GENETIC ANALYSIS OF HIV-1 IN THE ALTAI KRAY: THE FURTHER SPREAD OF THE CRF63_02A1 VARIANT IN WESTERN SIBERIA

IThe aim of this study was to characterize HIV-1 genetic strains currently circulating in Altay Kray (Western Siberia) and to analyze the HIV resistance on this territory.

Materials and methods. Blood samples were collected, with informed consent, in 2017 from 82 HIV infected persons living in Altai Kray. Sequences of pol gene fragments coding protease and part of reverse transcriptase were obtained by in house system and Sanger sequencing. Genotyping, phylogenetic and recombinant analyses were carried out by HIVdbProgram: Sequence Analysis, COMET HIV-1, REGA HIV-1 Subtyping Tool (V 3.0), MEGA 5.05, RIP and jpHMM.

Results and discussion. The results of genotype analysis revealed that the circulating recombinant form CRF63_02A1 dominated in Altay Kray (61%), subtype А was identified in 33%, the remaining subtypes, such as B, G, URF, accounted for 6%. According to phylogenetic analysis results, CRF63_02A1 sequences formed the common branch with nucleotide sequences of strains found in other regions of Siberia and Far East. All of HIV-1 variants belonging to subtype A clustered together with nucleotide sequences of A6 dominating in Russia. RIP analysis allowed to identify three unique recombinant forms (URFs), formed by CRF63_02A1 and A6. Drug resistance mutations were identified in 8 of 21 ART patients (8/21, 38%). The prevalence of drug resistance mutations in naïve patients equaled to 5,1%.

 Conclusion. Currently, the process of changing the dominant strain to CRF63_02A1 is ongoing in the Altai Kray, where 13 years ago the main variant was HIV sub-subtype A6 (IDU-A).

1. Foley B.T., Leitner T., Paraskevis D., Peeters M. Primate immunodeficiency virus classification and nomenclature: Review // Infect. Genet. Evol. 2016. Vol. 46. Р. 150–158.

2. Bobkov A.F., Kazennova E.V., Selimova L.M., Khanina T.A., Ladnaia N.N., Bobkova M.R., Kravchenko A.V., Riabov G.S., Sukhanova A.L., Buravtsova E.V., Pokrovski V.V., Weber G.N. The molecular and virological specificities of the epidemic of HIV infections in Russia and other CIS countries. Bulletin of the Russian Academy of Medical Sciences, 2003, No. 12, рр. 83–85 (In Russ.).

3. Baryshev P.B, Bogachev V.V., Gashnikova N.M. Genetic characterization of an isolate of HIV type 1 AG recombinant form circulating in Siberia, Russia // Arch. Virol. 2012. Vol. 12. Р. 2335–2341.

4. Laga V.Iu., Kazennova E.V., Vasil’ev A.V., Lapovok I.A., Ismailova A., Be sheeva N., Asybalieva N., Bobkova M.R. Molecular genetic character- ization of the HIV-1 variants abundant in Kirgiziia. Problems of Virology, 2012, No. 5, рр. 26–32 (In Russ.).

5. Murankina V.P., Vlasov E.V., Ivlev V.V., Totmenin A.V., Gashnikova M.P., Mirjamalova F.O., Sokolov Yu.V., Kazaeva E.V., Gashnikova N.M. Current moni- toring data of HIV epidemic infection in Novosibirsk areas. Molecular diagnostics-2017, Proceedings of the IX Russian scientific-practical con- ference with international participation, 2017, рр. 476–477 (In Russ.).

6. Gashnikova N.M., Bogachev V.V., Baryshev P.B., Totmenin A.V., Gashnikova M.P., Kazachinskaya A.G., Ismailova T.N., Stepanova S.A., Chernov A.S., Mikheev V.N. A rapid expansion of HIV-1 CRF63_02A1 among newly diagnosed HIV-infected individuals in the Tomsk Region, Russia // AIDS Res Hum Retroviruses. 2015. Vol. 4. Р. 456–460.

7. Gashnikova N.M., Zyryanova D.P., Astakhova E.M., Ivlev V.V., Gashnikova M.P., Pustylnikov S.V., Bocharov E.F., Totmenin A.V., Moskaleva N.V., Aikin S.S., Bulatova T.N. Predominance of CRF63_02A1 and multiple patterns of unique recombinant forms of CRF63_A1 among individuals with newly diagnosed HIV-1 infection in Kemerovo oblast, Russia // Archives of Virology. 2017. Vol. 2. Р. 379–390.

8. Kotova V.O., Trotsenko O.E., Balakhontseva L.A., Bazykina E.A., Yanovich O.A., Schikanov Yu.V., Pavlova M.N., Shmakova T.I. Molecular-epidemiological characteristics of HIV-1 variants circulating in the Jewish Autonomous Region territory. HIV Infection and Immunosuppressive Disorders, 2018, No. 4, рр. 90–99 (In Russ.).

9. Totmenin A.V., Astakhova E.M., Ivlev V.V., Zyryanova D.P., Gashnikova M.P., Vlasov E.V., Murankina V.R., Gashnikova N.M. Features of HIV-1 genotyping with regard to the development of modern territorial epidemic. Molecular diagnostics 2017, works of the IX Russian scientific-practical conference with international participation. 2017. Р. 477–478 (In Russ.).

10. Kazennova E., Laga V., Lapovok I., Glushchenko N., Neshumaev D., Vasilyev A., Bobkova M. HIV-1 Genetic Variants in the Russian Far East // AIDS Res. Hum. Retroviruses. 2014. Vol. 8. Р. 742–752.

