Genetic features of the Puumala virus (Hantaviridae: Orthohantavirus) identified in the Moscow region
- Authors: Blinova E.A.1,2, Makenov M.T.1, Morozkin E.S.1, Kholodilov I.S.2, Fedorova M.V.1, Zhurenkova O.B.1, Roev G.V.1,3, Khafizov K.F.1, Karan L.S.1
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Affiliations:
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
- Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of poliomyelitis)
- Moscow Institute of Physics and Technology (National Research University)
- Issue: Vol 68, No 4 (2023)
- Pages: 283-290
- Section: ORIGINAL RESEARCH
- URL: https://journals.rcsi.science/0507-4088/article/view/133987
- DOI: https://doi.org/10.36233/0507-4088-177
- EDN: https://elibrary.ru/nuunok
- ID: 133987
Cite item
Abstract
Introduction. Puumala virus (family Hantaviridae, genus Orthohantavirus) is distributed in most regions of the European part of Russia. However, information about its genetic variants circulating on the territory of the Central Federal District is extremely scarce.
Materials and methods. Rodents’ tissue samples were tested after reverse transcription by PCR for the presence of hantaviral RNA. The amplified fragments of the L segment were sequenced by the Sanger method. For two samples, sequences of all three segments were obtained using the NGS method. Phylogenetic trees were built in the MEGA-X software.
Results. Puumala virus was found in six samples. Based on the phylogenetic analysis of sequences of three segments, the obtained genetic variants belong to the sublineage previously designated as W-RUS.
Conclusion. A genetic variant of the Puumala virus, belonging to the subline W-RUS, circulates on the territory of the Volokolamsk district of Moscow region.
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##article.viewOnOriginalSite##About the authors
Ekaterina A. Blinova
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing; Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of poliomyelitis)
Author for correspondence.
Email: blinova.e@cmd.su
ORCID iD: 0000-0002-0735-5627
research associate; PhD student
Russian Federation, 111123, Moskow; 108819, MoscowMarat T. Makenov
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: makenov@cmd.su
ORCID iD: 0000-0002-6835-4572
PhD, research associate
Russian Federation, 111123, MoskowEvgeny S. Morozkin
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: morozkin@cmd.su
ORCID iD: 0000-0001-8407-2623
PhD, research associate
Russian Federation, 111123, MoskowIvan S. Kholodilov
Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of poliomyelitis)
Email: ivan-kholodilov@bk.ru
ORCID iD: 0000-0002-3764-7081
PhD, research associate
Russian Federation, 108819, MoscowMarina V. Fedorova
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: culicidae@mail.ru
ORCID iD: 0000-0002-1232-1624
PhD, research associate
Russian Federation, 111123, MoskowOlga B. Zhurenkova
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: Zhurenkova@cmd.su
ORCID iD: 0000-0003-1571-4826
research associate
Russian Federation, 111123, MoskowGerman V. Roev
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing; Moscow Institute of Physics and Technology (National Research University)
Email: roev@cmd.su
ORCID iD: 0000-0002-2353-5222
research associate; Student
Russian Federation, 111123, Moskow; 141701, MoscowKamil F. Khafizov
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: khafizov@cmd.su
ORCID iD: 0000-0001-5524-0296
PhD, Head of the Laboratory
Russian Federation, 111123, MoskowLudmila S. Karan
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: karan@cmd.su
ORCID iD: 0000-0002-5927-460X
Group Leader
Russian Federation, 111123, MoskowReferences
