Генетическое разнообразие вируса гепатита С и распространенность мутаций резистентности к ингибиторам NS5А в Красноярском крае

Цель – исследовать молекулярно‐генетические особенности популяции ВГС, циркулирующей среди ВИЧ‐инфицированных жителей Красноярского края, включая анализ мутаций вируса, связанных с резистентностью к ингибиторам NS5А. Из 94 образцов плазмы крови ВИЧ/ВГС‐инфицированных жителей края выделена суммарная РНК, получены и расшифрованы нуклеотидные последовательности областей гена Core/E1 и гена NS5А, которые использовали для генотипирования и поиска мутаций резистентности.

В изученной выборке ВГС зарегистрирована циркуляция пяти субтипов вируса: 1b (47,9 %), 3a (37,2 %), 1a (10,6 %), 2a (3,2 %) и 2k (1,1 %). Филогенетический анализ ВГС выявил частичную кластеризацию внутри субтипов 1а и 3a по территориальному принципу. ВГС субтипа 1b, 2а и 2k группировались с другими ВГС, выделенными ранее в России, Армении и Кыргызстане. Среди исследованных ВГС не было найдено кластеров, общих для ВИЧ‐инфицированных лиц с одним путем заражения. Среди пациентов, не имевших опыта приема ПППД, мутации резистентности ВГС в области NS5A для лиц, инфицированных вирусом субтипа 3a, были обнаружены у 42,3 % случаев, для инфицированных ВГС субтипа 1b – в 75,6 % случаев.

Выполненный анализ разнообразия и встречаемости мутаций лекарственной устойчивости ВГС к препаратам прямого противовирусного действия крайне важен для разработки тактики эффективного лечения ХГС. Высокий уровень распространенности полиморфных мутаций, влияющих на чувствительность к ПППД, указывает на актуальность внедрения анализа резистентности ВГС в клиническую практику.

1. Bertino G., et al. Chronic hepatitis C: This and the new era of treatment // World journal of hepatology. 2016. V. 8. N 2. P. 92. DOI: 10.4254/wjh.v8.i2.92

2. Dubuisson J. Hepatitis C virus proteins // World journal of gastroenterology: WJG. 2007. V. 13. N 17. P. 2406. DOI: 10.3748/wjg.v13.i17.2406

3. Schulze zur Wiesch J., et al. The proteins of the Hepatitis C virus: Their features and interactions with intracellular protein phosphorylation // Archives of virology. 2003. V. 148. P. 1247–1267. DOI: 10.1007/s00705‐003‐0115‐8

4. Simmonds P. Genetic diversity and evolution of hepatitis C virus–15 years on // Journal of General Virology. 2004. V. 85. N 11. P. 3173–3188. DOI: 10.1099/vir.0.80401‐0

5. Correction Naghavi M., et al. Global, regional, and national age‐sex specific all‐cause and cause‐specific mortality for 240 causes of death, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013 // The Lancet. 2015. V. 38. N 9963. P. 117–171. DOI: 10.1016/S0140‐6736(14)61682‐2

6. Thursz M., Fontanet A. HCV transmission in industrialized countries and resource‐constrained areas // Nature reviews Gastroenterology & hepatology. 2014. V. 11. N 1. P. 28–35. DOI: 10.1038/nrgastro.2013.179

7. Pawlotsky J.M., Chevaliez S., McHutchison J.G. The hepatitis C virus life cycle as a target for new antiviral therapies // Gastroenterology. 2007. V. 132. N 5. P. 1979– 1998. DOI: 10.1053/j.gastro.2007.03.116

8. Hassany M., Elsharkawy A. HCV treatment failure in the Era of DAAs // INTECH open science. 2017. P. 117–129. DOI: 10.5772/67149

9. Svarovskaia E.S., et al. Infrequent development of resistance in genotype 1–6 hepatitis C virus–infected subjects treated with sofosbuvir in phase 2 and 3 clinical trials // Clinical Infectious Diseases. 2014. V. 59. N 12 P. 1666–1674. DOI: 10.1093/cid/ciu697

10. Wyles D., et al. Post‐treatment resistance analysis of hepatitis C virus from phase II and III clinical trials of ledipasvir/sofosbuvir // Journal of hepatology. 2017. V. 66. N 4. P. 703–710. DOI: 10.1016/j.jhep.2016.11.022

11. Wyles D.L., Luetkemeyer A.F. Understanding hepatitis C virus drug resistance: clinical implications for current and future regimens // Topics in antiviral medicine. 2017. V. 25. N 3. P. 103. PMID: 28820725

12. Pawlotsky J.M. NS5A inhibitors in the treatment of hepatitis C // Journal of hepatology. 2013. V. 59. N 2. P. 375–382. DOI: 10.1016/j.jhep.2013.03.030

13. Jimmerson L.C. The clinical pharmacology of ribavirin: intracellular effects on endogenous nucleotides and hemolytic anemia: diss. University of Colorado Denver, Anschutz Medical Campus. 2016.

