1
|
Campos LB, de Almeida NAA, de Santana CG, Barbosa ENP, Horta MAP, Amendola Pires M, Brandão Mello CE, de Paula VS, de Barros JJF. Before Direct-Acting Antivirals for Hepatitis C Virus: Evaluation of Core Protein R70Q and L/C91M Substitutions in Chronically Infected Brazilian Patients Unresponsive to IFN and/or RBV. Viruses 2023; 15:187. [PMID: 36680226 PMCID: PMC9863677 DOI: 10.3390/v15010187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Although chronic hepatitis C has been effectively treated with direct-acting antivirals (DAAs), the use of conventional therapy with peg-interferon (Peg-IFN) or (predominantly) ribavirin (RBV), remains widespread. R70Q/H and L/C91M amino acid substitutions in the hepatitis C virus (HCV) core protein may modulate responses to IFN and/or RBV, and are associated with cirrhosis, hepatocellular carcinoma (HCC), insulin resistance, and liver steatosis. We evaluated the R70Q/H and L/C91M substitutions, clinical and epidemiological profiles, and risk factors of Brazilian patients chronically infected with HCV subgenotypes 1a and 1b (HCV-GT1a and HCV-GT1b) unresponsive to IFN and/or RBV therapy. Sequencing and pyrosequencing analyses and sociodemographic and clinical predictive variables were used to assess the relationship between R70Q/H and L/C91M substitutions. Leukocyte counts, ALT levels, and ALT/AST ratios were significantly reduced in treated individuals, but more of these patients had advanced fibrosis and cirrhosis. L91M was more prevalent (19.7%), occurring only in HCV-GT1b, followed by R70Q/P (11.5%) and R70P (1.4%). R70Q/P exhibited higher mean AST, ALT, and GGT values, whereas L91M showed higher mean GGT values. Pyrosequencing of the L91M position revealed mutant subpopulations in 43.75% of samples.
Collapse
Affiliation(s)
- Letícia Bomfim Campos
- Laboratory of Molecular Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | | | - Catarina Góis de Santana
- Gaffrée and Guinle University Hospital, Ambulatory of Liver Disease, Rio de Janeiro State Federal University/UniRio, Rio de Janeiro 20270-004, Brazil
| | | | | | - Márcia Amendola Pires
- Gaffrée and Guinle University Hospital, Ambulatory of Liver Disease, Rio de Janeiro State Federal University/UniRio, Rio de Janeiro 20270-004, Brazil
| | - Carlos Eduardo Brandão Mello
- Gaffrée and Guinle University Hospital, Ambulatory of Liver Disease, Rio de Janeiro State Federal University/UniRio, Rio de Janeiro 20270-004, Brazil
| | - Vanessa Salete de Paula
- Laboratory of Molecular Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | | |
Collapse
|
2
|
Khan A, Nawaz M, Ullah S, Rehman IU, Khan A, Saleem S, Zaman N, Shinwari ZK, Ali M, Wei DQ. Core amino acid substitutions in HCV-3a isolates from Pakistan and opportunities for multi-epitopic vaccines. J Biomol Struct Dyn 2022; 40:3753-3768. [PMID: 33246391 DOI: 10.1080/07391102.2020.1850353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatitis C virus (HCV), which infected 71 million worldwide and about 5%-6% are from Pakistan, is an ssRNA virus, responsible for end-stage liver disease. To date, no effective therapy is available to cure this disease. Hence, it is important to study the most prevalent genotypes infecting human population and design novel vaccine or small molecule inhibitors to control the infections associated with HCV. Therefore, in this study clinical samples (n = 35; HCV-3a) from HCV patients were subjected to Sanger sequencing method. The sequencing of the core gene, which is generally considered as conserved, involved in the detection, quantitation and genotyping of HCV was performed. Multiple mutations, that is, R46C, R70Q, L91C, G60E, N/S105A, P108A, N110I, S116V, G90S, A77G and G145R that could be linked with response to antiviral therapies were detected. Phylogenetic analysis suggests emerging viral isolates are circulating in Pakistan. Using ab initio modelling technique, we predicted the 3D structure of core protein and subjected