Detection of the RNA for new multicomponent virus in patients with Crimean-Congo hemorrhagic fever in southern Russia

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Abstract


Background. Recently, a new multicomponent RNA-containing virus was described and called as Jingmen tick virus (JMTV) supposedly belonging to flaviviruses. A virus contains of four viral particles and JMTV was firstly isolated from ticks in China.

Aims. Detection viral RNA specific for JMTV complex, sequencing genome fragments and taxonomy identification novel virus from JMTV complex in patients with Crimean-Congo hemorrhagic fever (CCHF) from southern European part of Russia.

Methods. Panel of 20 randomly selected sera from patients with confirmed Crimean-Congo hemorrhagic fever was collected in 2016 and was used for detection JMTV and CCHF viral RNA by PCR with experimental primers. Subsequent sequencing of isolated fragments of viral genomes was used for identification JMTV and CCHF virus genetic materials and phylogenetic analyses.

Results. The RNA of the CCHF virus and JMTV were detected in sera of four patients. Sequencing of the PCR fragments from S segment CCHF virus were identifying these isolates as members of Europa 1 clade. The nucleotide sequences of segment 2 (GP glycoprotein) of novel JMTV isolates clustered together by phylogenetic analysis. The level nucleotide identity for discovered JMTV isolates was only about 81−82% with comparison to the previously described European variants (Kosovo) of JMTV.

Conclusions. The results allow us to conclude that in CCHF patients the RNA of the CCHF virus and RNA of the novel multicomponent JMTV flavivirus were detected in serum.


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About the authors

Vladimir A. Ternovoi

State Research Center for Virology and Biotechnology “Vector” Rospotrebnadzor

Author for correspondence.
Email: tern@vector.nsc.ru
ORCID iD: 0000-0003-1275-171X
SPIN-code: 1328-5960
ResearcherId: A-6497-2014

Russian Federation, Novosibirsk region, Koltsovo

Ph. D. in Biology

Anastasia V. Gladysheva

State Research Center for Virology and Biotechnology “Vector” Rospotrebnadzor

Email: Nastya95.ru@list.ru
ORCID iD: 0000-0002-7396-3954
SPIN-code: 5214-3421

Russian Federation, Novosibirsk region, Koltsovo

стажер-исследователь

Alexandra O. Sementsova

State Research Center for Virology and Biotechnology “Vector” Rospotrebnadzor

Email: sementsova_ao@vector.nsc.ru
ORCID iD: 0000-0002-7188-5948
SPIN-code: 3387-9642

Russian Federation, Novosibirsk region, Koltsovo

младший научный сотрудник

Anna V. Zaykovskaya

State Research Center for Virology and Biotechnology “Vector” Rospotrebnadzor

Email: zaykovskaya_av@vector.nsc.ru
ORCID iD: 0000-0002-7188-5948
SPIN-code: 9339-6505

