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Wentao Zhu, Jing Yang, Shan Lu, Yuyuan Huang, Dong Jin, Ji Pu, Liyun Liu, Zhenjun Li, Mang Shi and Jianguo Xu. Novel pegiviruses infecting wild birds and rodents[J]. Virologica Sinica.
Citation: Wentao Zhu, Jing Yang, Shan Lu, Yuyuan Huang, Dong Jin, Ji Pu, Liyun Liu, Zhenjun Li, Mang Shi, Jianguo Xu. Novel pegiviruses infecting wild birds and rodents [J].VIROLOGICA SINICA.

Novel pegiviruses infecting wild birds and rodents

  • Pegivirus (family Flaviviridae) is a genus of small enveloped RNA viruses that mainly causes blood infections in various mammals including human. Herein, we carried out an extensive survey of pegiviruses from a wide range of wild animals mainly sampled in the Qinghai-Tibet Plateau of China. Three novel pegiviruses, namely Passer montanus pegivirus, Leucosticte brandti pegivirus and Montifringilla taczanowskii pegivirus, were identified from different wild birds, and one new rodent pegivirus, namely Phaiomys leucurus pegivirus, was identified from Blyth’s vole. Interestingly, the pegiviruses of non-mammalian origin discovered in this study substantially broaden the host range of Pegivirus to avian species. Co-evolutionary analysis showed virus-host co-divergence over long evolutionary timescales, and indicated that pegiviruses largely followed a virus-host co-divergence relationship. Overall, this work extends the biodiversity of the Pegivirus genus to those infecting wild birds and hence revises the host range and evolutionary history of genus Pegivirus.

Novel pegiviruses infecting wild birds and rodents

  • Pegivirus (family Flaviviridae) is a genus of small enveloped RNA viruses that mainly causes blood infections in various mammals including human. Herein, we carried out an extensive survey of pegiviruses from a wide range of wild animals mainly sampled in the Qinghai-Tibet Plateau of China. Three novel pegiviruses, namely Passer montanus pegivirus, Leucosticte brandti pegivirus and Montifringilla taczanowskii pegivirus, were identified from different wild birds, and one new rodent pegivirus, namely Phaiomys leucurus pegivirus, was identified from Blyth’s vole. Interestingly, the pegiviruses of non-mammalian origin discovered in this study substantially broaden the host range of Pegivirus to avian species. Co-evolutionary analysis showed virus-host co-divergence over long evolutionary timescales, and indicated that pegiviruses largely followed a virus-host co-divergence relationship. Overall, this work extends the biodiversity of the Pegivirus genus to those infecting wild birds and hence revises the host range and evolutionary history of genus Pegivirus.

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    1. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120

    2. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60

    3. Burgin CJ, Colella JP, Kahn PL, Upham NS. How many species of mammals are there? Journal of Mammalogy. 2018;99:1–14

    4. Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R. Jane: a new tool for the cophylogeny reconstruction problem. Algorithms Mol Biol. 2010;5:16

    5. Firth C, Bhat M, Firth MA, Williams SH, Frye MJ, Simmonds P, Conte JM, Ng J, Garcia J, Bhuva NP, Lee B, Che X, Quan PL, Lipkin WI. Detection of zoonotic pathogens and characterization of novel viruses carried by commensal Rattus norvegicus in New York City. mBio. 2014;5:e01933–01914

    6. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–652

    7. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–321

    8. Hameed M, Wahaab A, Nawaz M, Khan S, Nazir J, Liu K, Wei J, Ma Z. Potential Role of Birds in Japanese Encephalitis Virus Zoonotic Transmission and Genotype Shift. Viruses. 2021;13:357

    9. Han BA, Schmidt JP, Bowden SE, Drake JM. Rodent reservoirs of future zoonotic diseases. Proc Natl Acad Sci U S A. 2015;112:7039–7044

    10. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–589

    11. Kapoor A, Simmonds P, Scheel TK, Hjelle B, Cullen JM, Burbelo PD, Chauhan LV, Duraisamy R, Sanchez Leon M, Jain K, Vandegrift KJ, Calisher CH, Rice CM, Lipkin WI. Identification of rodent homologs of hepatitis C virus and pegiviruses. mBio. 2013;4:e00216–00213