to molecular dynamics simulation to extract the most stable conformation of the structure for further analysis. Immunoinformatic approaches were used to propose a multi-epitopes vaccine against HCV by using core protein. The vaccine constructs consist of nine CTL and three HTL epitopes joined by different linkers were docked against the two reported Toll-like receptors (TLR-3 and TLR-8). Docking of vaccine construct with TLR-3 and TLR-8 shows proper binding and in silico expression of the vaccine resulted in a CAI value of 0.93. These analyses suggest that specific immune responses may be produced by the proposed vaccine.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ayyaz Khan
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Mehboob Nawaz
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Saeed Ullah
- Saidu Group of Teaching Hospital, Swat, Pakistan
| | - Irshad Ur Rehman
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Shoaib Saleem
- National Center for Bioinformatics, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Nasib Zaman
- Center of Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Zabta Khan Shinwari
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.,Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China
| |
Collapse
|
3
|
Primary HCV Drug Resistance Mutations in Patients with Newly Diagnosed HIV Infection. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2020. [DOI: 10.21055/0370-1069-2020-3-97-105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Objective of our work was to assess prevalence of the primary HCV drug resistance mutations in the NS5b gene in patients with newly diagnosed HIV infection.Materials and methods. The study material was 196 blood plasma samples from patients living in the North-Western Federal District with newly diagnosed HIV. Samples were examined for the anti-HCV antibodies and HCV RNA presence. If HCV RNA was detected, amplification was performed using three primers pairs that co-flanked the NS5b gene. After sequencing the indicated gene nucleotide sequence, the virus subtype was determined and drug resistance mutations were detected.Results and discussion. Antibodies to HCV were detected in 18.87 % of HIV-infected individuals. HCV RNA was detected in 18.36 % of the patients, including 89.18 % anti-HCV-positive and 1.88 % anti-HCV-negative. It was shown that co-infection is more common in men (77.8 %) compared to women (22.2 %) – χ2 = 3.996 at p = 0.0456, df = 2. The difference in the HIV viral load between the groups with HIV monoinfection and with HIV + HCV coinfection was demonstrated (χ2 = 6.284 at p = 0.0432, df = 2). A significant difference between the groups by the CD4 + lyphocytes number was shown. In the phylogenetic analysis, the HCV subtypes are distributed as follows: HCV 1b – 47.2 %, HCV 3a – 30.6 %, HCV 1a – 13.9 %, HCV 2a – 5.5 % and only one sample was defined as HCV 2k – 2.8 %, respectively. Nine samples (25 %) presented NS5b mutations in the positions related to the development of drug resistance of HCV, including two samples among HCV genotypes 1a and 3a (i.e., 5.6 % of the total HIV + HCV group), as well as five samples among HCV 1b (13.9 % of the total group). Mutations among HCV 1a were C316Y and N444D substitutions. Among HCV 1b, C316N, C451S, S556N/G substitutions were identified. Among patients with HCV 3a, 2 samples (5.6 %) with a D310N mutation associated with an unfavorable disease prognosis were found. The introduction of direct sequencing of HCV nucleotide sequences into the routine laboratory diagnostics will allow us to estimate the primary drug resistance mutations prevalence in risk groups to predict the HCV life-threatening complications development – fibrosis, cirrhosis, hepatocellular carcinoma, as well as the outcome of antiviral therapy prognosis. The data obtained can be rationally used to assess the dynamics of the HCV primary pharmacoresistance prevalence among HIV-infected individuals.