- Bernshteyn A.D., Gavrilovskaya I.N., Apekina N.S., Dzagurova T.K., Tkachenko E.A. Features of the natural focality of hantavirus zoonoses. Epidemiologiya i vaktsinoprofilaktika. 2010; (2): 5–13. https://www.elibrary.ru/micwyl (in Russian)
- Kuhn J.H., Schmaljohn C.S. A brief history of bunyaviral family hantaviridae. Diseases. 2023; 11(1): 38. https://doi.org/10.3390/diseases11010038
- Lee G.Y., Kim W.K., Park K., Lee S.H., Hwang J., No J.S., et al. Phylogeographic diversity and hybrid zone of Hantaan orthohantavirus collected in Gangwon Province, Republic of Korea. PLoS Negl. Trop. Dis. 2020; 14(10): e0008714. https://doi.org/10.1371/journal.pntd.0008714
- Vetter P., L’Huillier A.G., Montalbano M.F., Pigny F., Eckerle I., Torriani G., et al. Puumala virus infection in family, Switzerland. Emerg. Infect. Dis. 2021; 27(2): 658–60. https://doi.org/10.3201/eid2702.203770
- Tkachenko E.A., Ishmukhametov A.A., Dzagurova T.K., Bernshtein A.D., Morozov V.G., Siniugina A.A., et al. Hemorrhagic fever with renal syndrome, Russia. Emerg. Infect. Dis. 2019; 25(12): 2325–8. https://doi.org/10.3201/eid2512.181649
- Szabó R., Radosa L., Ličková M., Sláviková M., Heroldová M., Stanko M., et al. Phylogenetic analysis of Puumala virus strains from Central Europe highlights the need for a full-genome perspective on hantavirus evolution. Virus Genes. 2017; 53(6): 913–7. https://doi.org/10.1007/s11262-017-1484-5
- Garanina S.B., Platonov A.E., Zhuravlev V.I., Murashkina A.N., Yakimenko V.V., Korneev A.G., et al. Genetic diversity and geographic distribution of hantaviruses in Russia. Zoonoses Public Health. 2009; 56(6-7): 297–309. https://doi.org/10.1111/j.1863-2378.2008.01210.x
- Kabwe E., Davidyuk Y., Shamsutdinov A., Garanina E., Martynova E., Kitaeva K., et al. Orthohantaviruses, emerging zoonotic pathogens. Pathogens. 2020; 9(9): 775. https://doi.org/10.3390/pathogens9090775
- Klempa B. Reassortment events in the evolution of hantaviruses. Virus Genes. 2018; 54(5): 638–46. https://doi.org/10.1007/s11262-018-1590-z
- Castel G., Chevenet F., Razzauti M., Murri S., Marianneau P., Cosson J.F., et al. Phylogeography of Puumala orthohantavirus in Europe. Viruses. 2019; 11(8): 679. https://doi.org/10.3390/v11080679
- Dekonenko A., Yakimenko V., Ivanov A., Morozov V., Nikitin P., Khasanova S., et al. Genetic similarity of Puumala viruses found in Finland and western Siberia and of the mitochondrial DNA of their rodent hosts suggests a common evolutionary origin. Infect. Genet. Evol. 2003; 3(4): 245–57. https://doi.org/10.1016/s1567-1348(03)00088-1
- Sironen T., Vaheri A., Plyusnin A. Molecular evolution of Puumala hantavirus. J. Virol. 2001; 75(23): 11803–10. https://doi.org/10.1128/JVI.75.23.11803-11810.2001
- Blinova E., Deviatkin A., Kurashova S., Balovneva M., Volgina I., Valdokhina A., et al. A fatal case of haemorrhagic fever with renal syndrome in Kursk Region, Russia, caused by a novel Puumala virus clade. Infect. Genet. Evol. 2022; 102: 105295. https://doi.org/10.1016/j.meegid.2022.105295
- Yashina L.N., Tregubchak T.V., Malyshev B.S., Smetannikova N.A., Grishchenko I.V., Dol’skiy A.A., et al. Study of the exosomal microrna-126 and microrna-218 expression profiles in patients with hemorrhagic fever with renal syndrome (hfrs). Problemy osobo opasnykh infektsiy. 2021; (4): 150–6. https://doi.org/10.21055/0370-1069-2021-4-150-156 https://elibrary.ru/dxxsey (in Russian)
- Kabwe E., Al Sheikh W., Shamsutdinov A.F., Ismagilova R.K., Martynova E.V., Ohlopkova O.V., et al. Analysis of Puumala orthohantavirus genome variants identified in the territories of Volga federal district. Trop. Med. Infect. Dis. 2022; 7(3): 46. https://doi.org/10.3390/tropicalmed7030046
