the context of heart transplantation. METHODS We searched MEDLINE, EMBASE, OVIDE JOURNAL, and GOOGLE SCHOLAR for papers published between 01.01.2011 and 01.06.2019 using key words "heart transplantation" associated with "hepatitis C." RESULTS After removing duplicates, we screened 78 articles and retained 16 for primary analysis and 20 for sustained virologic response 12 weeks after completion of the DAA therapy (SVR-12). The data from 62 patients were extracted from these publications. Fifty-six (90%) patients had donor-derived hepatitis C and 6 (10%) patients were chronically infected with hepatitis C before transplantation. All living transplanted patients achieved SVR-12, defined as hepatitis C virus RNA below the limit of detection 12 weeks after treatment completion. Treatment duration ranged from 4 to 24 weeks. Clinically relevant modification to the dosing of immunosuppressive mediations during DAA therapy was documented in only 1 patient (1.6%). Six (14%) patients experienced rejection during DAA therapy. CONCLUSIONS Despite different timings of initiation of DAA therapy across the included studies, there were no differences in sustained viral clearance. Early commencement of DAA with a potentially shorter treatment duration (<8 wk) is appealing; however, further studies are required before recommending this approach.
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Affiliation(s)
- Schnegg Bruno
- Department of Cardiology, Center for advance heart failure, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Heart and Lung Transplant Unit, St Vincent's Hospital, 390 Victoria St., Darlinghurst, NSW, Australia
| | - Bart Nicole
- Heart and Lung Transplant Unit, St Vincent's Hospital, 390 Victoria St., Darlinghurst, NSW, Australia
| | - Dharan Nila J
- HIV, Immunology and Infectious Disease Unit, St Vincent's Hospital, 390 Victoria St., Darlinghurst, NSW, Australia
| | - Matthews Gail
- HIV, Immunology and Infectious Disease Unit, St Vincent's Hospital, 390 Victoria St., Darlinghurst, NSW, Australia
| | - Nadel James
- Heart and Lung Transplant Unit, St Vincent's Hospital, 390 Victoria St., Darlinghurst, NSW, Australia
| | - Macdonald Peter S
- Heart and Lung Transplant Unit, St Vincent's Hospital, 390 Victoria St., Darlinghurst, NSW, Australia
| | - Hayward Christopher S
- Heart and Lung Transplant Unit, St Vincent's Hospital, 390 Victoria St., Darlinghurst, NSW, Australia
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15
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Ghazy AA, Osman EM, Rashwan EA, Gaballah AH, Mostafa H, Tawfik S. Relation between microRNA-21, transforming growth factor β and response to treatment among chronic hepatitis C patients. J Med Virol 2019; 91:2166-2173. [PMID: 31368531 DOI: 10.1002/jmv.25559] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Persistence of hepatitis C virus (HCV) infection and response to antiviral therapy has been shown to be associated with inappropriate levels of cytokines and microRNAs (miRNAs). miRNA levels have been reported to fluctuate during treatment. Thus they could be useful predictors for responses to treatment among HCV infected patients, thereby reducing ineffective treatments. AIM The current study aimed to investigate the relation between miRNA-21 expression profiles, transforming growth factor β (TGF-β) serum levels and response to treatment with the new direct antiviral drugs (sofosbuvir + daclatasvir ± ribavirin), among HCV infected Egyptian patients. SUBJECTS AND METHODS This prospective study was conducted on 50 HCV infected patients (before and after treatment) and 20 healthy volunteers. miRNA expression profiles were determined by real-time polymerase chain reaction and TGF-β1 serum levels were measured by using enzyme-linked immunosorbent assay. RESULTS There was a significant increase in serum albumin, platelets count and a significant decrease in liver enzymes, serum bilirubin, and prothrombin time after treatment. Significant reduction of viral load among HCV patients after receiving the treatment was reported. Concomitantly, there was an increase in the relative quantity of miRNA-21 (P = .001*) and serum levels of TGF-β1 ( P = .337) among HCV patients after receiving treatment. CONCLUSION Nearly all responders to direct antiviral drugs showed increased levels of both miRNA-21 and TGF-β1. This may indicate an interplay between TGF-β1 and miRNA-21 during remission or progression of viral infection. Thus miRNA-21 could be used as promising serum biomarker, for assessment of antiviral treatment efficacy and improvement of fibrosis among chronically infected HCV patients.
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Affiliation(s)
- Amany A Ghazy
- Microbiology and Medical Immunology Unit, Pathology Departments, College of Medicine, Jouf University, Sakaka, Saudi Arabia.,Department of Microbiology & Medical Immunology, Faculty of Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Eman M Osman
- Department of Immunology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Eman A Rashwan
- Department of Immunology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Ahmed H Gaballah
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Hanan Mostafa
- Department of Internal Medicine, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Salwa Tawfik
- Department of Internal Medicine, National Research Center, Cairo, Egypt
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16
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Oestringer BP, Bolivar JH, Claridge JK, Almanea L, Chipot C, Dehez F, Holzmann N, Schnell JR, Zitzmann N. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features. Sci Rep 2019; 9:8383. [PMID: 31182749 PMCID: PMC6557816 DOI: 10.1038/s41598-019-44413-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022] Open
Abstract
The hepatitis C virus (HCV) viroporin p7 oligomerizes to form ion channels, which are required for the assembly and secretion of infectious viruses. The 63-amino acid p7 monomer has two putative transmembrane domains connected by a cytosolic loop, and has both N- and C- termini exposed to the endoplasmic reticulum (ER) lumen. NMR studies have indicated differences between p7 structures of distantly related HCV genotypes. A critical question is whether these differences arise from the high sequence variation between the different isolates and if so, how the divergent structures can support similar biological functions. Here, we present a side-by-side characterization of p7 derived from genotype 1b (isolate J4) in the detergent 6-cyclohexyl-1-hexylphosphocholine (Cyclofos-6) and p7 derived from genotype 5a (isolate EUH1480) in n-dodecylphosphocholine (DPC). The 5a isolate p7 in conditions previously associated with a disputed oligomeric form exhibits secondary structure, dynamics, and solvent accessibility broadly like those of the monomeric 1b isolate p7. The largest differences occur at the start of the second transmembrane domain, which is destabilized in the 5a isolate. The results show a broad consensus among the p7 variants that have been studied under a range of different conditions and indicate that distantly related HCVs preserve key features of structure and dynamics.
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Affiliation(s)
- Benjamin P Oestringer
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RY, United Kingdom
| | - Juan H Bolivar
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Jolyon K Claridge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Latifah Almanea
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Chris Chipot
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois, 61801, United States
| | - François Dehez
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Nicole Holzmann
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Jason R Schnell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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17
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Ammari M, McCarthy F, Nanduri B. Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome. ACTA ACUST UNITED AC 2019; 61:8.26.1-8.26.12. [PMID: 30040202 DOI: 10.1002/cpbi.44] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An increasing proportion of curated host-pathogen interaction (HPI) information is becoming available in interaction databases. These data represent detailed, experimentally-verified, molecular interaction data, which may be used to better understand infectious diseases. By their very nature, HPIs are context dependent, where the outcome of two proteins as interacting or not depends on the precise biological conditions studied and approaches used for identifying these interactions. The associated biology and the technical details of the experiments identifying interacting protein molecules are increasing being curated using defined curation standards but are overlooked in current HPI network modeling. Given the increase in data size and complexity, awareness of the process and variables included in HPI identification and curation, and their effect on data analysis and interpretation is crucial in understanding pathogenesis. We describe the use of HPI data for network modeling, aspects of curation that can help researchers to more accurately model specific infection conditions, and provide examples to illustrate these principles. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Mais Ammari
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
| | - Fiona McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
| | - Bindu Nanduri
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi.,College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi
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18
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Hepatitis C Infection in Hemodialysis Patients. CURRENT HEALTH SCIENCES JOURNAL 2019; 44:107-112. [PMID: 30746156 PMCID: PMC6320456 DOI: 10.12865/chsj.44.02.02] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/27/2018] [Indexed: 01/01/2023]
Abstract
Three centuries after the identification of hepatitis C virus (HCV), specialized literature has outlined the epidemiology, viral kinetics and clinical manifestations of this infection. A major cause of morbidity-mortality in patients with renal transplantation and in hemodialysis patients is HCV infection. In high seroprevalence countries, internal accounts are not uniform. The European trend is to decrease the incidence and prevalence of HCV in hemodialysis patients. In Europe, the prevalence of HCV infection among hemodialysis patients tends to be higher than that of the general population, but it is variable by region. Some studies indicate a decrease in incidence in parallel with prevalence in dialysis centers over the last 10 years, while others maintain a high incidence. In some countries, as is the case with Romania, both prevalence and incidence remain high, with the major route of transmission being nosocomial, probably due to limited resources for a rapidly growing dialyzed population. Some authors recommend more isolation measures to be taken in centers with high prevalence of infection.