Collapse
|
4
|
Factors Influencing the Prevalence of Resistance-Associated Substitutions in NS5A Protein in Treatment-Naive Patients with Chronic Hepatitis C. Biomedicines 2020; 8:biomedicines8040080. [PMID: 32272736 PMCID: PMC7235841 DOI: 10.3390/biomedicines8040080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/24/2020] [Accepted: 04/05/2020] [Indexed: 12/12/2022] Open
Abstract
Direct-acting antivirals (DAAs) revolutionized treatment of hepatitis C virus (HCV) infection. Resistance-associated substitutions (RASs) present at the baseline impair response to DAA due to rapid selection of resistant HCV strains. NS5A is indispensable target of the current DAA treatment regimens. We evaluated prevalence of RASs in NS5A in DAA-naïve patients infected with HCV 1a (n = 19), 1b (n = 93), and 3a (n = 90) before systematic DAA application in the territory of the Russian Federation. Total proportion of strains carrying at least one RAS constituted 35.1% (71/202). In HCV 1a we detected only M28V (57.9%) attributed to a founder effect. Common RASs in HCV 1b were R30Q (7.5%), L31M (5.4%), P58S (4.4%), and Y93H (5.4%); in HCV 3a, A30S (31.0%), A30K (5.7%), S62L (8.9%), and Y93H (2.2%). Prevalence of RASs in NS5A of HCV 1b and 3a was similar to that worldwide, including countries practicing massive DAA application, i.e., it was not related to treatment. NS5A with and without RASs exhibited different co-variance networks, which could be attributed to the necessity to preserve viral fitness. Majority of RASs were localized in polymorphic regions subjected to immune pressure, with selected substitutions allowing immune escape. Altogether, this explains high prevalence of RAS in NS5A and low barrier for their appearance in DAA-inexperienced population.
Collapse
|
5
|
Khan MA, Khan SA, Hamayun M, Ali M, Idrees M. Sequence variability of HCV 3a isolates based on core gene in patients from Lahore, Pakistan. Future Virol 2019. [DOI: 10.2217/fvl-2019-0086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aim: To investigate the HCV 3a core sequence variation and amino acid substitutions of patients from Lahore, Pakistan. Materials & methods: Blood samples from HCV positive patients (n = 232) were collected for viral genotypes. Moreover, the nucleotide sequencing was performed for core gene of 20 samples. Results: Viral genotyping showed that 69.82% (n = 162) belonged to 3a genotype, 9.05% (1a; n = 21), 2.15% (3b; n = 5) and 18.98% were untypable (n = 44). Phylogenetic analyses suggest majority of our isolates clustered with previously reported reference isolates from Pakistan. The remaining isolates clustered with HCV-core sequences reported from Vietnam, Japan, Thailand, Iran, USA, Bangladesh, Malaysia and Morocco. Conclusion: We report HCV-core substitutions (G60E, R70Q, C91A, A94Q and Q63E/D) that could be associated with treatment response in Pakistani patients.
Collapse
Affiliation(s)
- Muhammad Ajmal Khan
- Center for Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sumera Afzal Khan
- Center for Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Idrees
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
6
|
Kyuregyan KK, Malinnikova EY, Soboleva NV, Isaeva OV, Karlsen AA, Kichatova VS, Potemkin IA, Schibrik EV, Gadjieva OA, Bashiryan BA, Lebedeva NN, Serkov IL, Yankina A, Galli C, Mikhailov MI. Community screening for hepatitis C virus infection in a low-prevalence population. BMC Public Health 2019; 19:1038. [PMID: 31375104 PMCID: PMC6679455 DOI: 10.1186/s12889-019-7388-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/26/2019] [Indexed: 12/22/2022] Open
Abstract
Background Age cohort screening for hepatitis C virus (HCV) might be an effective strategy if the majority of undiagnosed cases are concentrated in a particular age group. The objective of this study was to determine HCV prevalence in different age cohorts of the general population in the Central European part of Russia and second, to assess feasibility of HCV antigen testing for community screening programs. Methods Sera from 2027 volunteers were tested for anti-HCV (Architect Anti-HCV, Abbott Laboratories). All anti-HCV reactive samples were confirmed in an immunoblot and tested for HCV Ag (ARCHITECT HCV Ag, Abbott Laboratories), HCV RNA and HCV viral load. Results Out of 31 individuals with anti-HCV reactive result, 22 (71%) were confirmed by immunoblot, six were false positives and three were indeterminate. Active infection was observed in 73% of anti-HCV confirmed positives. Five out of 16 individuals had low HCV-RNA levels (< 10,000 IU/mL) and one of those had a very low level (594 IU/mL). Agreement between HCV Ag and HCV RNA was 100%. Total anti-HCV and active HCV infection rates were 1.09% (22/2027) and 0.79% (16/2027), respectively. The peak rates were observed in people 60 years or older (anti-HCV: 2.84% [95% CI: 1.66–4.74%], 13/319; HCV RNA/HCV Ag: 2.23% [95% CI: 1.20–4.00%], 10/319). Conclusions Overall HCV prevalence is low, except in people 60 years or older. The latter should be considered as a target group for HCV screening. The high agreement between HCV RNA and HCV Ag suggests the utility of HCV Ag testing to confirm active infection in screening programs.
