Frequency of Interferon-Resistance Conferring Substitutions in Amino Acid Positions 70 and 91 of Core Protein of the Russian HCV 1b Isolates Analyzed in the T-Cell Epitopic Context

Funding Information: This study was supported by the grant of the Russian Science Foundation (Project ID 15-15-30039). Mobility and training of the researchers was supported by the grants of the Swedish Institute (TP 09272/2013 and PI 19806/2016). Publisher Copyright: © 2018 V. S. Kichatova et al.Amino acid substitutions R70Q/H and L91M in HCV subtype 1b core protein can affect the response to interferon and are associated with the development of hepatocellular carcinoma. We found that the rate of R70Q/H in HCV 1b from Russia was 31.2%, similar to that in HCV strains from Asia (34.0%), higher than that in the European (18.0%, p=0.0010), but lower than that in the US HCV 1b strains (62.8%, p<0.0001). Substitution L91M was found in 80.4% of the Russian HCV 1b isolates, higher than in Asian isolates (43.8%, p<0.0001). Thus, a significant proportion of Russian HCV 1b isolates carry the unfavorable R70Q/H and/or L91M substitution. In silico analysis of the epitopic structure of the regions of substitutions revealed that both harbor clusters of T-cell epitopes. Peptides encompassing these regions were predicted to bind to a panel of HLA class I molecules, with substitutions impairing peptide recognition by HLA I molecules of the alleles prevalent in Russia. This indicates that HCV 1b with R70Q/H and L91M substitutions may have evolved as the immune escape variants. Impairment of T-cell recognition may play a part in the negative effect of these substitutions on the response to IFN treatment.Peer reviewe

Factors influencing the prevalence of resistance-associated substitutions in NS5A protein in treatment-naive patients with chronic hepatitis C

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.Fil: Kyuregyan, Karen K.. Russian Academy Of Sciences; Rusia. Russian Medical Academy Of Continuous Professional Education; Rusia. I. I. Mechnikov Research Institute For Vaccines And Sera; RusiaFil: Kichatova, Vera S.. Russian Medical Academy Of Continuous Professional Education; Rusia. Russian Academy Of Sciences; Rusia. I. I. Mechnikov Research Institute For Vaccines And Sera; RusiaFil: Karlsen, Anastasiya A.. I. I. Mechnikov Research Institute For Vaccines And Sera; Rusia. Russian Medical Academy Of Continuous Professional Education; Rusia. Russian Academy Of Sciences; RusiaFil: Isaeva, Olga V.. I. I. Mechnikov Research Institute For Vaccines And Sera; Rusia. Russian Medical Academy Of Continuous Professional Education; RusiaFil: Solonin, Sergei A.. N.V. Sklifosovsky Research Institute for Emergency Medicine; RusiaFil: Petkov, Stefan. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Isaguliants, Maria G.. Russian Academy Of Sciences; Rusia. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Mikhailov, Mikhail I.. Russian Medical Academy Of Continuous Professional Education; Rusia. I. I. Mechnikov Research Institute For Vaccines And Sera; Rusi

Coverage with timely administered vaccination against hepatitis b virus and its influence on the prevalence of HBV infection in the regions of different endemicity

Funding Information: Funding: This research was funded by grant of the Russian Science Foundation (ID-20-15-00148). Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Universal hepatitis B vaccination of newborns was implemented in Russia starting from 1998. From 1998 to 2019, the incidence of acute hepatitis B reduced from 43.8 to 0.57 cases per 100,000 population. Here, we assessed the timely coverage of newborns with the birth dose (HepB-BD), second dose (HepB-2nd), and three vaccine doses (HepB3) in two remote regions of Russia with low (Belgorod Oblast) and high (Yakutia) levels of hepatitis B virus (HBV) endemicity. Vaccination data were obtained from the medical records of 1000 children in Yakutia and 2182 children in Belgorod Oblast. Sera of healthy volunteers from Belgorod Oblast (n = 1754) and Yakutia (n = 1072) across all age groups were tested for serological markers of HBV to assess the infection prevalence and herd immunity. Average HepB-BD coverage was 99.2% in Yakutia and 89.4% in Belgorod Oblast (p < 0.0001) and in both regions varied significantly, from 66% to 100%, between medical centers. The principal reason for the absence of HepB-BD was parent refusal, which accounted for 63.5% of cases of non-vaccination (83/123). While timely HepB-2nd coverage was only 55.4%–64.7%: HepB3 coverage by the age of one year exceeded 90% in both study regions. HBV surface antigen (HBsAg) prevalence in the 1998–2019 birth cohort was 0.2% (95% CI: 0.01–1.3%) in Belgorod Oblast and 3.2% (95% CI: 1.9–5.2%) in Yakutia. The proportion of persons testing negative for both antibodies to HBsAg (anti-HBs) and antibodies to HBV core antigen (anti-HBc) in the 1998–2019 birth cohort was 26.2% (125/481) in Belgorod Oblast and 32.3% (162/501) in Yakutia. We also assessed the knowledge of and attitude towards vaccination among 782 students and teachers of both medical and non-medical specialties from Belgorod State University. Only 60% of medical students knew that hepatitis B is a vaccine-preventable disease. Both medical and nonmedical students, 37.8% and 31.3%, respectively, expressed concerns about safety and actual necessity of vaccination. These data indicate the need to introduce a vaccine delivery audit system, improve medical education with respect to vaccination strategies and policies, and reinforce public knowledge on the benefits of vaccination.Peer reviewe

