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Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia

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Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
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Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Lusaka 10101, Zambia
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Department of Para-Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
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Center for Research in Infectious Disease, University College Dublin, Dublin, Ireland
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International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
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Global Virus Network, Baltimore, MD 21201, USA
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Department of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
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Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, 1090 Vienna, Austria
*
Authors to whom correspondence should be addressed.
Viruses 2020, 12(9), 1017; https://doi.org/10.3390/v12091017
Received: 15 July 2020 / Revised: 8 September 2020 / Accepted: 8 September 2020 / Published: 11 September 2020
(This article belongs to the Section Insect Viruses)
To monitor the arthropod-borne virus transmission in mosquitoes, we have attempted both to detect and isolate viruses from 3304 wild-caught female mosquitoes in the Livingstone (Southern Province) and Mongu (Western Province) regions in Zambia in 2017. A pan-flavivirus RT-PCR assay was performed to identify flavivirus genomes in total RNA extracted from mosquito lysates, followed by virus isolation and full genome sequence analysis using next-generation sequencing and rapid amplification of cDNA ends. We isolated a newly identified Barkedji virus (BJV Zambia) (10,899 nt) and a novel flavivirus, tentatively termed Barkedji-like virus (BJLV) (10,885 nt) from Culex spp. mosquitoes which shared 96% and 75% nucleotide identity with BJV which has been isolated in Israel, respectively. These viruses could replicate in C6/36 cells but not in mammalian and avian cell lines. In parallel, a comparative genomics screening was conducted to study evolutionary traits of the 5′- and 3′-untranslated regions (UTRs) of isolated viruses. Bioinformatic analyses of the secondary structures in the UTRs of both viruses revealed that the 5′-UTRs exhibit canonical stem-loop structures, while the 3′-UTRs contain structural homologs to exoribonuclease-resistant RNAs (xrRNAs), SL-III, dumbbell, and terminal stem-loop (3′SL) structures. The function of predicted xrRNA structures to stop RNA degradation by Xrn1 exoribonuclease was further proved by the in vitro Xrn1 resistance assay. View Full-Text
Keywords: Barkedji virus; Barkedji-like virus; dISFVs; 5′-UTR; 3′-UTR; RNA secondary structure Barkedji virus; Barkedji-like virus; dISFVs; 5′-UTR; 3′-UTR; RNA secondary structure
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MDPI and ACS Style

Wastika, C.E.; Harima, H.; Sasaki, M.; Hang’ombe, B.M.; Eshita, Y.; Qiu, Y.; Hall, W.W.; Wolfinger, M.T.; Sawa, H.; Orba, Y. Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia. Viruses 2020, 12, 1017. https://doi.org/10.3390/v12091017

AMA Style

Wastika CE, Harima H, Sasaki M, Hang’ombe BM, Eshita Y, Qiu Y, Hall WW, Wolfinger MT, Sawa H, Orba Y. Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia. Viruses. 2020; 12(9):1017. https://doi.org/10.3390/v12091017

Chicago/Turabian Style

Wastika, Christida E., Hayato Harima, Michihito Sasaki, Bernard M. Hang’ombe, Yuki Eshita, Yongjin Qiu, William W. Hall, Michael T. Wolfinger, Hirofumi Sawa, and Yasuko Orba. 2020. "Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia" Viruses 12, no. 9: 1017. https://doi.org/10.3390/v12091017

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