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19
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Hua R, Jiang X, Qi L, Guan S, Kuai Z, Qiao Y, Xu Y, Gong X, Shi Y, Kong W, Niu J, Zhang H, Shan Y. Screening HCV genotype-specific epitope peptides based on conserved sequence analysis and B cell epitope prediction in HCV E2 region. Immunol Res 2019; 66:67-73. [PMID: 29151181 DOI: 10.1007/s12026-017-8962-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The high mutation rate of the hepatitis C virus (HCV) genome increases the genotype diversity and renders the detection of the virus more difficult. Therefore, prediction and assessment of highly conserved and strongly antigenic epitope polypeptide sequences have become a focus of current research. The E2 region is the target binding region of neutralizing antibodies. HCV genomics, especially the high mutation rate of E2 region sequence, makes its genotyping more and more diverse, and the detection of HCV and genotype is becoming more and more strict. In this study, four HCV B cell epitope polypeptides were constructed based on assessment of conserved sequences in the HCV E2 region and prediction of B cell epitopes, including sequences specific to genotype 1A (DC-13: 434-DTGWLAGLFYYHK-446), genotype 1B (HC-13: 434-HTGFLAALFYAKS-446), genotype 4D (NC-13: 434-NTGFLASLFYTHK-446), and a consensus sequence (FC-9: 447-FNSSGCPER-455). Epitope polypeptides combined with serum from 29 HCV-infected or 25 non-HCV-infected individuals were assayed by enzyme-linked immunosorbent assay (ELISA), and differences were analyzed by T/T' test methods in SPSS v20.0 software. Binding levels of genotype 1A, 4D, and consensus epitope polypeptides with sera of HCV-infected patients were higher than those of non-infected individuals. Moreover, binding of genotype 1B epitope polypeptides with serum of HCV 1B-infected patients was higher than that of HCV 2A-infected patients. While the screening results of HCV genotype-specific epitope polypeptides were preliminary, these findings indicated that we successfully established an HCV and genotype serological ELISA detection method. Such an approach would facilitate the discovery of epitope polypeptides which may become new antigen candidates in peptide vaccine development for the prevention of HCV infection.
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Affiliation(s)
- Rui Hua
- Department of Hepatology, The First Hospital, Jilin University, Changchun, Jilin, China
| | - Xiaoyu Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Lingxia Qi
- Department of Hepatology, The First Hospital, Jilin University, Changchun, Jilin, China
| | - Shanshan Guan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Ziyu Kuai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yongbo Qiao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yan Xu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Xin Gong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yuhua Shi
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China.,Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Junqi Niu
- Department of Hepatology, The First Hospital, Jilin University, Changchun, Jilin, China
| | - Hao Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China. .,Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin, China.
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20
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Ganta NM, Gedda G, Rathnakar B, Satyanarayana M, Yamajala B, Ahsan MJ, Jadav SS, Balaraju T. A review on HCV inhibitors: Significance of non-structural polyproteins. Eur J Med Chem 2018; 164:576-601. [PMID: 30639895 PMCID: PMC7185800 DOI: 10.1016/j.ejmech.2018.12.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022]
Abstract
Hepatitis C virus (HCV) mortality and morbidity is a world health misery with an approximate 130–150 million chronically HCV tainted and suffering individuals and it initiate critical liver malfunction like cirrhosis, hepatocellular carcinoma or liver HCV cancer. HCV NS5B protein one of the best studied therapeutic target for the identification of new drug candidates to be added to the combination or multiple combination medication recently approved. During the past few years, NS5B has thus been an important object of attractive medicinal chemistry endeavors, which induced to the surfacing of betrothal preclinical drug molecules. In this scenario, the current review set limit to discuss research published on NS5B and few other therapeutic functional inhibitors concentrating on hit investigation, hit to lead optimization, ADME parameters evaluation, and the SAR data which was out for each compound type and similarity taken into consideration. The discussion outlined in this specific review will surly helpful and vital tool for those medicinal chemists investigators working with HCV research programs mainly pointing on NS5B and set broad spectrum identification of creative anti HCV compounds. This mini review also tells each and every individual compound ability related how much they are active against NS5B and few other targets. Hepatitis C infection causes severe liver cirrhosis and carcinoma. The new acute HCV infections are raising every year and mortality rate become serious concern. The plausible list of anti-HCV drugs and clinical agents were listed in this review. The divergent medicinal scaffolds as anti-HCV agents were presented as per their targets.
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Affiliation(s)
- Narayana Murthy Ganta
- Department of Pharmaceutical Chemistry, Vishnu Institute of Pharmaceutical Education and Research, Narsapur, Medak, Telangana, 502313, India
| | - Gangaraju Gedda
- Department of Chemistry, School of Science, GITAM deemed to be University, Rudraram, Patancheru Mandal, Hyderabad, Telangana, Sangareddy Dist. 502329, India
| | - Bethi Rathnakar
- Department of Pharmaceutical Chemistry, Telangana University, Nizamabad, Telangana, 503322, India
| | - Mavurapu Satyanarayana
- Department of Pharmaceutical Chemistry, Telangana University, Nizamabad, Telangana, 503322, India
| | - Bhaskar Yamajala
- Department of Chemistry, School of Science, GITAM deemed to be University, Rudraram, Patancheru Mandal, Hyderabad, Telangana, Sangareddy Dist. 502329, India
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 62529, Saudi Arabia
| | - Surender Singh Jadav
- CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, India.
| | - Tuniki Balaraju
- Deapartment of Chemistry, Material Science Centre, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, WB, 741 246, India.
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21
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Akaberi D, Bergfors A, Kjellin M, Kameli N, Lidemalm L, Kolli B, Shafer RW, Palanisamy N, Lennerstrand J. Baseline dasabuvir resistance in Hepatitis C virus from the genotypes 1, 2 and 3 and modeling of the NS5B-dasabuvir complex by the in silico approach. Infect Ecol Epidemiol 2018; 8:1528117. [PMID: 30319736 PMCID: PMC6179053 DOI: 10.1080/20008686.2018.1528117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/13/2018] [Indexed: 02/08/2023] Open
Abstract
Background: Current combination treatments with direct-acting antiviral agents (DAAs) can cure more than 95% of hepatitis C virus (HCV) infections. However, resistance-associated substitutions (RASs) may emerge and can also be present in treatment-naïve patients. Methods, results and discussion: In this study, a semi-pan-genotypic population sequencing method was developed and used to assess all NS5B amino acid variants between residue positions 310 and 564. Our method successfully sequenced more than 90% of genotype (GT) 1a, 1b, 2b and 3a samples. By using the population sequencing method with a cut-off of 20%, we found the dasabuvir RASs A553V and C445F to be a baseline polymorphism of GT 2b (8 out of 8) and GT 3a (18 out of 18) sequences, respectively. In GT 1a and 1b treatment-naïve subjects (n=25), no high-fold resistance polymorphism/RASs were identified. We further predicted dasabuvir’s binding pose with the NS5B polymerase using the in silico methods to elucidate the reasons associated with the resistance of clinically relevant RASs. Dasabuvir was docked at the palm-I site and was found to form hydrogen bonds with the residues S288, I447, Y448, N291 and D318. The RAS positions 316, 414, 448, 553 and 556 were found to constitute the dasabuvir binding pocket.
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Affiliation(s)
- Dario Akaberi
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Assar Bergfors
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Midori Kjellin
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Nader Kameli
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Microbiology, NUTRIM school of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Louise Lidemalm
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Bhavya Kolli
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Robert W Shafer
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Navaneethan Palanisamy
- HBIGS, University of Heidelberg, Heidelberg, Germany.,Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Johan Lennerstrand
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Elsebai MF, Abass K, Hakkola J, Atawia AR, Farag MA. The wild Egyptian artichoke as a promising functional food for the treatment of hepatitis C virus as revealed via UPLC-MS and clinical trials. Food Funct 2018; 7:3006-16. [PMID: 27296047 DOI: 10.1039/c6fo00656f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Infection by hepatitis C virus (HCV) and its subsequent complications are a major cause of mortality worldwide. The water extract of the wild Egyptian artichoke (WEA) (Cynara cardunculus L. var. sylvestris (Lam.) Fiori) leaves is a freely available herbal product that is used for treatment of HCV-infection complications such as jaundice and ascites. The purpose of this study was to evaluate whether WEA exhibits activity against HCV, identify bioactive chemicals in its extract and to tentatively examine the potential inhibitory interactions of WEA with human drug-metabolizing enzymes. The current pilot clinical trial revealed that the water extract of a WEA plant decreased the HCV viral load below the detection level in 12 out of 15 patients. Furthermore, the liver enzymes ALT and AST, as well as the level of bilirubin were normalized. The total WEA extract inhibited CYP2B6 (OH-BUP) and CYP2C19 (5-OH-OME) with high affinity, IC50 ∼ 20 μg ml(-1), while moderate inhibitory interactions were observed for CYP1A2, CYP2D6, CYP2E1 and CYP3A4. Results presented herein suggest that the WEA exhibits strong antiviral activity against HCV and may be useful for its treatment. Compared to the artichoke product "Hepar SL Forte(®)", WEA was found to be more enriched in sesquiterpenes versus the abundance of phenolic compounds, especially flavonoids in Hepar SL Forte(®) as revealed via UPLC-MS analysis coupled to chemometrics.
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Affiliation(s)
| | - Khaled Abass
- Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, FIN-90014, Oulu, Finland and Centre for Arctic Medicine, Thule Institute, University of Oulu, FIN-90014, Finland and Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, FIN-90014, Oulu, Finland
| | - Jukka Hakkola
- Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, FIN-90014, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, FIN-90014, Oulu, Finland
| | - Ahmed Rezk Atawia
- Department of Horticulture, Faculty of Agriculture, Moshtohor, Benha University, Egypt
| | - Mohamed A Farag
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, 11562, Cairo, Egypt.
