Characterization of the Full-Length Genome Sequences and Phylogenetic Analysis of HDV Strains Isolated from Patients with Chronic HBV and HDV Infection in Kyrgyz Republic

Objective. The purpose of our work was molecular genetic characterization of the hepatitis D virus isolates, circulating in the region with high prevalence of HBV + HDV super-infection. Materials and methods. The study material was 64 blood serum samples obtained from Kyrgyz Republic residents - patients with chronic viral hepatitis B+D. The hepatitis D virus complete genomes were sequenced, followed by phylogenetic analysis. Results and discussion. Based on the phylogenetic analysis of 64 HDV samples, it was shown that HDV genotype 1 (96.9 %) predominates in the examined group compared with HDV genotype 2 (3.1 %). Sequences were submitted to GenBank under access No MN984407 through MN984470. When assessing the genetic variability over the examined HDV genotype 1 samples, the maximum genetic distance was 12,49 %, and the minimum – 7,41 %. Within individual clusters, the genetic distance averaged from 2.6 % to 8.5 %. Among the sequences in GenBank, the closest resemblance to the HDV-2 Kyr41 and Kyr43 samples (nucleotide identity was 92.31 % and 89.57 %, respectively) was shown for the virus described earlier in Yakutia (AJ309880). To study the genetic relationships between the analyzed HDV genotype 1 strains in comparison with the HDV reference sequences, the predicted amino acid sequence was studied (111–214). Although hepatitis B preventive measures, including vaccination, have reduced the hepatitis D incidence, there is no effective way to prevent HDV infection in HBV carriers in endemic areas. The HDV sequence molecular-genetic characterization in this study, as well as the viral genomic sequence phylogenetic analysis, will help identify pathogen transmission pathways to control and / or prevent the spread of infection.

Hepatitis D virus, hepatitis delta virus, hepatitis B virus, co-infection, molecular epidemiology, sequencing, Kyrgyzstan

1. Casaca A., Fardilha M., da Cruz e Silva E., Cunha C. The heterogeneous ribonuclear protein C interacts with the hepatitis delta virus small antigen. Virol. J. 2011; 8:358. DOI: 10.1186/1743-422-X-8-358.

2. Giersch K., Dandri M. Hepatitis B and delta virus: Advances on studies about interactions between the two viruses and the in- fected hepatocyte. J. Clin. Transl. Hepatol. 2015; 3(3):220–9. DOI: 10.14218/JCTH.2015.00018.

3. Koytak E.S., Yurdaydin C., Glenn J.S. Hepatitis D. Curr. Treat. Options Gastroenterol. 2007; 10:456–63. DOI: 10.1007/s11938-007-0045-8.

4. Ni Y., Zhang Z., Engelskircher L., Verch G., Tu T., Lempp F.A., Urban S. Generation and characterization of a stable cell line persistently replicating and secreting the human hepatitis delta virus. Sci. Rep. 2019; 9:10021. DOI: 10.1038/s41598-019-46493-1.

5. Chen H.Y., Shen D.T., Ji D.Z., Han P.C., Zhang W.M., Ma J.F., Chen W.S., Goyal H., Pan S., Xu H.G. Prevalence and burden of hepatitis D virus infection in the global population: a systematic review and meta-analysis. Gut. 2018; 68:512–21. DOI: 10.1136/gutjnl-2018-316601.

6. Sagnelli E., Sagnelli C., Pisaturo M., Macera M., Coppola N. Epidemiology of acute and chronic hepatitis B and delta over the last 5 decades in Italy. World J. Gastroenterol. 2014; 20(24):7635– 43. DOI: 10.3748/wjg.v20.i24.7635.

7. Khodjaeva M., Ibadullaeva N., Khikmatullaeva A., Joldasova E., Ismoilov U., Colombo M., Caviglia G.P., Rizzetto M., Musabaev E. The medical impact of hepatitis D virus infection in Uzbekistan. Liver Int. 2019; 39(11):2077–81. DOI: 10.1111/liv.14243.

8. Wranke A., Pinheiro Borzacov L.M., Parana R., Lobato C., Hamid S., Ceausu E., Dalekos G.N., Rizzetto M., Turcanu A., Niro G.A., Lubna F., Abbas M., Ingiliz P., Buti M., Ferenci P., Vanwolleghem T., Hayden T., Dashdorj N., Motoc A., Cornberg M., Abbas Z., Yurdaydin C., Manns M.P., Wedemeyer H., Hardtke S., Hepatitis Delta International Network. Clinical and virological heterogeneity of hepatitis delta in different regions world-wide: the Hepatitis Delta International Network (HDIN). Liver Int. 2018; 38(5):842–50. DOI: 10.1111/liv.13604.

9. De Sousa B.C., Cunha C. Development of mathematical models for the analysis of hepatitis delta virus viral dynamics. PLoS One. 2010; 5(9):e12512. DOI: 10.1371/journal.pone.0012512.

