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Pimenov N, Kostyushev D, Komarova S, Fomicheva A, Urtikov A, Belaia O, Umbetova K, Darvina O, Tsapkova N, Chulanov V. Epidemiology and Genotype Distribution of Hepatitis C Virus in Russia. Pathogens 2022; 11:pathogens11121482. [PMID: 36558817 PMCID: PMC9781887 DOI: 10.3390/pathogens11121482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The hepatitis C virus (HCV) causes both acute and chronic infection of the liver that can lead to liver cirrhosis, cancer, and liver failure. HCV is characterized by high genetic diversity and substantial variations in the prevalence of specific HCV genotypes throughout the world. Many effective regimens of direct-acting antivirals (DAAs), including pan-genotypic, can successfully treat HCV infection. Additionally, genotype-specific treatments for HCV are being actively employed in national plans for eliminating HCV infection around the world. The evaluation of HCV genotype prevalence in a given country is necessary for the successful implementation of the HCV elimination plans and for allocating financial resources to the DAAs which are the most effective against those specific HCV genotypes prevalent in a given country. Here, we analyzed HCV genotypes, subgenotypes, and recombinants in 10,107 serum samples collected in 2015-2017 from patients with chronic HCV infection living in all federal districts of Russia. This is the first and largest evaluation of HCV genotypes performed on samples from all territories of Russia, from its Central federal district to the Far East. Moreover, we have updated retrospective epidemiological analysis of chronic and acute HCV infection in Russia from 2001 to 2021. We demonstrate that the incidence of acute HCV (AHC) infection in Russia decreased from 16.7 cases per 100,000 people in 2001 to 0.6/100,000 in 2021. The number of cases of chronic HCV (CHC) infection also decreased from 29.5 to 16.4 per 100,000 people during this period. The HCV genotype analysis indicated that HCV genotype 1 dominates in Russia (53.6%), while genotypes 3 and 2 were detected in 35.4% and 7.8% of patients, respectively. These proportions are virtually identical in all regions of Russia except for the Far East, where HCV genotype 2 was detected in only 1% of the samples. HCV genotypes 1 and 2 are more widespread in women, and HCV genotype 3 in men. Genotype 3 was the most prevalent in 31-40-year-olds (44.9%), and genotype 1 was most prevalent in those over 70 years of age (72.2%). HCV genotype 2 was predominant among HCV-infected persons older than 40 years. Discriminating between HCV genotype 2 and recombinant RF1_2k/1b, which are frequently misclassified, is important for successful antiviral treatment. For the first time, we demonstrate, here, countrywide prevalence of HCV RF1_2k/1b in different regions of Russia. HCV RF1_2k/1b makes up 3.2% of HCV genotypes, reaching 30% among samples classified as genotype 2 by some commercial genotyping tests. The highest proportion of HCV RF1_2k/1b was detected in the North-West (60%), Southern (41.6%), and Central (31.6%) federal districts; its frequency in the Far Eastern and North Caucasus districts was ~14.3%. HCV RF1_2k/1b, and it was not detected in the Volga, Ural, or Siberian districts. To conclude, this is the first and most complete evaluation of HCV epidemiology and genotype/subgenotype distribution in Russia.
