Abstract
The first report about Ebinur Lake orthotobunyavirus (EBIV) detected in mosquito pools in the northern provinces of China was published in 2014. The south of the European part of the Russian Federation is a known area of some arboviral infection foci such as West Nile Fever due to favorable climatic and geographic conditions and being a part of the bird’s migratory pathways. But very little is known about the spread of other bird-associated viruses. We describe here the first case of EBIV detection in the Volgograd region, Russia. The genomic RNA of EBIV was detected in bird brain tissues, mosquitoes (including overwintering ones) and ticks pools using metagenomic sequencing technique. Belonging of the detected RNA to EBIV (Orthobunyavirus, Peribunyaviridae) was confirmed by phylogenetic analysis. The simultaneous existence of EBIV and other arboviruses such as West Nile virus (WNV) and Sindbis virus (SINV) in environmental samples was revealed. The obtained results indicate the need for further studies of the EBIV circulation in the Volgograd region and possible epidemiological risks.
REFERENCES
Platonov, A., Outbreak of West Nile virus infection, Volgograd region, Russia, 1999, Emerging Infect. Dis., 2001, vol. 7, no. 1, pp. 128–132. https://doi.org/10.3201/eid0701.010118
Napp, S., Petrić, D, and Busquets, N., West Nile virus and other mosquito-borne viruses present in Eastern Europe, Pathog. Global Health, 2018, vol. 112, no. 5, pp. 233–248. https://doi.org/10.1080/20477724.2018.1483567
Camp, J. and Nowotny, N., The knowns and unknowns of West Nile virus in Europe: what did we learn from the 2018 outbreak?, Expert Rev. Anti-Infect. Ther., 2020, vol. 18, no. 2, pp. 145–154. https://doi.org/10.1080/14787210.2020.1713751
Platonov, A., Karan, L., Shopenskaia, T., Fedorova, M., Koliasnikova, N., Rusakova, N., et al., Genotyping of West Nile fever virus strains circulating in southern Russia as an epidemiological investigation method: principles and results, Zh. Mikrobiol., Epidemiol. Immunobiol., 2011, no. 2, pp. 29–37. PMID.21598612.
Subbotina, E. and Loktev, V., Molecular evolution of West Nile virus, Mol. Genet., Microbiol. Virol., 2014, vol. 29, no. 1, pp. 34–41. https://doi.org/10.3103/S0891416814010054
Molchanova, E., Luchinin, D., Negodenko, A., Prilepskaya, D., Boroday, N., Konovalov, P., et al., Monitoring studies of arbovirus infections transmitted by mosquitoes on the territory of the Volgograd region, Zdorov’e Naseleniya i Sreda Obitaniya, 2019, no. 6, pp. 60–66.
Romanowski, V., Taxonomy of the order Bunyavirales: update 2019, Arch. Virol., 2019, vol. 164, no. 7, pp. 1949–1965. https://doi.org/10.1007/s00705-019-04253-6
Elliott, R., Orthobunyaviruses: recent genetic and structural insights, Nat. Rev. Microbiol., 2014, vol. 12, no. 10, pp. 673–685. https://doi.org/10.1038/nrmicro3332
Liu, R., Zhang, G., Yang, Y., Dang, R., and Zhao, T., Genome sequence of Abbey Lake virus, a novel Orthobunyavirus isolated from China, Genome Announce., 2014, vol. 2, no. 3, p. e00433-14. https://doi.org/10.1128/genomeA.00433-14
Liu, R., Zhang, G., Sun, X., Zheng, Z., Liu, X., Zhao, Y., et al., Isolation and molecular characterization on Abbey Lake Orthobunyavirus (Bunyaviridae) in Xinjiang, China, Zhonghua Liuxingbingxue Zazhi, 2014, vol. 35, no. 8, pp. 939–942. PMID.25376687.
Xia, H., Liu, R., Zhao, L., Sun, X., Zheng, Z., Atoni, E., Hu, X., Zhang, B., Zhang, G., and Yuan, Z., Characterization of Ebinur Lake virus and its human seroprevalence at the China-Kazakhstan Border, Front. Microbiol., 2020, vol. 10, p. 3111. https://doi.org/10.3389/fmicb.2019.03111
Zhao, L., Luo, H., Huang, D., Yu, P., Dong, Q., Mwaliko, C., et al., Pathogenesis and immune response of Ebinur Lake virus: A newly identified orthobunyavirus that exhibited strong virulence in mice, Front. Microbiol., 2021, vol. 11, p. 625661. https://doi.org/10.3389/fmicb.2020.625661
Wright, M., Stockwell, T., Beck, E., Busam, D., Bajaksouzian, S., Jacobs, M., et al., SISPA-Seq for rapid whole genome surveys of bacterial isolates, Infect., Genet. Evol., 2015, vol. 32, pp. 191–198. https://doi.org/10.1016/j.meegid.2015.03.018
Moser, L., Ramirez-Carvajal, L., Puri, V., Pauszek, S., Matthews, K., Dilley, K., et al., A universal next-generation sequencing protocol to generate noninfectious barcoded cDNA libraries from high-containment RNA viruses, mSystems, 2016, vol. 1, no. 3. https://doi.org/10.1128/mSystems.00039-15
Martin, M., Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J., 2011, vol. 17, no. 1, p. 10. https://doi.org/10.14806/ej.17.1.200
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al., The sequence Alignment/Map format and SAMtools, Bioinformatics, 2009, vol. 25, no. 16, pp. 2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Danecek, P., Bonfield, J., Liddle, J., Marshall, J., Ohan, V., Pollard, M., et al., Twelve years of SAMtools and BCFtools, GigaScience, 2021, vol. 10, no. 2, p. giab008. https://doi.org/10.1093/gigascience/giab008
Li, H. and Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 2009, vol. 25, no. 14, pp. 1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A., Dvorkin, M., Kulikov, A., et al., SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol., 2012, vol. 19, no. 5, pp. 455–477. https://doi.org/10.1089/cmb.2012.0021
Nurk, S., Bankevich, A., Antipov, D., Gurevich, A., Korobeynikov, A., Lapidus, A., et al., Assembling single-cell genomes and mini-metagenomes from chimeric MDA products, J. Comput. Biol., 2013, vol. 20, no. 10, pp. 714–737. https://doi.org/10.1089/cmb.2013.0084
Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D., Basic local alignment search tool, J. Mol. Biol., 1990, vol. 215, no. 3, pp. 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Katoh, K. and Standley, D., MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 2013, vol. 30, no. 4, pp. 772–780. https://doi.org/10.1093/molbev/mst010
Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K., MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 2018, vol. 35, no. 6, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096
Letunic, I. and Bork, P., Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation, Nucleic Acids Res., 2021, vol. 49, no. W1, pp. W293-W296. https://doi.org/10.1093/nar/gkab301
ACKNOWLEDGMENTS
The authors are grateful to virologist A.O. Negodenko for collaborative work on virus isolation in Volgograd Plague Control Research Institute.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest. The authors declare that they have no conflicts of interest.
This article does not contain any studies involving human participants or animals as research subjects.
About this article
Cite this article
Avdiusheva, E.F., Luchinin, D.N., Borodai, N.V. et al. The First Detection of Ebinur Lake Virus (Orthobunyavirus, Peribunyaviridae) in Russia. Mol. Genet. Microbiol. Virol. 38, 41–46 (2023). https://doi.org/10.3103/S0891416823010020
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.3103/S0891416823010020