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Consequence of HIV and HCV co-infection on host immune response, persistence and current treatment options. Virusdisease 2018; 29:19-26. [PMID: 29607354 DOI: 10.1007/s13337-018-0424-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/13/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is a common opportunistic pathogen especially among Human immunodeficiency virus (HIV) infected patients. Due to incongruous studies, the pathological effect of HCV on HIV induced disease are still not fully understood. While some studies have showed no effect of HCV on HIV infection, others reported a defined role of HCV in aggravating the rates of AIDS-related illnesses and mortality. The explanation of such variances may be due to the host immune response, viral genotypes, sub-type and quasi-species distribution. The factors that complicate the management of HIV/HCV patients are: (1) reduced HCV antibody production, (2) drug interactions, (3) liver disease and (4) different epidemiologic characteristics. However, it is abundantly clear that the morbidity and mortality caused by HCV have increased since the introduction of highly active antiretroviral therapy (HAART) against HIV. In this review, the consequence of HIV/HCV co-infection on host immune response, viral replication, disease progression, mortality and morbidity, viral load, persistence and current treatment options have been discussed. Based on the clinical studies, it is necessary to evaluate the effect of HCV therapy on HIV progression and to provide a fully active HCV treatment for patients receiving HIV treatment. In conclusion, it is recommended to provide fully active HAART therapy in combination with a known HCV therapy.
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Ombitasvir/paritaprevir/ritonavir + dasabuvir ± ribavirin for treatment of chronic hepatitis C 1 genotype in the Republic of Belarus. Clin Exp Hepatol 2017; 3:164-168. [PMID: 29062907 PMCID: PMC5649486 DOI: 10.5114/ceh.2017.70281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/04/2017] [Indexed: 01/16/2023] Open
Abstract
AIM OF THE STUDY Aim of the study is to evaluate real-world efficacy of the ombitasvir/ paritaprevir/ ritonavir + dasabuvir ± ribavirin for treatment of chronic hepatitis C 1 genotype. MATERIAL AND METHODS The study included 27 patients according to inclusion criteria. Main laboratory studies were performed in all patients at the baseline and during the treatment. RESULTS Efficacy of the antiviral therapy was assessed by measuring the SVR12 and the SVR24 along with measuring of viral load during the treatment. The SVR12 and SVR24 rate was 100% (27/27). DISCUSSION The results of the treatment were comparable to the results of pivotal, large-scale, randomized clinical trials. There were no serious adverse events during the treatment.
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Jin G, Lee J, Lee K. Chemical genetics-based development of small molecules targeting hepatitis C virus. Arch Pharm Res 2017; 40:1021-1036. [PMID: 28856597 DOI: 10.1007/s12272-017-0949-3] [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: 05/19/2017] [Accepted: 08/20/2017] [Indexed: 12/21/2022]
Abstract
Hepatitis C virus (HCV) infection is a major worldwide problem that has emerged as one of the most significant diseases affecting humans. There are currently no vaccines or efficient therapies without side effects, despite today's advanced medical technology. Currently, the common therapy for most patients (i.e. genotype 1) is combination of HCV-specific direct-acting antivirals (DAAs). Up to 2011, the standard of care (SOC) was a combination of peg-IFNα with ribavirin (RBV). After approval of NS3/4A protease inhibitor, SOC was peg-IFNα and RBV with either the first-generation DAAs boceprevir or telaprevir. In the past several years, various novel small molecules have been discovered and some of them (i.e., HCV polymerase, protease, helicase and entry inhibitors) have undergone clinical trials. Between 2013 and 2016, the second-generation DAA drugs simeprevir, asunaprevir, daclatasvir, dasabuvir, sofosbuvir, and elbasvir were approved, as well as the combinational drugs Harvoni®, Zepatier®, Technivie®, and Epclusa®. A number of reviews have been recently published describing the structure-activity relationship (SAR) in the development of HCV inhibitors and outlining current therapeutic approaches to hepatitis C infection. Target identification involves studying a drug's mechanism of action (MOA), and a variety of target identification methods have been developed in the past few years. Chemical biology has emerged as a powerful tool for studying biological processes using small molecules. The use of chemical genetic methods is a valuable strategy for studying the molecular mechanisms of the viral lifecycle and screening for anti-viral agents. Two general screening approaches have been employed: forward and reverse chemical genetics. This review reveals information on the small molecules in HCV drug discovery by using chemical genetics for targeting the HCV protein and describes successful examples of targets identified with these methods.
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Affiliation(s)
- Guanghai Jin
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jisu Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Kyeong Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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Up-regulation of circulating miRNA146a correlates with viral load via IRAK1 and TRAF6 in hepatitis C virus-infected patients. Virus Res 2017; 238:24-28. [PMID: 28587864 DOI: 10.1016/j.virusres.2017.05.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 05/18/2017] [Accepted: 05/30/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) is a life threatening human pathogen. It has been found that miRNA146a regulates innate immunity, inflammatory response and antiviral pathway. We evaluated miRNA146a expression by real-time PCR and IL-1 receptor associated kinase 1 (IRAK1) and TNF receptor-associated factor 6 (TRAF6) levels by ELISA in serum of 36 HCV viremia patients and 42 age and gender matched healthy controls. RESULTS miRNA146a expression was significantly higher in HCV patients with a best cut off value 1.63 to discriminate between HCV patients and healthy controls. Meanwhile, it was negatively correlated to IRAK1 and TRAF6 levels and positively correlated to viral load in HCV patients. CONCLUSIONS miRNA146a has a potential role in HCV infection and viral replication through IRAK1 and TRAF6. It can also serve as a new screening method for HCV.
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Martin MT, Deming P. Closing the Gap: The Challenges of Treating Hepatitis C Virus Genotype 3 Infection. Pharmacotherapy 2017; 37:735-747. [PMID: 28374965 DOI: 10.1002/phar.1933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The efficacy of hepatitis C virus (HCV) treatment has increased over the last 5 years to nearly 100% for many patient groups. Patients with genotype (GT) 3 HCV infection, however, and specifically cirrhotic or treatment-experienced patients, have lower sustained virologic response (SVR) rates than patients with other GTs. Because GT 3 presents more clinical challenges than other GTs, this review focuses on the evolution and efficacy of direct-acting antiviral (DAA) treatment options for HCV GT 3 infection after the historical standard of care with pegylated interferon and ribavirin. Our objective was to review the SVR rates with available and late-pipeline DAAs for HCV GT 3 infection and discuss challenges with successful GT 3 treatment. Authors performed a literature search of the PubMed/MEDLINE database (inception to March 27, 2017) and narrowed the field to clinical trials published in English. Trials that evaluated alternative treatments, non-DAA historical treatment, and DAAs not currently indicated for HCV were excluded. Trials only involving patients with human immunodeficiency virus/HCV coinfection were also excluded. Additional trials were identified from a review of the ClinicalTrials.gov database. Authors further identified references from a review of literature citations and reviewed annual meeting abstracts from the American Association for the Study of Liver Diseases and the European Association for the Study of the Liver for pipeline and real-world GT 3 data. Phase III trial data were not available to support all GT 3 treatment recommendations found in the guidelines. The SVR rates were lower in treatment-experienced and cirrhotic patients with GT 3 than other HCV populations. Treatment failure was associated with resistance to current treatment regimens. Clinical studies included patients with various levels of advanced liver disease, but few patients with decompensated cirrhosis were represented. Recent advances in pharmacologic treatment with DAAs have greatly increased SVR rates in patients with all HCV GTs, but SVR rates for treatment-experienced cirrhotic patients with GT 3 are lower than for other GTs. Given the limited data and observed SVR rates in this patient population, the optimal therapy for patients with decompensated cirrhotic GT 3 HCV infection is not yet established. Newer agents and recommendations regarding baseline resistance are likely to evolve treatment strategies in the near future.
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Affiliation(s)
- Michelle T Martin
- University of Illinois Hospital & Health Sciences System, Chicago, Illinois.,University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois
| | - Paulina Deming
- College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
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Tracing the epidemic history of hepatitis C virus genotypes in Saudi Arabia. INFECTION GENETICS AND EVOLUTION 2017; 52:82-88. [PMID: 28458032 DOI: 10.1016/j.meegid.2017.04.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 01/11/2023]
Abstract
HCV genotype 4 is highly prevalent in many Middle Eastern countries, yet little is known about the genotype's epidemic history at the subtype-level in this region. To address the dearth of data from Saudi Arabia (SA) we genotyped 230 HCV isolates in the core/E- and NS5B-region and analyzed using Bayesian phylogenetic approaches. HCV genotype 4 (HCV/4) was positive in 61.7% (142/230) of isolates belonging to 7 different subtypes with the predominance of 4d (73/142; 51.4%) followed by 4a (51/142; 35.9%). Phylogenetic analysis also revealed a distinct epidemiological cluster of HCV/4d for Saudi Arabia. HCV/1 appeared as the second most prevalent genotype positive in 31.3% (72/230) of isolates with the predominance of 1b (53/72; 73.6%) followed by 1a (16/72; 22.2%), and 1g (3/72; 4.1%). A small proportion of isolates belonged to HCV/3a (12/230; 5.2%), and HCV/2a (4/230; 1.7%). We estimate that the genotype 4 common ancestor existed around 1935 (1850-1985). Genotype 4 originated plausibly in Central Africa and multiple subtypes disseminated across African borders since ~1970, including subtype 4d which dominates current HCV infections in Saudi Arabia. The Bayesian skyline plot (BSP) analysis showed that genotype 4d entered the Saudi population in 1900. The effective number of HCV infections grew gradually until the second half of the 1950s and more rapidly until the early-80s through the use of imported blood units and blood products. Subsequently, the rate of HCV infection in the Saudi Arabian population was stabilized through effective screening of blood and infection control measures.