Russian Federation, Novosibirsk region, Koltsovo

Ph. D. in Biology

Anna S. Volynkina

Stavropol Anti-plague Institute

Email: volyn444@mail.ru
ORCID iD: 0000-0001-5554-5882
SPIN-code: 3387-4340

Russian Federation, 13-15, Sovetskaya street, Stavropol, 355035

Ph. D. in Biology

Egor S. Kotenev

Stavropol Anti-plague Institute

Email: egor_kotenev@mail.ru
ORCID iD: 0000-0002-8036-8926
SPIN-code: 1562-9580

Russian Federation, 13-15, Sovetskaya street, Stavropol, 355035

Ph. D. in Biology

Alexander P. Agafonov

State Research Center for Virology and Biotechnology “Vector” Rospotrebnadzor

Email: agafonov@vector.nsc.ru
ORCID iD: 0000-0003-2577-0434
SPIN-code: 2112-2920

Russian Federation, Novosibirsk region, Koltsovo

Doct. of Biology

Valeriy B. Loktev

State Research Center for Virology and Biotechnology “Vector” Rospotrebnadzor

Email: valeryloktev@gmail.com
ORCID iD: 0000-0002-0229-321X
SPIN-code: 3496-8857

Russian Federation, Novosibirsk region, Koltsovo

Doct. of biology Professor

References

  1. Qin X-C, Shi M, Tian J-H, Lin X-D, et al. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proc Natl Acad Sci U S A. 2014;111(18):6744–6749. doi: 10.1073/pnas.1324194111.
  2. Maruyama SR, Castro-Jorge LA, Ribeiro JM, et al. Characterisation of divergent flavivirus NS3 and NS5 protein sequences detected in Rhipicephalus microplus ticks from Brazil. Mem Inst Oswaldo Cruz. 2014;109(1):38–50. doi: 10.1590/0074-0276130166.
  3. Villa EC, Maruyama SR, de Miranda-Santos IKF, et al. Complete coding genome sequence for Mogiana tick virus, a Jingmenvirus isolated from ticks in Brazil. Genome Announc. 2017;5(18):e00232-17. doi: 10.1128/genomeA.00232-17.
  4. Ladner JT, Wiley MR, Beitzel B, et al. A multicomponent animal virus isolated from mosquitoes. Cell Host Microbe. 2016;20(3):357–367. doi: 10.1016/j.chom.2016.07.011.
  5. Emmerich P, Jakupi X, von Possel R, et al. Viral metagenomics, genetic and evolutionary characteristics of Crimean-Congo hemorrhagic fever orthonairovirus in humans, Kosovo. Infect Genet Evol. 2018;65:6–11. doi: 10.1016/j.meegid.2018.07.010.
  6. Meng F, Ding M, Tan Z, et al. Virome analysis of tick-borne viruses in Heilongjiang Province, China. Ticks Tick Borne Dis. 2019;10(2):412−420. doi: 10.1016/j.ttbdis.2018.12.002.
  7. Na Jia, Hong-Bo Liu, Xue-Bing Ni, et al. Emergence of human infection with Jingmen tick virus in China: A retrospective study. EBio Medicine. 2019;43:317−324. doi: 10.1016/j.ebiom.2019.04.004.
  8. Wang ZD, Wang B, Wei F, et al. New segmented virus associated with human febrile illness in China. N Engl J Med. 2019;380(22):2116−2125. doi: 10.1056/NEJMoa1805068.
  9. Whitehouse CA. Crimean-Congo hemorrhagic fever. Antiviral Res. 2014;64(3):145–160. doi: 10.1016/j.antiviral.2004.08.001.
  10. Fajs L, Jakupi X, Ahmeti S, et al. Molecular epidemiology of Crimean-Congo hemorrhagic fever virus in Kosovo. PLoS Negl Trop Dis. 2014;8(1):e2647.
  11. Fajs L, Humolli I, Saksida A, et al. Prevalence of Crimean-Congo hemorrhagic fever virus in healthy population, livestock and ticks in Kosovo. PLoS One. 2014;9(11):e110982. doi: 10.1371/journal.pone.0110982.
  12. Sherifi K, Cadar D, Muji S, et al. Crimean-Congo hemorrhagic fever virus clades V and VI (Europe 1 and 2) in ticks in Kosovo, 2012. PLoS Negl Trop Dis. 2014;8(10):e3168. eCollection. doi: 10.1371/journal.pntd.0003168.
  13. Вакалова Е.В., Волынкина А.С., Котенев Е.С., и др. Детекция и генетическая характеристика РНК-изолятов вируса Крымской-Конго геморрагической лихорадки, выделенных из клещей Hyalomma marginatum в Астраханской области (2016 г.) // Эпидемиология и инфекционные болезни. — 2017. — Т.22. — №5. — С. 248−253. [Vakalova EV, Volynkina AS, Korenev ES, et al. Detecrion and genetic characteristics of RNA isolates of Crimean-Congo haemorrhagic fever virus from the hyalomma marginatum ticks collected in the Astrakhan region (2016). Epidemiology and infectious diseases. 2017;22(5):248−253. (In Russ).] doi: 10.1882/1560-9529-2017-22-5-248-253.
  14. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870−1874. doi: 10.1093/molbev/msw054.
  15. Morovvati A, Ghalyanchi-Langeroudi A, Soleimani M, et al. Emergence of a new genotype of crimean-congo hemorrhagic fever virus in Iran. Iranian J Virol. 2012;6(3):24−29.

Supplementary files

Supplementary Files Action
1.
Fig. 1. Phylogenetic analysis of the CCHF virus based on the S-segment (1450 nucleotides). The analysis was carried out by the Neighbor-joining method using a two-parameter Kimura model. The significance of the constructed tree was estimated using bootstrap analysis with 1000 repetitions.

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2.
Fig. 2. The phylogenetic tree of the JMTV group, built on the basis of known nucleotide sequences. The analysis was carried out by the Neighbor-joining method using a two-parameter Kimura model. Original names of strains deposited in GenBank are given. The Alongshan virus sequence (MH158416) was used as an external group. The significance of the constructed tree was estimated using bootstrap analysis with 1000 repetitions.

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