Prevalence of resistance-associated substitutions and phylogenetic analysis of hepatitis C virus infection in Russia

Isakov, Vasily; Hedskog, Charlotte; Wertheim, Joel O.; Hostager, Reilly; Parhy, Bandita; Schneider, Adriano de Bernardi; Suri, Vithika; Mo, Hongmei; Geivandova, Natalia; Морозов, В. Г.; Bessonova, E. I.; Gankina, Natalya; Жданов, К. В.; Abdurakhmanov, Dzhamal; Svarovskaia, Evguenia S.

doi:10.1016/j.ijid.2021.09.041

Cited by 7 publications

(3 citation statements)

References 45 publications

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“…To the best of our knowledge, this is the largest study to date of the concordance between a probe-based HCV genotyping assay and assignment of HCV subtypes making use of full-length genomes. Surprisingly, the older and newer versions of the assay showed similar concordance profiles, and while the frequency, and types of RASs were similar to those previously reported [19,20], rates of treatment failure with Zepatier were considerably higher [21].…”

Section: Discussionsupporting

confidence: 81%

Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Christensen

Pierard

Beuselinck

et al. 2022

Journal of Clinical Virology

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Section: Discussionsupporting

confidence: 81%

Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Christensen

Pierard

Beuselinck

et al. 2022

Journal of Clinical Virology

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“…The HCV subtype 1b dominates epidemics in the neighboring Russian Federation (1a – 2.1%; 1b – 52.8%; 3 – 36.3%) and several Central Asian countries, such as Uzbekistan and Azerbaijan, whilst 1a is more commonly found in western Europe [ 20 ]. Higher 1a prevalence amongst HIV co-infected patients compared to the general population has been linked to IDU mediated transmission elsewhere [ 30 ], and thus is expected in our study population, where HIV/HCV coinfection was prevalent. The increase in 1a prevalence in our study, reflected in the most recent growth of this subtype compared to subtypes 1b and 3a as estimated by our reconstructed Bayesian Skyline plots, follows the increase in HIV transmission in PWID [ 31 ].…”

Section: Discussionmentioning

confidence: 83%

Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020

et al. 2023

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Background Due to practical challenges associated with genetic sequencing in low-resource environments, the burden of hepatitis C virus (HCV) in forcibly displaced people is understudied. We examined the use of field applicable HCV sequencing methods and phylogenetic analysis to determine HCV transmission dynamics in internally displaced people who inject drugs (IDPWID) in Ukraine. Methods In this cross-sectional study, we used modified respondent-driven sampling to recruit IDPWID who were displaced to Odesa, Ukraine, before 2020. We generated partial and near full length genome (NFLG) HCV sequences using Oxford Nanopore Technology (ONT) MinION in a simulated field environment. Maximum likelihood and Bayesian methods were used to establish phylodynamic relationships. Results Between June and September 2020, we collected epidemiological data and whole blood samples from 164 IDPWID (PNAS Nexus.2023;2(3):pgad008). Rapid testing (Wondfo® One Step HCV; Wondfo® One Step HIV1/2) identified an anti-HCV seroprevalence of 67.7%, and 31.1% of participants tested positive for both anti-HCV and HIV. We generated 57 partial or NFLG HCV sequences and identified eight transmission clusters, of which at least two originated within a year and a half post-displacement. Conclusions Locally generated genomic data and phylogenetic analysis in rapidly changing low-resource environments, such as those faced by forcibly displaced people, can help inform effective public health strategies. For example, evidence of HCV transmission clusters originating soon after displacement highlights the importance of implementing urgent preventive interventions in ongoing situations of forced displacement.

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“…HCV phylogenetic analyses identified similarities between Russian HCV isolates and those from Europe and Asia. RF1_2k/1b was found to be related to European strains [38]. The relative prevalence of HCV genotypes likely reflects the European influence and major socio-political, historical events associated with massive migration of the population [21,39,40].…”

Section: Discussionmentioning

confidence: 95%

Epidemiology and Genotype Distribution of Hepatitis C Virus in Russia

Pimenov¹,

Kostyushev

Komarova³

et al. 2022

Pathogens

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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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Prevalence of resistance-associated substitutions and phylogenetic analysis of hepatitis C virus infection in Russia

Cited by 7 publications

References 45 publications

Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020

Epidemiology and Genotype Distribution of Hepatitis C Virus in Russia

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