14. Hernandez D., et al. Natural prevalence of NS5A polymorphisms in subjects infected with hepatitis C virus genotype 3 and their effects on the antiviral activity of NS5A inhibitors // Journal of Clinical Virology. 2013. V. 57. N 1. P. 13–18. DOI: 10.1016/j.jcv.2012.12.020

15. Krishnan P., et al. Analysis of hepatitis C virus genotype 1b resistance variants in Japanese patients treated with paritaprevir‐ritonavir and ombitasvir // Antimicrobial agents and chemotherapy. 2016. V. 60. N 2. P. 1106–1113. DOI: 10.1128/aac.02606‐15

16. Trickey A., et al. Guidelines for the care and treatment of persons diagnosed with chronic hepatitis C virus infection: web annex 4: modelling analyses // World Health Organization. 2018. N. WHO/CDS/HIV/18.38.

17. Tamura K., Stecher G., Kumar S. MEGA11: molecular evolutionary genetics analysis version 11 // Molecular biology and evolution. 2021. V. 38. N 7. P. 3022–3027. DOI: 10.1093/molbev/msab120

18. Larsson A. AliView: a fast and lightweight alignment viewer and editor for large datasets // Bioinformatics. 2014. V. 30. N 22. P. 3276–3278. DOI: 10.1093/bioinformatics/btu531

19. Katoh K., Rozewicki J., Yamada K.D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization // Briefings in bioinformatics. 2019. V. 20. N 4. P. 1160–1166. DOI: 10.1093/bib/bbx108

20. von Haeseler A., et al. IQ‐TREE: A fast and effective stochastic algorithm for estimating maximum‐likelihood phylogenies // Molecular Biology and Evolution. 2014. V. 32. Iss. 1. P. 268–274. DOI: 10.1093/molbev/msu300

21. Singer J.B., et al. GLUE: a flexible software system for virus sequence data // BMC bioinformatics. 2018. V. 19. P. 1–18. DOI: 10.1186/s12859‐018‐2459‐9

22. Singer J.B., et al. Interpreting viral deep sequencing data with GLUE // Viruses. 2019. V. 11. N 4. P. 323. DOI: 10.3390/v11040323

23. Кашникова А.Д. и др. Молекулярно‐генетический мониторинг как компонент эпидемиологического надзора за гепатитом С // Здоровье населения и среда обитания. 2022. Т. 30. N 11. С. 76–81. DOI: 10.35627/2219‐5238/2022‐30‐11‐76‐81

24. Кочнева Г.В. и др. О возможности искоренения гепатита C в России // Молекулярная генетика, микробиология и вирусология. 2021. Т. 39. N 1. С. 31–41. DOI: 10.17116/molgen20213901131

25. Базыкина Е.А. и др. Оценка эпидемиологических особенностей ВИЧ‐инфекции и генотипического разнообразия вируса гепатита С у ВИЧ‐инфицированных граждан в субъектах Дальневосточного федерального округа // Эпидемиология и вакцинопрофилактика. 2021. Т. 20. N 5. С. 79–88. DOI: 10.31631/2073‐3046‐2021‐20‐579‐88

26. Котова В.О. и др. Генетическое разнообразие вируса гепатита С среди населения Нанайского района Хабаровского края // Инфекция и иммунитет. 2021. Т. 11. N 1. С. 148–156. DOI: 10.15789/2220‐7619‐GDO‐1265

27. Pawlotsky J.M., et al. EASL recommendations on treatment of hepatitis C 2018 // Journal of hepatology. 2018. V. 69. N 2. P. 461–511. DOI: 10.1016/j.jhep.2018.03.026

28. Lahser F., et al. Interim analysis of a 3‐year follow‐up study of NS5A and NS3 resistance‐associated substitutions after treatment with grazoprevir‐containing regimens in participants with chronic HCV infection // Antiviral therapy. 2018. V. 23. N 7. P. 593–603. DOI: 10.3851/IMP3253