10. Nogoibaeva K.A., Tobokalova S.T., Bekenova D.S., Nazarbaeva Zh.N. Chronic hepatitis B without/with a delta agent in Kyrgyzstan (epidemic situation, clinical features). Infektsiya i Immunitet [Russian Journal of Infection and Immunity]. 2019. 9(3– 4):577–82. DOI: 10.15789/2220-7619-2016-2-141-150.

11. Niro G.A., Smedile A. Current concept in the pathophysiology of hepatitis delta infection. Curr. Infect. Dis. Rep. 2012; 14:9–14. DOI: 10.1007/s11908-011-0233-5.

12. Lempp F.A., Ni Y., Urban S. Hepatitis delta virus: in- sights into a peculiar pathogen and novel treatment options. Nat. Rev. Gastroenterol. Hepatol. 2016; 13:580–9. DOI: 10.1038/nrgastro.2016.126.

13. Le Gal F., Gault E., Ripault M.P., Serpaggi J., Trinchet J.C., Gordien E., Dény P. Eighth major clade for hepatitis delta virus. Emerg. Infect. Dis. 2006; 12(9):1447–50. DOI: 10.3201/eid1209.060112.

14. Wedemeyer H., Manns M.P. Epidemiology, pathogenesis and management of hepatitis D: update and challenges ahead. Nat. Rev. Gastroenterol. Hepatol. 2010; 7(1):31–40. DOI: 10.1038/nrgastro.2009.205.

15. Hsu S.C., Syu W.J., Sheen I.J., Liu H.T., Jeng K.S., Wu J.C. Varied assembly and RNA editing efficiencies between genotypes I and II hepatitis D virus and their implications. Hepatology. 2002; 35(3):665–72. DOI: 10.1053/jhep.2002.31777.

16. Gomes-Gouvêa M.S., Soares M.C., Bensabath G., de Carvalho-Mello I.M., Brito E.M., Souza O.S., Queiroz A.T., Carrilho F.J., Pinho J.R. Hepatitis B virus and hepatitis delta virus genotypes in outbreaks of fulminant hepatitis (Labrea black fever) in the west- ern Brazilian Amazon region. J. Gen. Virol. 2009; 90(11):2638–43. DOI: 10.1099/vir.0.013615-0.

17. Semenov A.V., Ostankova Yu. V., Nogoybaeva K.A., Kasymbekova K.T., Lavrentieva I.N., Tobokalova S.T., Totolyan A.A. Molecular epidemiology features of HBV/HDV co-infection in Kyrgyzstan. Infektsiya i Immunitet [Russian Journal of Infection and Immunity]. 2016. 6(2):141–50.DOI: 10.15789/2220-7619-2016- 2-141-150.

18. Kumar S., Stecher G., Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016; 33(7):1870–4. DOI: 10.1093/molbev/msw054.

19. Hong S., Chen P. Phosphorylation of Serine 177 of the Small Hepatitis Delta Antigen Regulates Viral Antigenomic RNA Replication by Interacting with the Processive RNA polymerase II. J. Virol. 2010; 84(3):1430–8. DOI: 10.1128/JVI.02083-09.

20. Perveen S., Nasir M.I., Shahid S.M., Azhar A., Khan O.Y. Phylogenetic analysis of HDV isolates from HBsAg positive patients in Karachi, Pakistan. Virol J. 2012; 9:162. DOI: 10.1186/1743-422- X-9-162.

21. Le Gal F., Badur S., Hawajri N.A., Akyüz F., Kaymakoglu S., Brichler S., Zoulim F., Gordien E., Gault E., Deny P. Current hepatitis delta virus type 1 (HDV1) infections in central and eastern Turkey indicate a wide genetic diversity that is probably linked to different HDV1 origins. Arch. Virol. 2012; 157:647–59. DOI: 10.1007/s00705-011-1212-8.

22. Ivaniushina V., Radjef N., Alexeeva M., Gault E., Semenov S., Salhi M., Kiselev O., Dény P. Hepatitis delta virus genotypes I and II cocirculate in an endemic area of Yakutia, Russia. J. Gen. Virol. 2001; 82(11):2709–18. DOI: 10.1099/0022-1317-82-11-2709.

23. Sadeghian H., Varasteh N., Esmaeelzadeh A., Nomani H., Alimardani M., Davoodnejad M., Meshkat M., Ahadi M., Sepahi S., Rostami S., Meshkat Z. Distribution of hepatitis delta virus genotypes in Mashhad, northeast Iran. Jundishapur J. Microbiol. 2015; 8(2):e14908. DOI: 10.5812/jjm.14908.

24. Anarbaeva Zh.A., Tashpolotova A.Sh., Suranbaeva G.S., Zhakisheva E.M., Maksytov S.T. Chronic viral hepatitis Delta. [Healthcare in Kyrgyzstan]. 2017; 2:9–13.

25. Yashechkin Y.I., Naydenova E.V., Bugorkova T.V., Shcherbakova S.A. Setting-up of the Database on the Nucleotide Sequences of the Genomes of the Strains of Bacterial and Viral Infections Agents of the I–II Pathogenicity Groups. Problemy Osobo Opasnykh Infektsii [Problems of Particularly Dangerous Infections]. 2013; (1):70–3. DOI: 10.21055/0370-1069-2013-1-70-73.