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29
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Win NN, Nakamoto S, Kanda T, Takahashi H, Takahashi-Nakaguchi A, Yasui S, Nakamura M, Wu S, Imazeki F, Mikami S, Yokosuka O, Gonoi T, Shirasawa H. Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences. Int J Mol Sci 2017; 18:ijms18010172. [PMID: 28106726 PMCID: PMC5297804 DOI: 10.3390/ijms18010172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 01/31/2023] Open
Abstract
Determination of hepatitis C virus (HCV) genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4) region and 5'-untranslated region (5'-UTR), respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results. Deep sequencing was also performed for the corresponding HCV NS4 regions. Seventeen out of 18 discrepant samples could be sequenced by the Sanger method. Both HCV core and NS4 sequences were concordant with that of genotyping in the 5'-UTR in all 17 samples. In cloning analysis of the HCV NS4 region, there were several amino acid variations, but each sequence was much closer to the peptide with the same genotype. Deep sequencing revealed that minor clones with different subgenotypes existed in two of the 17 samples. Genotyping by genome amplification showed high consistency, while several false reactions were detected by serotyping. The deep sequencing method also provides accurate genotyping results and may be useful for analyzing discrepant cases. HCV genotyping should be correctly determined before antiviral treatment.
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Affiliation(s)
- Nan Nwe Win
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Shingo Nakamoto
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Tatsuo Kanda
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.
| | | | - Shin Yasui
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Masato Nakamura
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Shuang Wu
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Fumio Imazeki
- Safety and Health Organization, Chiba University, Chiba 263-8522, Japan.
| | - Shigeru Mikami
- Department of Gastroenterology, Kikkoman General Hospital, Noda 278-0005, Japan.
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.
| | - Hiroshi Shirasawa
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan.
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Igarashi A, Tang W, Cure S, Guerra I, Marié L, Lopresti M, Tsutani K. Cost-utility analysis of sofosbuvir for the treatment of genotype 2 chronic hepatitis C in Japan. Curr Med Res Opin 2017; 33:1-10. [PMID: 27608157 DOI: 10.1080/03007995.2016.1222512] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Across Japan, around 2 million people are infected with hepatitis C virus (HCV) with long-term complications such as cirrhosis, hepatocellular carcinoma (HCC) and liver transplant (LT). Current treatment options have several limitations due to side effects, interferon intolerability and ineligibility, long treatment durations and low sustained virological responses (SVR) rates, especially for the most severe patients. Sofosbuvir (SOF) is the first nucleotide analog NS5B polymerase inhibitor with pan-genotypic activity. SOF, administered in combination with ribavirin (RBV) with or without pegylated interferon (PEGIFN) resulted in high SVR rates across genotype (GT) 1-6 patients. It is also the first available regimen for patients that are unsuitable for interferon. This analysis assessed the cost-utility ratio of sofosbuvir in GT2 patients in Japan. RESEARCH DESIGN AND METHODS A Markov model followed a cohort of 10,000 GT2 patients until patients reached 100 years of age. Approximately 20% of patients initiated treatment at the cirrhotic stage. Comparators were based on the current recommendations in Japan, including PEGIFN with ribavirin (RBV), telaprevir (TVR) in combination with PEGIFN + RBV and no treatment. Costs and outcomes were discounted at 2%. RESULTS Sofosbuvir was cost-effective across all the studied indications, especially in patients unsuitable for interferon, with incremental cost-effectiveness ratios (ICERs) lower than JPY 5,000,000. Compared to the other treatments included in the analysis, SOF + RBV resulted in improved clinical outcomes. Results were robust to sensitivity analyses. CONCLUSION SOF combined with RBV was shown to be cost-effective in GT2 patients in Japan. Compared to PEGIFN + RBV, TVR + PEGIFN + RBV and no treatment SOF offers a more efficacious, shorter and better tolerated treatment option and extends treatment to reach HCV-infected patients who are ineligible for interferon-based regimens. Although adverse events were not included in the analyses, this would not make any changes to our conclusion.
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Affiliation(s)
- Ataru Igarashi
- a Graduate School of Pharmaceutical Sciences, The University of Tokyo , Tokyo , Japan
| | - Wentao Tang
- a Graduate School of Pharmaceutical Sciences, The University of Tokyo , Tokyo , Japan
| | | | | | | | | | - Kiichiro Tsutani
- a Graduate School of Pharmaceutical Sciences, The University of Tokyo , Tokyo , Japan
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Ismail NSM, Elzahabi HSA, Sabry P, Baselious FN, AbdelMalak AS, Hanna F. A study of the allosteric inhibition of HCV RNA-dependent RNA polymerase and implementing virtual screening for the selection of promising dual-site inhibitors with low resistance potential. J Recept Signal Transduct Res 2016; 37:341-354. [PMID: 27829320 DOI: 10.1080/10799893.2016.1248293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Structure-based pharmacophores were generated and validated using the bioactive conformations of different co-crystallized enzyme-inhibitor complexes for allosteric palm-1 and thumb-2 inhibitors of NS5B. Two pharmacophore models were obtained, one for palm-1 inhibitors with sensitivity = 0.929 and specificity = 0.983, and the other for thumb-2 inhibitors with sensitivity = 1 and specificity = 0.979. In addition, a quantitative structure activity relationship (QSAR) models were developed based on using the values of different scoring functions as descriptors predicting the activity on both allosteric binding sites (palm-1 and thumb-2). QSAR studies revealed good predictive and statistically significant two descriptor models (r2 = .837, r2adjusted = .792 and r2prediction = .688 for palm-1 model and r2 = .927, r2adjusted = .908 and r2prediction = .779 for thumb-2 model). External validation for the QSAR models assured their prediction power with r2ext = .72 and .89 for palm-1 and thumb-2, respectively. Different docking protocols were examined for their validity to predict the correct binding poses of inhibitors inside their respective binding sites. Virtual screening was carried out on ZINC database using the generated pharmacophores, the selected valid docking algorithms and QSAR models to find compounds that could theoretically bind to both sites simultaneously.
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Affiliation(s)
- Nasser S M Ismail
- a Pharmaceutical Chemistry Department, Faculty of Pharmaceutical Sciences and Pharmaceutical Industries , Future University , Cairo , Egypt
| | - Heba S A Elzahabi
- b Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Al-Azhar University , Cairo , Egypt
| | - Peter Sabry
- c National Organization for Drug Control and Research , Dokki , Cairo , Egypt
| | - Fady N Baselious
- d Department of Research and Development , Global Napi Pharmaceuticals , 6th October City , Giza , Egypt
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Shah SR, Rao PN, Sarin SK, Chowdhury A, Bhatia S, Dharamsi R, Goswami BD, Kapoor D, Luaia R, Mehta R, Mukewar S, Prasad VGM, Rai RR, Saigal S, Singh D, Trehanpati N, Chen S, Gaggar A, Knox SJ, Subramanian GM, Singh SP, Sood A, Varghese J, Venugopal RV. Chronic hepatitis C virus infection in India: Regional demographics and distribution of viral genotypes. Indian J Gastroenterol 2016; 35:469-477. [PMID: 27844277 DOI: 10.1007/s12664-016-0709-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/11/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Although chronic hepatitis C virus (HCV) infection affects millions of people in India, few studies have assessed host, viral, and disease characteristics of chronically infected patients at national and regional levels. Such information is critical to support large scale screening and treatment initiatives for chronic HCV infection in India. METHODS Patients with known chronic HCV infection making routine or for-cause visits to the participating study centers were enrolled in this observational study. Patients attended a single outpatient visit during which demographics and medical history were collected, a physical examination was performed, and blood and urine samples were collected for laboratory assessments. Samples were analyzed to determine HCV genotypes and subtypes, and genotypes of interferon lambda 3 (IFNL3) single nucleotide polymorphism. No therapeutic interventions were administered. RESULTS We enrolled 500 patients at 19 centers, categorized into four geographic regions (North, South, East, and West). All patients self-identified as Indian, and most (66 %) were male. Genotype 3 was the most common genotype overall (54 %); however, its prevalence varied greatly by region, ranging from 34 % in the South to 69 % in the East. Genotypes 1 (24 %) and 4 (6 %) were the next most common, and HCV genotype could not be determined for 16 % of patients. CONCLUSIONS This prospective survey suggests that demographics, viral, and host factors in patients with chronic HCV infection are highly variable in India and pose significant challenges for the implementation of broad-scale screening and treatment initiatives.