29. Krishnan P., et al. O057: Long‐term follow‐up of treatment‐emergent resistance‐associated variants in NS3, NS5A and NS5B with paritaprevir/r‐, ombitasvir‐and dasabuvir‐based regimens // Journal of hepatology. 2015. V. 62. P. S220. DOI: 10.1016/S0168‐8278(15)30071‐4

30. Wyles D., et al. Long‐term persistence of HCV NS5A resistance‐associated substitutions after treatment with the HCV NS5A inhibitor, ledipasvir, without sofosbuvir // Antiviral therapy. 2018. V. 23. N 3. P. 229–238. DOI: 10.3851/IMP3181

31. Mawatari S., et al. New resistance‐associated substitutions and failure of dual oral therapy with daclatasvir and asunaprevir // Journal of gastroenterology. 2017. V. 52. P. 855–867. DOI: 10.1007/s00535‐016‐1303‐0

32. Lopez Luis B.A., et al. Baseline hepatitis C virus NS5A resistance‐associated polymorphisms in patients with and without human immunodeficiency virus coinfection in Mexico // Microbial Drug Resistance. 2021. V. 27. N 9. P. 1195–1202. DOI: 10.1089/mdr.2020.0436

33. Seronello S., et al. Ethanol and reactive species increase basal sequence heterogeneity of hepatitis C virus and produce variants with reduced susceptibility to antivirals // PLoS One. 2011. V. 6. N 11. Article id: e27436. DOI: 10.1371/journal.pone.0027436

34. Wyles D.L., et al. Daclatasvir plus sofosbuvir for HCV in patients coinfected with HIV‐1 // New England Journal of Medicine. 2015. V. 373. N 8. P. 714–725. DOI: 10.1056/NEJMoa1503153

35. Nelson D.R., et al. All‐oral 12‐week treatment with daclatasvir plus sofosbuvir in patients with hepatitis C virus genotype 3 infection: ALLY‐3 phase III study // Hepatology. 2015. V. 61. N 4. P. 1127–1135. DOI: 10.1002/hep.27726

36. Liu R., et al. Susceptibilities of genotype 1a, 1b, and 3 hepatitis C virus variants to the NS5A inhibitor elbasvir // Antimicrobial agents and chemotherapy. 2015. V. 59. N 11. P. 6922–6929. DOI: 10.1128/aac.01390‐15

37. Poordad F., et al. High antiviral activity of NS 5A inhibitor ABT‐530 with paritaprevir/ritonavir and ribavirin against hepatitis C virus genotype 3 infection // Liver International. 2016. V. 36. N 8. P. 1125–1132. DOI: 10.1111/liv.13067

38. Hezode C., et al. Resistance analysis in patients with genotype 1–6 HCV infection treated with sofosbuvir/velpatasvir in the phase III studies // Journal of hepatology. 2018. V. 68. N 5. P. 895–903. DOI: 10.1016/j.jhep.2017.11.032

39. Cabral B.C.A., et al. Frequency distribution of HCV resistance‐associated variants in infected patients treated with direct‐acting antivirals // International Journal of Infectious Diseases. 2022. V. 115. P. 171–177. DOI: 10.1016/j.ijid.2021.12.320

40. Zeuzem S., et al. Daclatasvir plus simeprevir with or without ribavirin for the treatment of chronic hepatitis C virus genotype 1 infection // Journal of hepatology. 2016. V. 64. N 2. P. 292–300. DOI: 10.1016/j.jhep.2015.09.024

41. Curry M.P., et al. Sofosbuvir and velpatasvir for HCV in patients with decompensated cirrhosis // New England Journal of Medicine. 2015. V. 373. N 27. P. 2618–2628. DOI: 10.1056/NEJMoa1512614

42. Gottwein J.M., et al. Efficacy of NS5A inhibitors against hepatitis C virus genotypes 1–7 and escape variants // Gastroenterology. 2018. V. 154. N 5. P. 1435–1448. DOI: 10.1053/j.gastro.2017.12.015

43. Krishnan P., et al. In vitro and in vivo antiviral activity and resistance profile of ombitasvir, an inhibitor of hepatitis C virus NS5A // Antimicrobial agents and chemotherapy. 2015. V. 59. N 2. P. 979–987. DOI: 10.1128/aac.04226‐14

44. Nakamoto S., et al. Hepatitis C virus NS5A inhibitors and drug resistance mutations // World journal of gastroenterology: WJG. 2014. V. 20. N 11. P. 2902. DOI: 10.3748/wjg.v20.i11.2902