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Affiliation(s)
- Nikolay Pimenov
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Moscow 127473, Russia
| | - Dmitry Kostyushev
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
- Division of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia
- Correspondence:
| | - Svetlana Komarova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Moscow 127473, Russia
| | - Anastasia Fomicheva
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Moscow 127473, Russia
| | - Alexander Urtikov
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Moscow 127473, Russia
| | - Olga Belaia
- Department of Infectious Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Karina Umbetova
- Department of Infectious Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Olga Darvina
- Department of Infectious Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Natalia Tsapkova
- F. Erisman Institute of Public Health, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Vladimir Chulanov
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Moscow 127473, Russia
- Laboratory of Genetic Technologies, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
- Department of Infectious Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
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Akimov IA, Timofeev DI, Mavzyutov AR, Ivanov MK. Detection of circulating HCV recombinant form RF1_2k/1b in blood serum of patients by real-time RT-PCR. Klin Lab Diagn 2021; 66:122-128. [PMID: 33734647 DOI: 10.51620/0869-2084-2021-66-2-122-128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Globally, about 70 million people are infected with the hepatitis C virus (HCV), and about 400 thousand people die annually from chronic hepatitis C complications. The management of patients with chronic hepatitis C may require HCV genotyping, since the efficiency of some widely used antiviral drugs strongly depend on the viral genotype and/or subtype. The most prevalent HCV circulating recombinant form, RF1_2k/1b, is misclassified as genotype 2 by many commercial HCV genotyping kits, based on the RT-PCR analysis of the 5' untranslated region of the HCV genome. This leads to inappropriate patient treatment, since the accepted treatment schemes for HCV genotype 2 are ineffective for the RF1_2k/1b. Here we describe a method for detecting the RNA HCV RF1_2k/1b in blood samples by RT-PCR analysis of two regions in HCV genome (5'UTR and NS5b). The method was tested on 240 blood serum samples from HCV infected patients, in which HCV genotype was defined as 2 or mixed (2+1 or 2+3) by the two commercial genotyping kits "OT-Hepatogen-C genotype" ("DNA-Technology", Moscow) and "RealBest RNA HCV-1/2/3" ("Vector- Best ", Novosibirsk). 50 (20.8%) RF1_2k/1b cases were revealed, including three mixed infections: RF1_2k/1b + 1a, RF1_2k/1b + 3a, RF1_2k/1b + 1b. In all cases, the accuracy of HCV typing by the proposed method was confirmed by Sanger sequencing and phylogenetic analysis. The method is easy to implement into clinical practice and may be used in clinical settings equipped for RT-PCR analysis to correctly identify the recombinant variant RF1_2k/1b.
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Affiliation(s)
| | | | - A R Mavzyutov
- Research Center «Laboratory».,Bashkir State Medical University
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Zakalashvili M, Zarkua J, Gish RG, Zhamutashvili M, Sartania V, Weizenegger M, Bartel J, Raabe M, Gvinjilia L, Metreveli S, Barnova M, Abramishvili N, Rtskhiladze I, Metreveli D. Assessment of treatment options for patients with hepatitis C virus recombinant form 2k/1b. Hepatol Res 2021; 51:156-165. [PMID: 33207029 DOI: 10.1111/hepr.13587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Abstract
AIM Hepatitis C virus (HCV) intergenotype recombinant form (RF) 2k/1b has been actively circulating in HCV-infected patients, and the prevalence of this RF virus in the Republic of Georgia is one of the highest reported worldwide. The aim of this study was to define the optimal treatment regimen for patients with RF_2k/1b. METHODS We analyzed the data of 2735 patients who started treatment at the Medical Center Mrcheveli within Georgia's hepatitis C elimination program from May 2015 through December 2019. The patients were treated with sofosbuvir (SOF)-based regimens. For identification of RF_2k/1b variants, refinement of standard (INNO-LiPA) genotyping results for all patient samples assigned the unspecific HCV genotypes (GT) 2a/2c was carried out by sequencing of core and non-structural protein 5B genes. RESULTS Overall, 444 patients, representing 66% of GT2 and 16% of the total samples, were RF_2k/1b. Treatment of patients with RF_2k/1b with SOF/ledipasvir and SOF/velpatasvir was highly effective and viral cure rates did not differ among genotypes treated with the same regimen: RF_2k/1b, 99% (343/346); GT1, 99% (876/885); GT2, 96% (156/162); and GT3, 99% (545/552). A separate comparison analysis of sustained virologic response rate, treated with SOF plus ribavirin, showed significantly higher sustained virologic response (96%) in patients with confirmed GT2 (by sequencing) compared to unspecified GT2 (by INNO-LiPA) (79%) (P < 0.05). CONCLUSION Sofosbuvir-based regimens are highly effective for treatment of RF 2k/1b patients, and with availability of new pan-genotypic direct-acting antivirals, genotyping to identify RF 2k/1b patients might not be necessary.