ЛЕКАРСТВЕННО-РЕЗИСТЕНТНЫЕ ВАРИАНТЫ ВГС СУБТИПА 1B, ЦИРКУЛИРУЮЩИЕ НА ТЕРРИТОРИИ РОССИЙСКОЙ ФЕДЕРАЦИИ: АНАЛИЗ АМИНОКИСЛОТНЫХ МУТАЦИЙ В БЕЛКАХ NS5A И CORE

Aim. To determine the prevalence of amino acid substitutions in hepatitis C virus NS5a and core proteins which are associated with resistance to direct-acting antivirals and interferon in genotype 1b (HCV-1b) strains circulating in Russia. Materials and methods. Nucleotide sequences of NS5a (n=93) and core (n=30) of HCV-1b were obtained using direct sequencing of respective amplified genome fragments. The search for resistance associated substitutions was performed for amino acid positions 28, 29, 30, 31, 32, 58, 62, 92, 93 of NS5a, and 70 and 91 amino acid positions of core proteins, respectively. Results. The total proportion of HCV-1b strains carrying resistance associated substitutions in NS5a was 22,6% (21/93). The total detection rate of L31M and Y93H substitutions that are associated with resistance to the majority of NS5a inhibitors was 10,8%. Less clinically significant substitutions L28M, R30Q, P58S/T, A92T were detected too. The proportion of infections caused by HCV-1b strains that are potentially resistant both to interferon and NS5a inhibitors was 10% (10/30). Conclusion. Testing of HCV-1b infected patients for background resistance profile could be a useful tool to prevent the choosing of initially ineffective treatment regimen.Цель: определение распространенности штаммов вируса гепатита С субтипа 1b (ВГС-1b) на территории Российской Федерации, несущих аминокислотные мутации в белках NS5a и core, ассоциированные с лекарственной резистентностью к ингибиторам NS5a и препаратам интерферона соответственно. Материалы и методы: определение нуклеотидной последовательности белка NS5a (n=93), а также белка core (n=30) ВГС-1b проводилось методом прямого секвенирования амплифицированных фрагментов генома. Поиск мутаций, ассоциированных с лекарственной резистентностью, проводился в аминокислотных позициях 28, 29, 30, 31, 32, 58, 62, 92, 93 белка NS5a и аминокислотных позициях 70 и 91 белка core ВГС-1b. Результаты: 22,6% (21/93) исследованных изолятов ВГС-1b несли мутации, ассоциированные с лекарственной резистентностью к ингибиторам NS5a. В 10,8% последовательностей были выявлены замены L31M и Y93H, связанные с устойчивостью к большинству ингибиторов NS5a, а также менее значимые с клинической точки зрения замены L28M, R30Q, P58S/T, A92T. Доля лиц, инфицированных штаммами ВГС-1b, потенциально резистентными одновременно к препаратам интерферона и ингибиторам NS5a, составила 10% (10/30). Заключение: полученные данные свидетельствуют в пользу целесообразности предварительного исследования профиля резистентности ВГС-1b перед назначением терапии для предотвращения выбора заведомо неэффективного препарата