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Affiliation(s)
- Samir R Shah
- Global Hospitals, 35, Dr. E Borges Road, Parel, Mumbai, 400 012, India.
| | - P N Rao
- Asian Institute of Gastroenterology, 6-3-661, Somajiguda, Hyderabad, 500 082, India
| | - Shiv K Sarin
- Institute of Liver and Biliary Sciences, D-1, Vasant Kunj, New Delhi, Delhi, 110 070, India
| | - Abhijit Chowdhury
- Institute of Post Graduate Medical Education and Research, 244 A.J.C Bose Road, Kolkata, 700 020, India
| | - Shobna Bhatia
- Seth GS Medical College and KEM Hospital, Acharya Donde Marg, Parel, Mumbai, 400 012, India
| | - Rajesh Dharamsi
- Dharamsi Hospital, Chandni Chowk, South Shivaji Nagar, Nishant Colony, Sangli, 416 416, India
| | - B D Goswami
- Institute of Digestive and Liver Disease, Guwahati, Assam, India
| | | | - Rosang Luaia
- Civil Hospital, Dawrpui, Aizawl, Mizoram, 796 001, India
| | - Rajiv Mehta
- Liver Clinic, U-9 Jolly Plaza, Athwagate, Surat, 395 001, India
| | - Shrikant Mukewar
- Midas Institute of Gastroenterology, Midas Heights, Central Bazar Road, Ramdas Peth, Ramdaspeth, Nagpur, 440 012, India
| | - V G Mohan Prasad
- VGM Hospital, 2100, Trichy Road, Singanallur, Coimbatore, 641 005, India
| | - Ramesh Roop Rai
- Rai Speciality Care Centre, H-6, Janpath, Shyam Nagar, Ajmer Road, Sodala, Jaipur, 302 019, India
| | - Sanjiv Saigal
- Medanta-The Medicity, Sector 38, Gurgaon, Delhi (NCR), 122 018, India
| | | | - Nirupama Trehanpati
- Institute of Liver and Biliary Sciences, D-1, Vasant Kunj, New Delhi, Delhi, 110 070, India
| | - Sandra Chen
- Gilead Sciences, 333 Lakeside Dr, Foster City, CA, 94404, USA
| | - Anuj Gaggar
- Gilead Sciences, 333 Lakeside Dr, Foster City, CA, 94404, USA
| | - Steven J Knox
- Gilead Sciences, 333 Lakeside Dr, Foster City, CA, 94404, USA
| | | | - Shivaram Prasad Singh
- Department of Gastroenterology, S.C.B. Medical College, Manglabag, Cuttack, 753 007, India
| | - Ajit Sood
- Dayanand Medical College and Hospital, Tagore Nagar, Civil Lines, Ludhiana, 141 001, India
| | - Joy Varghese
- Global Hospitals and Health City, 439, Cheran Nagar, Perumbakkam, Chennai, 600 100, India
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Heterogeneous genomic locations within NS3, NS4A and NS4B identified for genotyping and subtyping of Hepatitis C virus: A simple genome analysis approach. INFECTION GENETICS AND EVOLUTION 2016; 44:61-68. [DOI: 10.1016/j.meegid.2016.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 01/05/2023]
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You Y, Kim HS, Bae IH, Lee SG, Jee MH, Keum G, Jang SK, Kim BM. New potent biaryl sulfate-based hepatitis C virus inhibitors. Eur J Med Chem 2016; 125:87-100. [PMID: 27657807 DOI: 10.1016/j.ejmech.2016.09.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
The discovery of a new series of potent hepatitis C virus (HCV) NS5A inhibitors containing biaryl sulfone or sulfate cores is reported. Structure-activity relationship (SAR) studies on inhibitors containing various substitution patterns of the sulfate or sulfone core structure established that m-,m'- substituted biaryl sulfate core-based inhibitors containing an amide moiety (compound 20) or an imidazole moiety (compound 24) showed extremely high potency. Compound 20 demonstrated double-digit pM potencies against both genotype 1b (GT-1b) and 2a (GT-2a). Compound 24 also exhibited double-digit pM potencies against GT-1b and sub nM potencies against GT-2a. Furthermore, compounds 20 and 24 exhibited no cardiotoxicity in an hERG ligand binding assay and showed acceptable plasma stability and no mutagenic potential in the Ames test. In addition, these compounds showed distinctive additive effects in combination treatment with the NS5B targeting drug sofosbuvir (Sovaldi®). The results of this study showed that the compounds 20 and 24 could be effective HCV inhibitors.
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Affiliation(s)
- Youngsu You
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Hee Sun Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Il Hak Bae
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Seung Gi Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Min Hyeok Jee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Gyochang Keum
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, South Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea.
| | - B Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, South Korea.
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Immunogenicity and functional characterization of Leishmania-derived hepatitis C virus envelope glycoprotein complex. Sci Rep 2016; 6:30627. [PMID: 27481352 PMCID: PMC4969751 DOI: 10.1038/srep30627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/06/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are the main inducers of a cross-neutralizing antibody response which plays an important role in the early phase of viral infection. Correctly folded and immunologically active E1E2 complex can be expressed in mammalian cells, though the production process might still prove restrictive, even if the immunological response of a vaccine candidate is positive. Here, we report a characterization and immunogenicity study of a full-length (fE1E2) and soluble version of the E1E2 complex (tE1E2) from genotype 1a, successfully expressed in the cells of Leishmania tarentolae. In a functional study, we confirmed the binding of both Leishmania-derived E1E2 complexes to the CD-81 receptor and the presence of the major epitopes participating in a neutralizing antibody response. Both complexes were proved to be highly immunogenic in mice and elicited neutralizing antibody response. Moreover, cross-reactivity of the mouse sera was detected for all tested HCV genotypes with the highest signal intensity observed for genotypes 1a, 1b, 5 and 6. Since the development of a prophylactic vaccine against HCV is still needed to control the global infection, our Leishmania-derived E1E2 glycoproteins could be considered a potential cost-effective vaccine candidate.
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Abstract
Soon after the hepatitis C virus (HCV) was identified in 1989, it was recognized that the prevalence of infection in patients with ESRD far exceeded that in the general population. Infection with HCV predisposes to the hepatic complications of cirrhosis and hepatocellular carcinoma. However, important extrahepatic manifestations include immune complex glomerular disease, accelerated progression of CKD, increases in cardiovascular event risk, and lymphoproliferative disorders. Advances in understanding the molecular biology of HCV have ushered in a new era in the treatment of this infection. Second generation direct-acting antiviral agents have revolutionized therapy, with sustained virologic response rates (undetectable viral load 12 weeks after completing therapy) of >90% in most patients. Studies using direct-acting antivirals in patients with CKD and those on dialysis are showing excellent safety and efficacy as well. In this context, it is imperative that nephrologists become familiar with this literature, reviewed here, so that the important decisions, including which patients should be treated and the optimal timing to initiate therapy, are vetted in association with the compounding issues of CKD, ESRD, and kidney transplantation.
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Affiliation(s)
- Marco Ladino
- Division of Nephrology and Hypertension, University of Miami Miller School of Medicine and the Miami Veterans Administration Hospital, Miami, Florida
| | - Fernando Pedraza
- Division of Nephrology and Hypertension, University of Miami Miller School of Medicine and the Miami Veterans Administration Hospital, Miami, Florida
| | - David Roth
- Division of Nephrology and Hypertension, University of Miami Miller School of Medicine and the Miami Veterans Administration Hospital, Miami, Florida
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Sargin Altunok E, Sayan M, Akhan S, Aygen B, Yildiz O, Tekin Koruk S, Mistik R, Demirturk N, Ural O, Kose Ş, Aynioglu A, Korkmaz F, Ersoz G, Tuna N, Ayaz C, Karakecili F, Keten D, Inan D, Yazici S, Koculu S, Yildirmak T. Protease Inhibitors Drug Resistance Mutations in Turkish Patients with Chronic Hepatitis C. Int J Infect Dis 2016; 50:1-5. [PMID: 27401586 DOI: 10.1016/j.ijid.2016.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/30/2016] [Accepted: 07/03/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Drug resistance development is an expected problem during treatment with protease inhibitors (PIs), this is largely due to the fact that Pls are low-genetic barrier drugs. Resistance-associated variants (RAVs) however may also occur naturally, and prior to treatment with Pls, the clinical impact of this basal resistance remains unknown. In Turkey, there is yet to be an investigation into the hepatitis C (HCV) drug associated resistance to oral antivirals. MATERIALS AND METHODS 178 antiviral-naïve patients infected with HCV genotype 1 were selected from 27 clinical centers of various geographical regions in Turkey and included in the current study. The basal NS3 Pls resistance mutations of these patients were analyzed. RESULTS In 33 (18.5%) of the patients included in the study, at least one mutation pattern that can cause drug resistance was identified. The most frequently detected mutation pattern was T54S while R109K was the second most frequently detected. Following a more general examination of the patients studied, telaprevir (TVR) resistance in 27 patients (15.2%), boceprevir (BOC) resistance in 26 (14.6%) patients, simeprevir (SMV) resistance in 11 (6.2%) patients and faldaprevir resistance in 13 (7.3%) patients were detected. Our investigation also revealed that rebound developed in the presence of a Q80K mutation and amongst two V55A mutations following treatment with TVR, while no response to treatment was detected in a patient with a R55K mutation. CONCLUSION We are of the opinion that drug resistance analyses can be beneficial and necessary in revealing which variants are responsible for pre-treatment natural resistance and which mutations are responsible for the viral breakthrough that may develop during the treatment.