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Affiliation(s)
- Mamuka Zakalashvili
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
| | - Jaba Zarkua
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
| | - Robert G Gish
- Hepatitis B Foundation, Doylestown, Pennsylvania, USA
| | - Maia Zhamutashvili
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
| | - Vakhtang Sartania
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
| | | | - Jan Bartel
- Medical Service Center Dr. Limbach & colleagues, Heidelberg, Germany
| | - Monika Raabe
- Medical Service Center Dr. Limbach & colleagues, Heidelberg, Germany
| | - Lia Gvinjilia
- TEPHINET independent contractor for Georgia Hepatitis C Elimination Program, Atlanta, Georgia, USA
| | - Sophia Metreveli
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
| | - Maka Barnova
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
| | - Nikoloz Abramishvili
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
| | - Irakli Rtskhiladze
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
| | - David Metreveli
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, Georgia
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Hostager R, Ragonnet-Cronin M, Murrell B, Hedskog C, Osinusi A, Susser S, Sarrazin C, Svarovskaia E, Wertheim JO. Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage. Virus Evol 2019; 5:vez041. [PMID: 31616569 PMCID: PMC6785677 DOI: 10.1093/ve/vez041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced twenty-one full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; n = 109) sampled in ninteen countries from public databases (102 individuals), additional newly sequenced genomic regions (from 48 of these 102 individuals), unpublished isolates with newly sequenced regions (5 additional individuals), and novel complete genomes (2 additional individuals) generated in this study. Analysis of this expanded dataset reconfirmed the monophyletic origin of 2k/1b with a recombination breakpoint at position 3,187 (95% confidence interval: 3,172–3,202; HCV GT1a reference strain H77). Phylogeography is a valuable tool used to reveal viral migration dynamics. Inference of the timed history of spread in a Bayesian framework identified Russia as the ancestral source of the CRF 2k/1b clade. Further, we found evidence for migration routes leading out of Russia to other former Soviet Republics or countries under the Soviet sphere of influence. These findings suggest an interplay between geopolitics and the historical spread of CRF 2k/1b.
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Affiliation(s)
- Reilly Hostager
- Department of Medicine, University of California, San Diego, CA, USA
| | | | - Ben Murrell
- Department of Medicine, University of California, San Diego, CA, USA
| | | | | | - Simone Susser
- Goethe-University Hospital, Medical Clinic, Frankfurt, Germany
| | - Christoph Sarrazin
- Gilead Sciences, Foster City, CA, USA.,St. Josefs-Hospital, Medical Clinic 2, Wiesbaden, Germany
| | | | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, USA
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Tagnouokam-Ngoupo PA, Ngoufack MN, Kenmoe S, Lissock SF, Amougou-Atsama M, Banai R, Ngono L, Njouom R. Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients. Virol J 2019; 16:101. [PMID: 31399103 PMCID: PMC6688274 DOI: 10.1186/s12985-019-1214-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
Background Current HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients. Methods All plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences. Results A total of 369 samples were received during the study period with high viral load values (median: 930,952 IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p = 0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region. Conclusions We found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1–4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.
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Affiliation(s)
| | - Marie Nicole Ngoufack
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Sebastien Kenmoe
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Simon Frédéric Lissock
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Marie Amougou-Atsama
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Robert Banai
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Laure Ngono
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Richard Njouom
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon.
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Zubkin ML, Shchepetkova GS, Balkarova OV, Chervinko VI, Kryukov EV. Successful Hepatitis C Virus Eradication in a Hemodialysis Patient With 2k/1b Chimera Genotype: A Case Report and Literature Review. Gastroenterology Res 2019; 12:176-180. [PMID: 31236161 PMCID: PMC6575136 DOI: 10.14740/gr1171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/05/2019] [Indexed: 01/04/2023] Open
Abstract
Treatment of hemodialysis patients infected with two or three hepatitis C virus (HCV) genotypes (Gt) with interferon-free regimens has not been possible until the recent introduction of pan-genotypic next generation therapy. The main reason is that sofosbuvir (SOF)-containing regimens are contraindicated in patients with low glomerular filtration rate. We describe here a case of a chronic HCV infection in a patient with end-stage renal disease, successfully treated with gleсaprevir/pibrentasvir (GLE/PIB). Limited published data are available regarding the efficacy of antiviral therapy in patients with rare HCV recombinant Gt 2k/1b. We were not able to identify any reports describing treatment of hemodialysis patients with this recombinant type of HCV. We present a 57-year-old patient with autosomal-dominant polycystic kidney disease with liver involvement with end-stage of kidney disease. He was infected with HCV Gt 2k/1b variant after initiation of hemodialysis. This subtype appeared in Russia (Soviet Union that times) as a result of high frequency of virus mutations, and actually is widely spread in some states of the post-Soviet space, as well as in the countries with intensive migration from Russia and other former Soviet republics. In this particular case, we observed a tendency to a rapid progression of liver fibrosis despite mild clinical activity of chronic hepatitis C. A 12-week course of GLE/PIB allowed achieving sustained virologic response (SVR) and was well tolerated.