РАСПРОСТРАНЕННОСТЬ ВИРУСА ГЕПАТИТА С СРЕДИ УСЛОВНО ЗДОРОВОГО НАСЕЛЕНИЯ РОССИЙСКОЙ ФЕДЕРАЦИИ

Aim. To determine the prevalence of hepatitis C virus (HCV) in different age groups of the conditionally healthy population of Russia.Materials and methods. Total 4764 serum samples from a conditionally healthy population of five regions of Russia (Moscow, Rostov, Sverdlovsk regions, Tyva Republic, and Sakha Republic (Yakutia) were tested. The study included persons of 10 age groups: &lt; 1 year, 1–4 years, 5–9 years, 10–14 years, 15–19 years, 20–29 years, 30–39 years, 40–49 years, 50–59 years old, ≥ 60 years. Anti-HCV was determined in ELISA with commercial test systems. Anti-HCV positive samples were tested for HCV RNA by RT-PCR. The genotype of HCV was determined based on the analysis of the nucleotide sequences of the core and NS5B regions of the viral genome.Results. The overall prevalence of anti-HCV in 5 regions of Russia was 2,6% (126/4764), and the proportion of people with HCV RNA was 1,1% (50/4764). The highest anti-HCV positivity rate was observed in Tyva and Yakutia (3,3% in both regions), in other regions its prevalence varied from 1,7% (Moscow region) to 3,0% (Sverdlovsk region). The highest frequency of HCV RNA detection was observerd in Tyva Republic and Rostov region (1.3% in both regions). No positive for HCV RNA cases was detected among persons aged 0–19 years in any region, except for Tyva Republic (1,0% (1/98) in age group 15–19 years). Peak positivity rates of HCV RNA were detected in the age groups 20–29 years and 30–39 years in the Rostov Region (3,9% and 3,0%, respectively); in Yakutia – in the group of 30–39 years (3,7%), in Tyva – in the group of 40–49 years (3,6%), in the Moscow region – in the groups of 20–29 and 30–39 years (2,9% and 2,5%, respectively).Conclusion. The results obtained indicate a high degree of HCV infection in virtually all age groups in the interval from 20 years to ≥60 years. Specific age cohorts that might benefit from inclusion in regional HCV screening programs were identified in each region. Цель. Определить долю инфицированных вирусом гепатита С (ВГС) лиц в различных возрастных группах условно здорового населения России.Материалы и методы. Исследованы 4764 образца сы- воротки крови от условно здорового населения пяти регионов РФ: Свердловской, Ростовской, Московской областей, Республики Тыва и Республики Саха (Якутия). В исследование были включены лица 10 возрастных групп: меньше 1 года, 1–4 года, 5–9 лет, 10–14 лет, 15–19 лет, 20–29 лет, 30–39 лет, 40–49 лет, 50–59 лет, старше 60 лет. Анти-ВГС определяли в ИФА с коммерческими тест-системами. В положительных по анти-ВГС образцах определяли РНК ВГС методом ОТ-ПЦР. Генотип ВГС определяли на основании анализа нуклеотидных последовательностей участков core и NS5B вирусного генома.Результаты. Общая распространенность анти-ВГС в 5 регионах РФ составила 2,6% (126/4764), доля лиц с РНК ВГС – 1,1% (50/4764). Наибольшая распространенность анти-ВГС выявлена в Республиках Тыва и Якутия (3,3%), в остальных регионах данный показатель варьировал от 1,7% (Московская область) до 3,0% (Свердловская область). Наибольшая частота выявления РНК ВГС отмечена в Республике Тыва и Ростовской области (1,3% в обоих регионах). Среди лиц в возрасте от 0 до 19 лет РНК ВГС не была выявлена ни в одном регионе, за исключением Республики Тыва (1% (1/98) в группе 15–19 лет). Пиковые показатели выявления РНК ВГС были вы- явлены в возрастных группах 20–29 лет и 30–39 лет в Ростовской области (3,9% и 3,0% соответственно); в Якутии – в группе 30–39 лет (3,7%), в Тыве – в группе 40–49 лет (3,6%), в Московской области – в группах 20–29 лет и 30–39 лет (2,9% и 2,5% соответственно).Заключение. Полученные результаты свидетельствуют о высокой степени пораженности ВГС практически всех возрастных групп в интервале от 20 лет до ≥ 60 лет. В каждом из обследованных регионов выявлены возрастные когорты, для которых целесообразно включение в региональные скрининговые программы.