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Affiliation(s)
- Elif Sargin Altunok
- Infectious Diseases and Clinical Microbiology, Bitlis Public Hospital, Bitlis 13000, Turkey
| | - Murat Sayan
- Clinical Laboratory, Kocaeli University Faculty of Medicine, Kocaeli 41380, Turkey; Near East University, Research Center of Experimental Health Sciences, Nicosia, Northern Cyprus
| | - Sila Akhan
- Infectious Diseases And Clinical Microbiology, Kocaeli University Faculty of Medicine, Kocaeli 41380, Turkey
| | - Bilgehan Aygen
- Infectious Diseases And Clinical Microbiology, Erciyes University Faculty of Medicine, Kayseri 38030, Turkey
| | - Orhan Yildiz
- Infectious Diseases And Clinical Microbiology, Erciyes University Faculty of Medicine, Kayseri 38030, Turkey
| | - Suda Tekin Koruk
- Infectious Diseases and Clinical Microbiology, Koc University Faculty of Medicine, İstanbul 34010, Turkey
| | - Resit Mistik
- Infectious Diseases and Clinical Microbiology, Uludag University Faculty of Medicine, Bursa, Turkey
| | - Nese Demirturk
- Infectious Diseases and Clinical Microbiology, Afyon Kocatepe University Faculty of Medicine, Afyonkarahisar, Turkey
| | - Onur Ural
- Infectious Diseases and Clinical Microbiology, Selçuk University Faculty of Medicine, Konya, Turkey
| | - Şükran Kose
- Infectious Diseases and Clinical Microbiology, Tepecik Training and Research Hospital, İzmir, Turkey
| | - Aynur Aynioglu
- Infectious Diseases and Clinical Microbiology, Zonguldak Ataturk Public Hospital, Zonguldak, Turkey
| | - Fatime Korkmaz
- Infectious Diseases and Clinical Microbiology, Konya Training and Research Hospital, Konya, Turkey
| | - Gülden Ersoz
- Infectious Diseases And Clinical Microbiology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Nazan Tuna
- Infectious Diseases and Clinical Microbiology, Sakarya University Faculty of Medicine, Sakarya, Turkey
| | - Celal Ayaz
- Infectious Diseases and Clinical Microbiology, Dicle University Faculty of Medicine, Diyarbakir, Turkey
| | - Faruk Karakecili
- Infectious Diseases and Clinical Microbiology, Erzincan University Faculty of Medicine, Erzincan, Turkey
| | - Derya Keten
- Infectious Diseases and Clinical Microbiology, Necip Fazil City Hospital, Kahramanmaraş, Turkey
| | - Dilara Inan
- Infectious Diseases and Clinical Microbiology, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Saadet Yazici
- Infectious Diseases and Clinical Microbiology, Göztepe Training and Research Hospital, İstanbul, Turkey
| | - Safiye Koculu
- Infectious Diseases and Clinical Microbiology, Giresun Public Hospital, Giresun, Turkey
| | - Taner Yildirmak
- Infectious Diseases and Clinical Microbiology, Okmeydanı Training and Research Hospital, İstanbul, Turkey
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Palanisamy N, Lennerstrand J. Biophysical Studies on HCV 1a NS3/4A Protease and Its Catalytic Triad in Wild Type and Mutants by the In Silico Approach. Interdiscip Sci 2016; 10:143-156. [PMID: 27311576 DOI: 10.1007/s12539-016-0177-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 05/17/2016] [Accepted: 06/01/2016] [Indexed: 02/05/2023]
Abstract
The hepatitis C virus (HCV), of the family flaviviridae, is one of the major causes of chronic liver diseases. Until the year 2012, HCV infections were treated using PEG-interferon and ribavirin combinations, which have a low cure rate and severe side effects. Currently, many direct-acting antivirals (DAAs) are available, e.g. protease inhibitors, NS5A and polymerase inhibitors. These drugs have proven to be efficient in interferon-free treatment combinations and capable of enhancing the cure rate to above 90 %. Unlike PEG-interferon and ribavirin combinations, DAAs select for resistance in HCV. The R155K mutation in the HCV was found to resist all the currently available protease inhibitors. Here, we studied biophysical parameters like pocket (cavity) geometries and stabilizing residues of HCV 1a NS3/4A protease in wild type and mutants. We also studied HCV 1a NS3/4A protease's catalytic residues: their accessibility, energy, flexibility and binding to Phase II oral protease inhibitor vedroprevir (GS-9451), and compared these parameters between wild type and mutant(s). All these studies were performed using various bioinformatics tools (e.g. Swiss-PdbViewer and Schrödinger's Maestro) and web servers (e.g. DoGSiteScorer, SRide, ASA-View, WHAT IF, elNémo, CABS-flex, PatchDock and PLIP). From our study, we found that introduction of R155K, A156T or D168A mutation to wild-type NS3/4A protease increases the pocket's volume, surface (in the R155K mutant, surface decreases), lipo surface and depth and decreases the number of stabilizing residues. Additionally, differences in catalytic residues' solvent accessibility, energy, root-mean-square deviation (RMSD) and flexibility between wild type and mutants might explain changes in the protease activity and the resistance to protease inhibitors.
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Affiliation(s)
- Navaneethan Palanisamy
- Synthetic Biology Group, Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 267 (BioQuant), 69120, Heidelberg, Germany.
- The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany.
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, 751 85, Uppsala, Sweden.
| | - Johan Lennerstrand
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, 751 85, Uppsala, Sweden
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Estimating the Size of the HCV Infection Prevalence: A Modeling Approach Using the Incidence of Cases Reported to an Official Notification System. Bull Math Biol 2016; 78:970-90. [PMID: 27160282 DOI: 10.1007/s11538-016-0170-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/21/2016] [Indexed: 10/21/2022]
Abstract
In this paper we propose two methods to give a first rough estimate of the actual number of hepatitis C virus (HCV)-infected individuals (prevalence) taking into account the notification rate of newly diagnosed infections (incidence of notification) and the size of the liver transplantation waiting list (LTWL) of patients with liver failure due to chronic HCV infection. Both approaches, when applied to the Brazilian HCV situation converge to the same results, that is, the methods proposed reproduce both the prevalence of reported cases and the LTWL with reasonable accuracy. We use two methods to calculate the prevalence of HCV that, as a first, and very crude approximation, assumes that the actual prevalence of HCV in Brazil is proportional to the reported incidence to the official notification system with a constant denoted [Formula: see text]. In the paper we discuss the limitations and advantages of this assumption. With the two methods we calculated [Formula: see text], which reproduces both the reported incidence and the size of the LTWL. With the value of [Formula: see text] we calculated the prevalence I(a) (the integral of which resulted in 1.6 million people living with the infection in Brazil, most of whom unidentified). Other variables related to HCV infection (e.g., the distribution of the proportion of people aged a who got infected n years ago) can be easily calculated from this model. These new variables can then be measured and the model can be recursively updated, improving its accuracy.
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Esmail MA, Hassuna NA, Amr KS, Ghazawy ER, Abdel-Hamid M. Polymorphisms at IL28B gene as predictors of viral relapse in genotype 4 Egyptian hepatitis C patients. J Med Virol 2016; 88:481-6. [PMID: 26280154 DOI: 10.1002/jmv.24354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2015] [Indexed: 12/23/2022]
Abstract
Chronic HCV is one of the commonest causes of chronic liver disease worldwide with about 15% of population infected in Egypt. Certain single nucleotide polymorphisms (SNPs) lying near the IL28B gene were found to affect the spontaneous clearance as well as treatment outcome of HCV. To examine the association between different IL28B variants and the relapse of HCV infection after combined therapy with ribavirin and pegylated interferon (pegIFN). Hundered HCV genotype four patients received 1.5 mg/kg/week peginterferon alfa-2b plus 800-1400 mg/d ribavirin (weight-adjusted) for 48 weeks. IL28B polymorphisms (rs12980275, rs12979860, and 1 rs8099917) were studied in responders and relapsers at week 72. Out of 69 patients receiving treatment, 13 (18.8%) were relapsers. By stratifying patients on the basis of the IL-28/60 genotype (CC vs. CT/TT), CC patients showed lower relapse rates (2.3%) compared with CT/TT patients (46.2%) (P < 0.001). On the basis of the IL-28/75 genotype (GG vs. GA/AA), the GG patients achieved higher relapse rates (62.5%) compared with GA/AA patients (13.1%) (P = 0.004). Moreover, no statistical significant difference was observed between the TT patients compared with GG/GT patients on the basis of the IL-28/17 genotype. SNPs at IL-28/60 and IL-28/75 are possible predictors of relapse in patients receiving dual treatment.