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Affiliation(s)
- Mikhail Leonidovich Zubkin
- Сlinical and Diagnostic Department, G.N. Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia
| | - Galina Sergeevna Shchepetkova
- Сlinical and Diagnostic Department, G.N. Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia
| | | | - Valeriy Ivanovich Chervinko
- Сlinical and Diagnostic Department, G.N. Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia
| | - Evgeniy Vladimirovich Kryukov
- Сlinical and Diagnostic Department, G.N. Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia
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Fernández-Caso B, Fernández-Caballero JÁ, Chueca N, Rojo E, de Salazar A, García Buey L, Cardeñoso L, García F. Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing. Sci Rep 2019; 9:9264. [PMID: 31239457 PMCID: PMC6592891 DOI: 10.1038/s41598-019-42605-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/01/2019] [Indexed: 12/21/2022] Open
Abstract
Current HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencing assay (Roche-NGS). Plasma samples collected from 139 HCV-infected patients tested with Abbott-RT-PCR, 114 with single genotype (GT) and 25 with mixed GTs were genotyped using Roche-NGS. Roche-NGS confirmed all single GTs obtained with Abbott-RT-PCR. One case of Abbott GT 4 was found as GT 1a using Roche-NGS. Genotype 5 was confirmed using Roche-NGS in 75% cases (3 out of 4 cases). Twenty-five patients were identified as having mixed HCVinfections using Abbott-RT-PCR. The concordance between Abbott-RT-PCR and Roche-NGS was 76% (19 out of 25 cases). Three mixed-GT infections identified with the Abbott assay (two (1b + 4); one (1a + 3)) were reported as pure 1b using Roche-NGS. Very divergent results were found for the other three samples. When compared to Roche-NGS, Abbott-RT-PCR has performed excellently for the determination of patients infected with single GTs. For patients that are categorized as having a mixed infection using Abbott-RT-PCR, we recommend an NGS assay as a confirmation test.
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Affiliation(s)
- Belén Fernández-Caso
- Servicio de Microbiologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Jose Ángel Fernández-Caballero
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Natalia Chueca
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Eukene Rojo
- Servicio de Aparato Digestivo - Unidad de Hepatologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Adolfo de Salazar
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Luisa García Buey
- Servicio de Aparato Digestivo - Unidad de Hepatologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Laura Cardeñoso
- Servicio de Microbiologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Federico García
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain.
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Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay. Sci Rep 2019; 9:3678. [PMID: 30842623 PMCID: PMC6403303 DOI: 10.1038/s41598-019-40099-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/27/2018] [Indexed: 12/19/2022] Open
Abstract
Accurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTime Genotype II (GT II) assay targeting the 5’NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with “not detected” results by GT Plus, or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 (n = 45) or just to GT II results if concordant (n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. “Not detected” results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples.