- Davidyuk Y., Shamsutdinov A., Kabwe E., Ismagilova R., Martynova E., Belyaev A., et al. Prevalence of the Puumala orthohantavirus strains in the Pre-Kama area of the Republic of Tatarstan, Russia. Pathogens. 2020; 9(7): 540. https://doi.org/10.3390/pathogens9070540
- Davidyuk Y.N., Kabwe E., Shamsutdinov A.F., Knyazeva A.V., Martynova E.V., Ismagilova R.K., et al. The Distribution of Puumala orthohantavirus genome variants correlates with the regional landscapes in the Trans-Kama area of the Republic of Tatarstan. Pathogens. 2021; 10(9): 1169. https://doi.org/10.3390/pathogens10091169
- Martynova E., Davidyuk Y., Kabwe E., Garanina E.E., Shakirova V., Pavelkina V., et al. Cytokine, chemokine, and metalloprotease activation in the serum of patients with nephropathia epidemica from the Republic of Tatarstan and the Republic of Mordovia, Russia. Pathogens. 2021; 10(5): 527. https://doi.org/10.3390/pathogens10050527
- Savitskaya T.A., Ivanova A.V., Isaeva G.Sh., Reshetnikova I.D., Trifonov V.A., Ziatdinov V.B., et al. Assessment of epidemiological situation on hemorhhagic fever with renal syndrome around the world and in Russia, forecast for 2020. Problemy osobo opasnykh infektsiy. 2020; (2): 62–70. https://doi.org/10.21055/0370-1069-2020-2-62-70 https://elibrary.ru/oqmbzo (in Russian)
- Shchipanov N.A. Universal live-trap for small mammals. Zoologicheskiy zhurnal. 1987; 66(5): 759–61. (in Russian)
- Mills J., Childs J., Ksiazek T., Peters C., Velleca W. Methods for trapping and sampling small mammals for virologic testing; 1995. Available at: https://stacks.cdc.gov/view/cdc/11507
- Klempa B., Fichet-Calvet E., Lecompte E., Auste B., Aniskin V., Meisel H., et al. Hantavirus in African wood mouse, Guinea. Emerg. Infect. Dis. 2006; 12(5): 838–40. https://doi.org/10.3201/eid1205.051487
- Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–20. https://doi.org/10.1093/bioinformatics/btu170
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011; 17(1): 10. https://doi.org/10.14806/ej.17.1.200
- Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012; 9(4): 357–9. https://doi.org/10.1038/nmeth.1923
- Wilm A., Aw P.P., Bertrand D., Yeo G.H., Ong S.H., Wong C.H., et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic. Acids. Res. 2012; 40(22): 11189–201. https://doi.org/10.1093/nar/gks918
- Danecek P., Bonfield J.K., Liddle J., Marshall J., Ohan V., Pollard M.O., et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2): giab008. https://doi.org/10.1093/gigascience/giab008
- Van der Auwera G.A., O’Connor B.D. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. O’Reilly Media; 2020.
- Kumar S., Stecher G., Li M., Knyaz C., Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol. Biol. Evol. 2018; 35(6): 1547–9. https://doi.org/10.1093/molbev/msy096
- Ivanov A.P., Dekonenko A.E., Dzagurova T.K., Malkin A.E., Shervarli I.V., Baranovskiy P.M., et al. Analysis of an outbreak of hemorrhagic fever with the renal syndrome in the Egoryevsk district of the Moscow region. Voprosy virusologii. 2000; 45(4): 33–6. (in Russian)
- Garanina S.B., Platonov A.E., Zhuravlev V.I., Murashkina A.N., Yakimenko V.V., Korneev A.G., et al. Genetic diversity and geographic distribution of hantaviruses in Russia. Zoonoses Public Health. 2009; 56(6-7): 297–309. https://doi.org/10.1111/j.1863-2378.2008.01210.x
- Razzauti M., Plyusnina A., Niemimaa J., Henttonen H., Plyusnin A. Co-circulation of two Puumala hantavirus lineages in Latvia: a Russian lineage described previously and a novel Latvian lineage. J. Med. Virol. 2012; 84(2): 314–8. https://doi.org/10.1002/jmv.22263
- Kabwe E., Shamsutdinov A.F., Suleimanova S., Martynova E.V., Ismagilova R.K., Shakirova V.G., et al. Puumala orthohantavirus reassortant genome variants likely emerging in the watershed forests. Int. J. Mol. Sci. 2023; 24(2): 1018. https://doi.org/10.3390/ijms24021018