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Affiliation(s)
| | - Noha A Hassuna
- Microbiology and Immunology Department, Faculty of Medicine, Minia University, Egypt
| | | | | | - Mohamed Abdel-Hamid
- Microbiology and Immunology Department, Faculty of Medicine, Minia University, Egypt
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Ederth J, Jern C, Norder H, Magnius L, Alm E, Rognsvåg BK, Sundin CG, Brytting M, Esbjörnsson J, Mild M. Molecular characterization of HCV in a Swedish county over 8 years (2002-2009) reveals distinct transmission patterns. Infect Ecol Epidemiol 2016; 6:30670. [PMID: 26854010 PMCID: PMC4744866 DOI: 10.3402/iee.v6.30670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 02/06/2023] Open
Abstract
Background Hepatitis C virus (HCV) is a major public health concern and data on its molecular epidemiology in Sweden is scarce. We carried out an 8-year population-based study of newly diagnosed HCV cases in one of Sweden's centrally situated counties, Södermanland (D-county). The aim was to characterize the HCV strains circulating, analyze their genetic relatedness to detect networks, and in combination with demographic data learn more about transmission. Methods Molecular analyses of serum samples from 91% (N=557) of all newly notified cases in D-county, 2002–2009, were performed. Phylogenetic analysis (NS5B gene, 300 bp) was linked to demographic data from the national surveillance database, SmiNet, to characterize D-county transmission clusters. The linear-by-linear association test (LBL) was used to analyze trends over time. Results The most prevalent subtypes were 1a (38%) and 3a (34%). Subtype 1a was most prevalent among cases transmitted via sexual contact, via contaminated blood, or blood products, while subtype 3a was most prevalent among people who inject drugs (PWIDs). Phylogenetic analysis revealed that the subtype 3a sequences formed more and larger transmission clusters (50% of the sequences clustered), while the 1a sequences formed smaller clusters (19% of the sequences clustered), possibly suggesting different epidemics. Conclusion We found different transmission patterns in D-county which may, from a public health perspective, have implications for how to control virus infections by targeted interventions.
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Affiliation(s)
- Josefine Ederth
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden;
| | - Camilla Jern
- Stockholm South General Hospital, Stockholm, Sweden
| | - Helené Norder
- Department of Infectious Medicine, Institute of Biomedicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars Magnius
- Department of Infectious Medicine, Institute of Biomedicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Alm
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | | | | | - Mia Brytting
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Joakim Esbjörnsson
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.,Nuffield Department Medicine, University of Oxford, Oxford, United Kingdom
| | - Mattias Mild
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
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Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing. Antiviral Res 2015; 126:81-9. [PMID: 26707078 DOI: 10.1016/j.antiviral.2015.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 11/05/2015] [Accepted: 12/15/2015] [Indexed: 01/03/2023]
Abstract
Development of Hepatitis C virus (HCV) resistance against direct-acting antivirals (DAAs), including NS5A inhibitors, is an obstacle to successful treatment of HCV when DAAs are used in sub-optimal combinations. Furthermore, it has been shown that baseline (pre-existing) resistance against DAAs is present in treatment naïve-patients and this will potentially complicate future treatment strategies in different HCV genotypes (GTs). Thus the aim was to detect low levels of NS5A resistant associated variants (RAVs) in a limited sample set of treatment-naïve patients of HCV GT1a and 3a, since such polymorphisms can display in vitro resistance as high as 60000 fold. Ultra-deep single molecule real time (SMRT) sequencing with the Pacific Biosciences (PacBio) RSII instrument was used to detect these RAVs. The SMRT sequencing was conducted on ten samples; three of them positive with Sanger sequencing (GT1a Q30H and Y93N, and GT3a Y93H), five GT1a samples, and two GT3a non-positive samples. The same methods were applied to the HCV GT1a H77-plasmid in a dilution series, in order to determine the error rates of replication, which in turn was used to determine the limit of detection (LOD), as defined by mean + 3SD, of minority variants down to 0.24%. We found important baseline NS5A RAVs at levels between 0.24 and 0.5%, which could potentially have clinical relevance. This new method with low level detection of baseline RAVs could be useful in predicting the most cost-efficient combination of DAA treatment, and reduce the treatment duration for an HCV infected individual.
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Pan-genotypic Hepatitis C Virus Inhibition by Natural Products Derived from the Wild Egyptian Artichoke. J Virol 2015; 90:1918-30. [PMID: 26656684 DOI: 10.1128/jvi.02030-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/25/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) infection is the leading cause of chronic liver diseases. Water extracts of the leaves of the wild Egyptian artichoke (WEA) [Cynara cardunculus L. var. sylvestris (Lam.) Fiori] have been used for centuries in the Sinai Peninsula to treat hepatitis symptoms. Here we isolated and characterized six compounds from the water extracts of WEA and evaluated their HCV inhibition capacities in vitro. Importantly, two of these compounds, grosheimol and cynaropicrin, inhibited HCV with half-maximal effective concentrations (EC50s) in the low micromolar range. They inhibited HCV entry into target cells and were active against both cell-free infection as well as cell-cell transmission. Furthermore, the antiviral activity of both compounds was pan-genotypic as HCV genotypes 1a, 1b, 2b, 3a, 4a, 5a, 6a, and 7a were inhibited. Thus, grosheimol and cynaropicrin are promising candidates for the development of new pan-genotypic entry inhibitors of HCV infection. IMPORTANCE Because there is no preventive HCV vaccine available today, the discovery of novel anti-HCV cell entry inhibitors could help develop preventive measures against infection. The present study describes two compounds isolated from the wild Egyptian artichoke (WEA) with respect to their structural elucidation, absolute configuration, and quantitative determination. Importantly, both compounds inhibited HCV infection in vitro. The first compound was an unknown molecule, and it was designated "grosheimol," while the second compound is the known molecule cynaropicrin. Both compounds belong to the group of sesquiterpene lactones. The mode of action of these compounds occurred during the early steps of the HCV life cycle, including cell-free and cell-cell infection inhibition. These natural compounds present promising candidates for further development into anti-HCV therapeutics.
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Tan WL, Yihui G, Abu Hassan MR. Demographic characteristics and intravenous drug use among hepatitis C patients in the Kota Setar district, Kedah, Malaysia. Epidemiol Health 2015. [PMID: 26212507 PMCID: PMC4616014 DOI: 10.4178/epih/e2015032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES: This study explored the demographic characteristics of hepatitis C patients in the Kota Setar (KS) district, Kedah, Malaysia, the prevalence of intravenous drug use (IVDU) as a risk factor among these patients, and the associations between IVDU and demographic characteristics. METHODS: Retrospective data pertaining to 713 patients from January 2009 to December 2013 were retrieved from hospital and disease notification records for analysis. The risk factors for hepatitis C virus (HCV) infection were grouped into IVDU and non-IVDU risk factors for analysis using multiple logistic regression. RESULTS: Of the hepatitis C patients included in this study, the most common age group was 31 to 40 years (30.2%), and male patients (91.2%) made up the overwhelming majority. Ethnic Malays constituted approximately 80.4% of the patients, and IVDU was the main risk factor (77.8%) for HCV infection. Multiple logistic regression showed that male patients were 59 times more likely to have IVDU as a risk factor for HCV infection. Single patients were 2.5 times more likely to have IVDU as a risk factor. Patients aged ≥71 years were much less likely than patients aged ≤30 years to have IVDU as a risk factor for HCV infection. CONCLUSIONS: IVDU was found to be an important risk factor for HCV infection among patients in the KS district. The factors associated with IVDU included age, sex, and marital status. Appropriate preventive measures should be developed to target the groups in which IVDU is most likely to be a risk factor for HCV infection.
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Affiliation(s)
- Wei Leong Tan
- Clinical Research Center, Sultanah Bahiyah Hospital, Kedah, Malaysia
| | - Goh Yihui
- Department of Opthalmology, Sultanah Bahiyah Hospital, Kedah, Malaysia
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Abstract
Hepatitis C virus (HCV) is a leading cause of chronic hepatitis and infects approximately three to four million people per year, about 170 million infected people in total, making it one of the major global health problems. In a minority of cases HCV is cleared spontaneously, but in most of the infected individuals infection progresses to a chronic state associated with high risk to develop liver cirrhosis, hepatocellular cancer, or liver failure. The treatment of HCV infection has evolved over the years. Interferon (IFN)-α in combination with ribavirin has been used for decades as standard therapy. More recently, a new standard-of-care treatment has been approved based on a triple combination with either HCV protease inhibitor telaprevir or boceprevir. In addition, various options for all-oral, IFN-free regimens are currently being evaluated. Despite substantial improvement of sustained virological response rates, some intrinsic limitations of these new direct-acting antivirals, including serious side effects, the risk of resistance development and high cost, urge the development of alternative or additional therapeutic strategies. Gene therapy represents a feasible alternative treatment. Small RNA technology, including RNA interference (RNAi) techniques and antisense approaches, is one of the potentially promising ways to investigate viral and host cell factors that are involved in HCV infection and replication. With this, newly developed gene therapy regimens will be provided to treat HCV. In this chapter, a comprehensive overview guides you through the current developments and applications of RNAi and microRNA-based gene therapy strategies in HCV treatment.
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Tong YQ, Liu B, Liu H, Zheng HY, Gu J, Liu H, Song EJ, Song C, Li Y. Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population. Clin Microbiol Infect 2015; 21:874.e9-874.e21. [PMID: 26055416 DOI: 10.1016/j.cmi.2015.05.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/10/2015] [Accepted: 05/26/2015] [Indexed: 12/21/2022]
Abstract
Nucleotide sequencing of the phylogenetically informative region of NS5B remains the gold standard for hepatitis C virus (HCV) genotyping. Here we developed a new methodology for sequencing new NS5B regions to increase the accuracy and sensitivity of HCV genotyping and subtyping. The eight new primers were identified by scanning the full-length NS5B regions from 1127 HCV genomic sequences found in HCV databases. The ability of each pair of primers to amplify HCV subtypes was scored, and the new primers were able to amplify the NS5B region better than the previously used primers, therefore more accurately subtyping HCV strains. Sequencing the DNA amplified by the new primer pairs can specifically and correctly detect the five standard HCV subtypes (1a, 2a, 3b, 6a and 1b). We further examined patient samples and found that the new primers were able to identify HCV subtypes in clinical samples with high sensitivity. This method was able to detect all subtypes of HCV in 567 clinical samples. Importantly, three novel HCV subtypes (1b-2a, 1b-2k and 6d-6k) were identified in the samples, which have not been previous reported in China. In conclusion, sequencing the NS5B region amplified by the new NS5B primers is a more reliable method of HCV genotyping and a more sensitive diagnostic tool than sequencing using the previously described primers, and could identify new HCV subtypes. Our research is useful for clinical diagnosis, guidance of clinical treatment, management of clinical patients, and studies on the epidemiology of HCV.