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Successful direct-acting antiviral treatment of three patients with genotype 2/1 recombinant hepatitis C virus. Clin J Gastroenterol 2018; 12:213-217. [PMID: 30446954 DOI: 10.1007/s12328-018-0922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
There have been a few reports on the treatment of patients infected with recombinant hepatitis C virus (HCV) genotype 2/1 strains with direct-acting antivirals (DAAs). We experienced three patients, with genotype 2/1 recombinant HCV, treated with DAAs successfully. The first, a 39-year-old man, was infected with recombinant HCV genotype 2a/1b, a rare variant. The sequence of the relapsed virus showed chimeric HCV 2a/1b with the recombinant breakpoint found at nucleotide +49 from the start of the NS3 region. Sofosbuvir plus ribavirin, a regimen recommended for HCV genotype 2, did not lead to a sustained viral response (SVR). Retreatment with grazoprevir plus elbasvir resulted in an SVR. The second case, a 70-year-old woman, was infected with recombinant HCV genotype 2b/1b. DAA therapy with sofosbuvir plus ledipasvir resulted in an SVR. The third case, a 48-year-old woman, was also infected with recombinant HCV genotype 2b/1b. DAA therapy with daclatasvir plus asunaprevir resulted in an SVR. The baseline sequences of the viruses from both the second and third cases showed chimeric HCV 2b/1b with the recombinant breakpoint found at nucleotide +10 from the NS3 start. We report three cases with 2/1 chimeras and discuss the prevalence and response to therapy.
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Kassela K, Karakasiliotis I, Kokkiou E, Souvalidou F, Mimidis P, Veletza S, Panopoulou M, Koskinas J, Mimidis K, Mavromara P. Intergenotypic 2k/1b hepatitis C virus recombinants in the East Macedonia and Thrace region of Greece. Ann Gastroenterol 2018; 32:88-92. [PMID: 30598597 PMCID: PMC6302191 DOI: 10.20524/aog.2018.0322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023] Open
Abstract
Background Intergenotypic recombinant hepatitis C virus (HCV) strains emerge rarely during coinfection of the same individual with two HCV genotypes. Few recombinant HCV strains have been identified to date and only one, CRF01 2k/1b, has become a worldwide concern. This study reevaluated the genotyping of three HCV genotype 2 strains from a group of patients with an unusually low rate of sustained virological response after pegylated interferon/ribavirin treatment. In addition, genetic determinants of host interferon resistance were evaluated. Methods The HCV type 2 strains from the patients’ serum were subjected to partial sequencing of the core-E1, NS2, NS5A and NS5B regions by reverse transcription polymerase chain reaction. Furthermore, the IFNL3 rs12979860 and the IFNL4 rs368234815 single nucleotide polymorphisms were defined in two of the three patients. Results All three strains were phylogenetically related to the Russia-derived CRF01 2k/1b while they encompassed the exact same 2k/1b junction site within NS2. Conclusion This is the first report of HCV 2k/1b recombinants in Greece and the greater area of the Balkans.
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Affiliation(s)
- Katerina Kassela
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara).,Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens (Katerina Kassela, Ioannis Karakasiliotis, Penelope Mavromara)
| | - Ioannis Karakasiliotis
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens (Katerina Kassela, Ioannis Karakasiliotis, Penelope Mavromara).,Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis (Ioannis Karakasiliotis, Stavroula Veletza)
| | - Eleni Kokkiou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara)
| | - Fani Souvalidou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara)
| | - Panayotis Mimidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara)
| | - Stavroula Veletza
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis (Ioannis Karakasiliotis, Stavroula Veletza)
| | - Maria Panopoulou
- Laboratory of Microbiology, Department of Medicine, Democritus University of Thrace, Alexandroupolis (Maria Panopoulou)
| | - John Koskinas
- Department of Internal Medicine, Medical School of Athens, Hippokration Hospital Athens (John Koskinas)
| | - Konstantinos Mimidis
- 1 Department of Internal Medicine, Democritus University of Thrace Medical School, Alexandroupolis (Konstantinos Mimidis), Greece
| | - Penelope Mavromara
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis (Katerina Kassela, Eleni Kokkiou, Fani Souvalidou, Panayotis Mimidis, Penelope Mavromara).,Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens (Katerina Kassela, Ioannis Karakasiliotis, Penelope Mavromara)
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Zarkua J, Zakalashvili M, Gish RG, Metreveli D. Identification of recombinant strains in HCV genotype 1 and 3: Is it needed? Liver Int 2018; 38:958. [PMID: 29479791 DOI: 10.1111/liv.13729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jaba Zarkua
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, GA, USA
| | - Mamuka Zakalashvili
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, GA, USA
| | - Robert G Gish
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University Medical Center, Stanford, CA, USA
| | - David Metreveli
- Hepatology and Gastroenterology Department, Medical Center Mrcheveli, Tbilisi, GA, USA
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