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Coverage with timely administered vaccination against hepatitis b virus and its influence on the prevalence of HBV infection in the regions of different endemicity

The principal reason for the absence of HepB-BD was parent refusal, which accounted for 63.5% of cases of non-vaccination (83/123). While timely HepB-2nd coverage was only 55.4%-64.7%: HepB3 coverage by the age of one year exceeded 90% in both study regions. HBV surface antigen (HBsAg) prevalence in the 1998-2019 birth cohort was 0.2% (95% CI: 0.01-1.3%) in Belgorod Oblast and 3.2% (95% CI: 1.9-5.2%) in Yakutia. The proportion of persons testing negative for both antibodies to HBsAg (anti-HBs) and antibodies to HBV core antigen (anti-HBc) in the 1998-2019 birth cohort was 26.2% (125/481) in Belgorod Oblast and 32.3% (162/501) in Yakuti

Drug resistant variants of hepatitis C virus genotype 1b in Russia: analysis of aminoacid substitutions in NS5a and core proteins

Aim. To determine the prevalence of amino acid substitutions in hepatitis C virus NS5a and core proteins which are associated with resistance to direct-acting antivirals and interferon in genotype 1b (HCV-1b) strains circulating in Russia. Materials and methods. Nucleotide sequences of NS5a (n=93) and core (n=30) of HCV-1b were obtained using direct sequencing of respective amplified genome fragments. The search for resistance associated substitutions was performed for amino acid positions 28, 29, 30, 31, 32, 58, 62, 92, 93 of NS5a, and 70 and 91 amino acid positions of core proteins, respectively. Results. The total proportion of HCV-1b strains carrying resistance associated substitutions in NS5a was 22,6% (21/93). The total detection rate of L31M and Y93H substitutions that are associated with resistance to the majority of NS5a inhibitors was 10,8%. Less clinically significant substitutions L28M, R30Q, P58S/T, A92T were detected too. The proportion of infections caused by HCV-1b strains that are potentially resistant both to interferon and NS5a inhibitors was 10% (10/30). Conclusion. Testing of HCV-1b infected patients for background resistance profile could be a useful tool to prevent the choosing of initially ineffective treatment regimen

MULTI-YEAR DYNAMICS OF SPREAD OF HEPATITIS C VIRUS GENOTYPES IN MOSCOW REGION

Aim. Determine spread of hepatitis C vims genotypes, circulating in Moscow Region over the last decade. Materials and methods. The presence of HCV RNA, genotype and subtype of the vims were determined in blood sera samples obtained in 2006 - 2014 from 2847 individuals with the presence of HCV infection, who had or did not have injectable dmg administration in anamnesis. Results, lb and 3a remain the main subtypes, circulating in the population over the last decade. A notable reduction of la subtype circulation took place among injectable dmg users (IDU). Recombinant form RFl_2k/lb of hepatitis vims is present only among this risk group and constitutes 2% of the overall amount of subtypes in both 2007 and 2014. Genotype 4d was detected in 2014, that is not typical for Russian Federation. Genotype 3a is dominant in IDU age groups of 20 - 29 and older than 40, and in the 30 - 39 group the main - subtype lb. Phylogenetic analysis has shown the lack of certain genetic variants of subtypes lb and 3a, characteristic for IDU, that gives evidence on a wide circulation of the main subtypes of the vims in the whole population of individuals, infected by HCV. Conclusion. Spread of main genotypes/subtypes of HCV in the overall population and among IDU in Moscow remains stable over the last decade

MODELLING OF HEPATITIS E IN MINI-PIGS

Aim. Experimental reproduction of HEV-infection in mini-pigs and comparative analysis of virological and immunological characteristics of experimental infection. Materials and methods. Wiesenauer minipigs (2 females and 4 males, age 50 - 60 days, weight 5-10 kg) were infected by HEV genotype 3 strain isolated from swine feces in Belgorod region in 2013. The virus was administered as a 10% clarified feces extract (800 pi). Blood (weekly) and feces (daily) were sampled from the animals for 49 days. Anti-HEV IgG were determined in sera samples using DS- ElA-ANTI-HEV-G (Diagnostic Systems) system, HEV RNA in samples of feces extracts and blood sera - RT-PCR. Results. Wiesenauer minipigs were sensitive to HEV genotype 3 infection, infection developed in all the animals after administration of the virus, that was accompanied by the presence of HEV RNA in feces for 2 weeks and seroconversion by anti-HEV. Comparative analysis of virological characteristics of experimental H EV-infection in mini- and standard pigs has shown, that the duration of the infection in mini-pigs is shorter, and seroconversion by anti-HEV occurs earlier. Conclusion. Sensitivity to HEV genotype 3 and lower weight make mini-pigs a comfortable alternative to standard swine and primates for modelling HEV infection in vivo