11. Gashnikova N.M., Astakhova E.M., Gashnikova M., Bocharov E.F., Totmenin A.V., Petrova S.V., Pun’ko O.A., Popkov A.V. HIV-1 epidemiology, genetic diversity, and primary drug resistance in the Tyumen oblast, Russia // BioMed Research International. 2016. 2016. 2496280. Epub 2016 Nov 13.

12. Grishechkin A.E., Kazennova E.V., Sukhanova A.L., Belykh S.I., Sultanov L.V., Dem’ianenko E.R., Plotnikova O.I., Ladnaia N.N., Pokrovski V.V., Bobkov A.F. Molecular and epidemiological characterization of HIV- infection in the Altai Territory Journal of Mikrobiology, Epidemiology and Immunobiology 2006. Vol. 1. Р. 15–19. (In Russ.).

13. Gifford R.J., Liu T.F., Rhee S.Y., Kiuchi M., Hue S., Pillay D, Shafer R.W. The calibrated population resistance tool: standardized genotypic esti- mation of transmitted HIV-1 drug resistance // Bioinformatics. 2009. Vol. 9. Р. 1197–1198.

14. Miller S.A., Dykes D.D., Polesky H.F. Miller S.A., Dykes D.D., Polesky H.F. A simple salting out procedure for extracting DNA from human nucleated cells // Nucleic Acids Res. 1988. Vol. 3. Р. 1215.

15. Struck D., Lawyer G., Ternes A.M., Schmit J.C., Bercoff D.P. COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identifica- tion // Nucleic Acids Res. 2014. Vol. 18. e144.

16. Pineda-Peña A.C., Faria N.R., Imbrechts S., Libin P., Abecasis A.B., Deforche K., Gómez-López A., Camacho R.J., de Oliveira T, Vandamme A.M. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools // Infect. Genet. Evol. 2013. Vol. 19. Р. 337–348.

17. Schultz A.K, Zhang M., Bulla I., Leitner T., Korber B., Morgenstern B., Stanke M. jpHMM: improving the reliability of recombination prediction in HIV-1 // Nucleic Acids Res. 2009. Vol. 37 (Web Server issue): W647–651.

18. Siepel A.C., Halpern A.L., Macken C., Korber B.T. A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences // AIDS Res. Hum. Retroviruses. 1995. Vol. 11. Р. 1413–1416.

19. Altschul S., Gish W., Miller W., Myers E., Lipman D. Basic local alignment search tool // Journal of Molecular Biology. 1990. Vol. 3. Р. 403–410.

20. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0 // Mol. Biol. Evol. 2013. Vol. 12. Р. 2725–2729.

21. Riva C., Romano L., Saladini F., Lai A., Carr J.K., Francisci D., Balotta C., Zazzi M. Identification of a possible ancestor of the subtype A1 HIV Type 1 variant circulating in the former Soviet Union // AIDS Research and Human Retroviruses. 2008. Vol. 10. Р. 1319–1325.

22. Tumanov A.S., Kazennova E.V., Gromov K.B., Lomakina E.A., Zozylya E.Y., Bersenev P.G., Bobkova M.R. The molecular epidemiological analysis of HIV infec- tion in Sakhalin region, Russia. HIV Infection and Immunosuppressive Disorders, 2017, Vol. 3, рр. 113–120 (In Russ.).

23. Kazennova E., Laga V., Gromov K., Lebedeva N., Zhukova E., Pronin A., Grezina L., Dement’eva N., Shemshura A., Bobkova M. Genetic variants of HIV type 1 in MSM in Russia // AIDS Res. Hum. Retroviruses. 2017. Vol. 10. Р. 1061–1064.

24. Bennett D.E., Camacho R.J., Otelea D., Kuritzkes D.R., Fleury H., Kiuchi M., Heneine W., Kantor R., Jordan M.R., Schapiro J.M., Vandamme A.M., Sandstrom P., Boucher C.A., van de Vijver D, Rhee S.Y., Liu T.F., Pillay D., Shafer R.W. Drug resistance mutations for sur- veillance of transmitted HIV-1 drugresistance: 2009 update // PLoS One. 2009. Vol. 4, No. 3. e4724.

25. Wolinsky S.M, Korber B.T., Neumann A.U., Daniels M., Kunstman K.J., Whetsell A.J., Furtado M.R., Cao Y., Ho D.D., Safrit J.T. Adaptive evolution of HIV type 1 during the natural course of infection // Science. 1996. Vol. 272. Р. 537–542.

26. Hofstra L.M., Schmit J.C., Wensing A.M.J. Transmission of HIV-1 drug resistance. Handbook of Antimicrobial Resistance. doi: 10.1007/978- 1-4939-0667-3_23-1 Springer Science+Business Media New York 2015.

27. Machnowska P., Meixenberger K., Schmidt D., Jessen H., Hillenbrand H., Gunsenheimer-Bartmeyer B., Hamouda O., Kücherer C., Bannert N. German HIV-1 Seroconverter Study Group // PLoS One. 2019. No. 1. e0209605. doi: 10.1371/journal.pone.0209605. eCollection 201.

28. Sluis-Cremer N., Jordan M.R., Huber K., Wallis C.L., Bertagnolio S., Mellors J.W., Parkin N.T., Harrigan P.R. E138A in HIV-1 reverse transcriptase is more common in subtype C than B: implications for rilpivirine use in resource-limited settings // Antiviral Res. 2014. Vol. 107. Р. 31–34.

29. Kazennova E.V., Lapovok I.A., Laga V.Yu, Vasilyev A.V., Bobkova M.R. Natural polymorphisms of HIV-1 IDU-A variant pol gene. HIV Infection and Immunosuppressive Disorders, 2012, No. 4, рр. 44–51 (In Russ.).