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Affiliation(s)
- Y-Q Tong
- Department of Clinical Laboratory, China; Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China
| | - B Liu
- Department of Pathology, Affiliated Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, China
| | - H Liu
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - H-Y Zheng
- Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China
| | - J Gu
- Department of Clinical Laboratory, China
| | - H Liu
- Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China
| | - E J Song
- Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, USA
| | - C Song
- Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, USA.
| | - Y Li
- Department of Clinical Laboratory, China; Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China.
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Shehat MG, Bahey-El-Din M, Kassem MA, Farghaly FA, Abdul-Rahman MH, Fanaki NH. Recombinant expression of the alternate reading frame protein (ARFP) of hepatitis C virus genotype 4a (HCV-4a) and detection of ARFP and anti-ARFP antibodies in HCV-infected patients. Arch Virol 2015; 160:1939-52. [PMID: 26036563 DOI: 10.1007/s00705-015-2465-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 05/23/2015] [Indexed: 01/27/2023]
Abstract
HCV is a single-stranded RNA virus with a single open reading frame (ORF) that is translated into a polyprotein that is then processed to form 10 viral proteins. An additional eleventh viral protein, the alternative reading frame protein (ARFP), was discovered relatively recently. This protein results from a translational frameshift in the core region during the expression of the viral proteins. Recombinant expression of different forms of ARFP was previously done for HCV genotypes 1 and 2, and more recently, genotype 3. However, none of the previous studies addressed the expression of ARFP of HCV genotype 4a, which is responsible for 80 % of HCV infections in the Middle East and Africa. Moreover, the direct detection of the ARFP antigen in HCV-infected patients was never studied before for any HCV genotype. In the present study, recombinant ARFP derived from HCV genotype 4a was successfully expressed in E. coli and purified using metal affinity chromatography. The recombinant ARFP protein and anti-ARFP antibodies were used for detection of ARFP antigen in patients' sera, employing competitive enzyme-linked immunosorbent assay (ELISA) procedures. Furthermore, the recombinant antigen was also used to detect and quantify anti-ARFP antibodies in HCV-infected Egyptian patients at different stages of pegylated interferon/ribavirin therapy, using an ELISA assay. The ARFP antigen was detectable in 69.4 % of RNA-positive sera, indicating that ARFP antigen is produced during the natural course of HCV infection. In addition, significant levels of anti-ARFP antibodies were present in 41 % of the serum samples tested. The important diagnostic value of the recombinant ARFP antigen was also demonstrated.
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Affiliation(s)
- Michael G Shehat
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
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Latli B, Hrapchak M, Chevliakov M, Li G, Campbell S, Busacca CA, Senanayake CH. Synthesis of deleobuvir, a potent hepatitis C virus polymerase inhibitor, and its major metabolites labeled with carbon-13 and carbon-14. J Labelled Comp Radiopharm 2015; 58:250-60. [PMID: 25964148 DOI: 10.1002/jlcr.3294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/10/2015] [Accepted: 04/01/2015] [Indexed: 01/09/2023]
Abstract
Deleobuvir, (2E)-3-(2-{1-[2-(5-bromopyrimidin-2-yl)-3-cyclopentyl-1-methyl-1H-indole-6-carboxamido]cyclobutyl}-1-methyl-1H-benzimidazol-6-yl)prop-2-enoic acid (1), is a non-nucleoside, potent, and selective inhibitor of hepatitis C virus NS5B polymerase. Herein, we describe the detailed synthesis of this compound labeled with carbon-13 and carbon-14. The synthesis of its three major metabolites, namely, the reduced double bond metabolite (2) and the acyl glucuronide derivatives of (1) and (2), is also reported. Aniline-(13) C6 was the starting material to prepare butyl (E)-3-(3-methylamino-4-nitrophenyl-(13) C6 )acrylate [(13) C6 ]-(11) in six steps. This intermediate was then used to obtain [(13) C6 ]-(1) and [(13) C6 ]-(2) in five and four more steps, respectively. For the radioactive synthesis, potassium cyanide-(14) C was used to prepare 1-cylobutylaminoacid [(14) C]-(23) via Buchrer-Bergs reaction. The carbonyl chloride of this acid was then used to access both [(14) C]-(1) and [(14) C]-(2) in four steps. The acyl glucuronide derivatives [(13) C6 ]-(3), [(13) C6 ]-(4) and [(14) C]-(3) were synthesized in three steps from the acids [(13) C6 ]-(1), [(13) C6 ]-(2) and [(14) C]-(1) using known procedures.
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Affiliation(s)
- Bachir Latli
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, CT, 06877-0368, USA
| | - Matt Hrapchak
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, CT, 06877-0368, USA
| | - Maxim Chevliakov
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, CT, 06877-0368, USA
| | - Guisheng Li
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, CT, 06877-0368, USA
| | - Scot Campbell
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, CT, 06877-0368, USA
| | - Carl A Busacca
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, CT, 06877-0368, USA
| | - Chris H Senanayake
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, CT, 06877-0368, USA
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Zhou L, Zhang HW, Tao S, Bassit L, Whitaker T, McBrayer TR, Ehteshami M, Amiralaei S, Pradere U, Cho JH, Amblard F, Bobeck D, Detorio M, Coats SJ, Schinazi RF. β-D-2'-C-Methyl-2,6-diaminopurine Ribonucleoside Phosphoramidates are Potent and Selective Inhibitors of Hepatitis C Virus (HCV) and Are Bioconverted Intracellularly to Bioactive 2,6-Diaminopurine and Guanosine 5'-Triphosphate Forms. J Med Chem 2015; 58:3445-58. [PMID: 25849312 PMCID: PMC7714489 DOI: 10.1021/jm501874e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The conversion of selected β-D-2,6-diaminopurine nucleosides (DAPNs) to their phosphoramidate prodrug (PD) substantially blocks the conversion to the G-analog allowing for the generation of two bioactive nucleoside triphosphates (NTPs) in human hepatocytes. A variety of 2'-C-methyl DAPN-PDs were prepared and evaluated for inhibition of HCV viral replication in Huh-7 cells, cytotoxicity in various cell lines, and cellular pharmacology in both Huh-7 and primary human liver cells. The DAPN-PDs were pan-genotypic, effective against various HCV resistant mutants, and resistant variants could not be selected. 2'-C-Me-DAPN-TP and 2'-C-Me-GTP were chain terminators for genotype 1b HCV-pol, and single nucleotide incorporation assays revealed that 2'-C-Me-DAPN-TP was incorporated opposite U. No cytotoxicity was observed with our DAPN-PD when tested up to 50 μM. A novel, DAPN-PD, 15c, has been selected for further evaluation because of its good virologic and toxicologic profile and its ability to deliver two active metabolites, potentially simplifying HCV treatment.
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Affiliation(s)
- Longhu Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Hong-wang Zhang
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Sijia Tao
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
| | - Tony Whitaker
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Tamara R. McBrayer
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Maryam Ehteshami
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Sheida Amiralaei
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Ugo Pradere
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Jong Hyun Cho
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
| | - Drew Bobeck
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Mervi Detorio
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
| | - Steven J. Coats
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
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50
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Purdy MA, Forbi JC, Sue A, Layden JE, Switzer WM, Opare-Sem OK, Phillips RO, Khudyakov YE. A re-evaluation of the origin of hepatitis C virus genotype 2 in West Africa. J Gen Virol 2015; 96:2157-2164. [PMID: 25888623 DOI: 10.1099/vir.0.000153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) is classified into seven genotypes based on genetic diversity, and most genotypes have been found in Africa. Infections with HCV genotype 2 (HCV2) are most prevalent in West Africa and it was suggested that HCV2 originated in West Africa. To better understand the evolutionary epidemiology of HCV2 in Africa, we examined new NS5B sequences of HCV2 strains obtained from Côte d'Ivoire, Ghana and Nigeria sequenced at the Centers for Disease Control and Prevention with those available from West, North and Central Africa. Bayesian phylogeographic analysis using a discrete trait model showed that Ghana was the most likely geographical region for the origin of HCV2. Spread of HCV2 from Ghana did not appear to be through diffusion to adjacent countries along the coast. Rather, it was transmitted from Ghana to many distant countries in Africa, suggesting that certain routes of geographical dissemination were historically more efficient than mere proximity and that the HCV2 epidemic history in West Africa is extremely complex.
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Affiliation(s)
- Michael A Purdy
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Joseph C Forbi
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Amanda Sue
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Jennifer E Layden
- Department of Public Health Sciences, Loyola University, Chicago, IL, 60660, USA
| | - William M Switzer
- Division of HIV/AIDS, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Ohene K Opare-Sem
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richard O Phillips
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yury E Khudyakov
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
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