Collapse
Affiliation(s)
- Karen K Kyuregyan
- Department of Viral Hepatitis, Russian Medical Academy of Continuing Professional Education, 125993, Moscow, Russia. .,Mechnikov Research Institute for Vaccines and Sera, 105064, Moscow, Russia.
| | - Elena Yu Malinnikova
- Department of Viral Hepatitis, Russian Medical Academy of Continuing Professional Education, 125993, Moscow, Russia.,Mechnikov Research Institute for Vaccines and Sera, 105064, Moscow, Russia
| | - Natalia V Soboleva
- Mechnikov Research Institute for Vaccines and Sera, 105064, Moscow, Russia
| | - Olga V Isaeva
- Department of Viral Hepatitis, Russian Medical Academy of Continuing Professional Education, 125993, Moscow, Russia.,Mechnikov Research Institute for Vaccines and Sera, 105064, Moscow, Russia
| | - Anastasia A Karlsen
- Department of Viral Hepatitis, Russian Medical Academy of Continuing Professional Education, 125993, Moscow, Russia.,Mechnikov Research Institute for Vaccines and Sera, 105064, Moscow, Russia
| | - Vera S Kichatova
- Department of Viral Hepatitis, Russian Medical Academy of Continuing Professional Education, 125993, Moscow, Russia.,Mechnikov Research Institute for Vaccines and Sera, 105064, Moscow, Russia
| | - Ilya A Potemkin
- Department of Viral Hepatitis, Russian Medical Academy of Continuing Professional Education, 125993, Moscow, Russia.,Mechnikov Research Institute for Vaccines and Sera, 105064, Moscow, Russia
| | - Elena V Schibrik
- Belgorod regional center for disease control and prevention, 308023, Belgorod, Russia
| | - Olga A Gadjieva
- BurdenkoNational Medical Research Center of Neurosurgery, 125047, Moscow, Russia
| | - Boris A Bashiryan
- BurdenkoNational Medical Research Center of Neurosurgery, 125047, Moscow, Russia
| | - Natalya N Lebedeva
- Moscow Regional Center for the Prevention and Control of AIDS and Infectious Diseases, 129110, Moscow, Russia
| | - Igor L Serkov
- Moscow Regional Center for the Prevention and Control of AIDS and Infectious Diseases, 129110, Moscow, Russia
| | - Anna Yankina
- Medical Communications, Abbott Diagnostics, 125171, Moscow, Russia
| | - Claudio Galli
- Medical Affairs Infectious Diseases, Abbott Diagnostics, 00144, Rome, Italy
| | - Mikhail I Mikhailov
- Department of Viral Hepatitis, Russian Medical Academy of Continuing Professional Education, 125993, Moscow, Russia.,Mechnikov Research Institute for Vaccines and Sera, 105064, Moscow, Russia
| |
Collapse
|