45. Uchida Y., et al. Development of rare resistance‐associated variants that are extremely tolerant against NS5A inhibitors during daclatasvir/asunaprevir therapy by a two‐hit mechanism // Hepatology Research. 2016. V. 46. N 12. P. 1234–1246. DOI: 10.1111/hepr.12673

46. Uchida Y., et al. “Reversi‐type virologic failure” involved in the development of non‐structural protein 5A resistance‐associated variants (RAVs) in patients with genotype 1b hepatitis C carrying no signature RAVs at baseline // Hepatology Research. 2017. V. 47. N 13. P. 1397–1407. DOI: 10.1111/hepr.12882

47. Kwo P., et al. Effectiveness of elbasvir and grazoprevir combination, with or without ribavirin, for treatmentexperienced patients with chronic hepatitis C infection // Gastroenterology. 2017. V. 152. N 1. P. 164–175. DOI: 10.1053/j.gastro.2016.09.045

48. Fourati S., et al. Viral kinetics analysis and virological characterization of treatment failures in patients with chronic hepatitis C treated with sofosbuvir and an NS 5A inhibitor // Alimentary pharmacology & therapeutics. 2018. V. 47. N 5. P. 665–673. DOI: 10.1111/apt.14478

49. Pelosi L.A., et al. Effect on hepatitis C virus replication of combinations of direct‐acting antivirals, including NS5A inhibitor daclatasvir // Antimicrobial agents and chemotherapy. 2012. V. 56. N 10. P. 5230–5239. DOI: 10.1128/aac.01209‐12

50. Kumada H., et al. The combination of elbasvir and grazoprevir for the treatment of chronic HCV infection in Japanese patients: a randomized phase II/III study // Journal of gastroenterology. 2017. V. 52. P. 520–533. DOI: 10.1007/s00535‐016‐1285‐y

51. Kozuka R., et al. The presence of multiple NS 5A RAS s is associated with the outcome of sofosbuvir and ledipasvir therapy in NS 5A inhibitor‐naïve patients with chronic HCV genotype 1b infection in a real‐world cohort // Journal of Viral Hepatitis. 2018. V. 25. N 5. P. 535–542. DOI: 10.1111/jvh.12850

52. Kao J.H., et al. All‐oral daclatasvir plus asunaprevir for chronic hepatitis C virus (HCV) genotype 1b infection: a sub‐analysis in Asian patients from the HALLMARK DUAL study // Liver International. 2016. V. 36. N 10. P. 1433– 1441. DOI: 10.1111/liv.13128

53. Dietz J., et al. Consideration of viral resistance for optimization of direct antiviral therapy of hepatitis C virus genotype 1‐infected patients // PloS one. 2015. V. 10. N 8. Article id: e0134395. DOI: 10.1371/journal.pone.0134395

54. Kwo P.Y., et al. Glecaprevir and pibrentasvir yield high response rates in patients with HCV genotype 1–6 without cirrhosis // Journal of hepatology. 2017. V. 67. N 2. P. 263– 271. DOI: 10.1016/j.jhep.2017.03.039

55. Zeuzem S., et al. NS5A resistance‐associated substitutions in patients with genotype 1 hepatitis C virus: prevalence and effect on treatment outcome // Journal of hepatology. 2017. V. 66. N 5. P. 910–918. DOI: 10.1016/j.jhep.2017.01.007

56. Рейнгардт Д.Э. и др. Распространенность мутаций лекарственной устойчивости вируса гепатита С среди пациентов с рецидивом заболевания на терапии препаратами прямого противовирусного действия // ВИЧ‐инфекция и иммуносупрессии. 2024. Т. 15. N 4. С. 86–93. DOI: 10.22328/2077‐9828‐2023‐15‐4‐86‐93

57. Кичатова В.С. и др. Лекарственно‐резистентные варианты ВГС субтипа 1b, циркулирующие на территории Российской Федерации: анализ аминокислотных мутаций в белках NS5a и core // Журнал инфектологии. 2018. Т. 10. N 4. С. 30–36. DOI: 10.22625/2072‐6732‐2018‐10‐4‐30‐36

58. Bartels D.J., et al. Hepatitis C virus variants with decreased sensitivity to direct‐acting antivirals (DAAs) were rarely observed in DAA‐naive patients prior to treatment // Journal of virology. 2013. V. 87. N 3. P. 1544–1553. DOI: 10.1128/jvi.02294‐12

59. Chen Z., et al. Global prevalence of pre‐existing HCV variants resistant to direct‐acting antiviral agents (DAAs): mining the GenBank HCV genome data // Scientific reports. 2016. V. 6. N 1. Article id: 20310. DOI: 10.1038/srep20310