    12. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–780

    13. Kumar S, Stecher G, Suleski M, Hedges SB. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. Mol Biol Evol. 2017;34:1812–1819

    14. Manigold T, Vial P. Human hantavirus infections: epidemiology, clinical features, pathogenesis and immunology. Swiss Med Wkly. 2014;144:w13937

    15. Merkle D, Middendorf M, Wieseke N. A parameter-adaptive dynamic programming approach for inferring cophylogenies. BMC Bioinformatics. 2010;11 Suppl 1:S60

    16. Porter AF, Pettersson JH, Chang WS, Harvey E, Rose K, Shi M, Eden JS, Buchmann J, Moritz C, Holmes EC. Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evol. 2020;6:veaa064

    17. Ramey AM, Reeves AB. Ecology of Influenza A Viruses in Wild Birds and Wetlands of Alaska. Avian Dis. 2020;64:109–122

    18. Rodrigues TCS, Subramaniam K, McCulloch SD, Goldstein JD, Schaefer AM, Fair PA, Reif JS, Bossart GD, Waltzek TB. Genomic characterization of a novel pegivirus species from free-ranging bottlenose dolphins (Tursiops truncatus) in the Indian River Lagoon, Florida. Virus Res. 2019;263:98–101

    19. Schaluder GG, Dawson GJ, Simons JN, Pilot-Matias TJ, Gutierrez RA, Heynen CA, Knigge MF, Kurpiewski GS, Buijk SL, Leary TP, et al. Molecular and serologic analysis in the transmission of the GB hepatitis agents. J Med Virol. 1995;46:81–90

    20. Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ. The evolutionary history of vertebrate RNA viruses. Nature. 2018;556:197–202

    21. Sibley SD, Lauck M, Bailey AL, Hyeroba D, Tumukunde A, Weny G, Chapman CA, O'Connor DH, Goldberg TL, Friedrich TC. Discovery and characterization of distinct simian pegiviruses in three wild African Old World monkey species. PLoS One. 2014;9:e98569

    22. Simmonds P, Becher P, Bukh J, Gould EA, Meyers G, Monath T, Muerhoff S, Pletnev A, Rico-Hesse R, Smith DB, Stapleton JT, Ictv Report C. ICTV Virus Taxonomy Profile: Flaviviridae. J Gen Virol. 2017;98:2–3

    23. Smith DB, Becher P, Bukh J, Gould EA, Meyers G, Monath T, Muerhoff AS, Pletnev A, Rico-Hesse R, Stapleton JT, Simmonds P. Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family. J Gen Virol. 2016;97:2894–2907

    24. Valiakos G, Plavos K, Vontas A, Sofia M, Giannakopoulos A, Giannoulis T, Spyrou V, Tsokana CN, Chatzopoulos D, Kantere M, Diamantopoulos V, Theodorou A, Mpellou S, Tsakris A, Mamuris Z, Billinis C. Phylogenetic Analysis of Bird-Virulent West Nile Virus Strain, Greece. Emerg Infect Dis. 2019;25:2323–2325

    25. Wang J, Han GZ. A Sister Lineage of Sampled Retroviruses Corroborates the Complex Evolution of Retroviruses. Mol Biol Evol. 2021;38:1031–1039

    26. Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, Irie N. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet. 2013;45:701–706

    27. Wu Z, Han Y, Liu B, Li H, Zhu G, Latinne A, Dong J, Sun L, Su H, Liu L, Du J, Zhou S, Chen M, Kritiyakan A, Jittapalapong S, Chaisiri K, Buchy P, Duong V, Yang J, Jiang J, Xu X, Zhou H, Yang F, Irwin DM, Morand S, Daszak P, Wang J, Jin Q. Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia. Microbiome. 2021;9:18

    28. Wu Z, Wu Y, Zhang W, Merits A, Simmonds P, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Liu Y, Zhang L, Yu Y, Tian B, Pan L, Rehman MU, Chen S, Cheng A. The First Nonmammalian Pegivirus Demonstrates Efficient In Vitro Replication and High Lymphotropism. J Virol. 2020;94:Zhu W, Song W, Fan G, Yang J, Lu S, Jin D, Luo XL, Pu J, Chen H, Xu J. Genomic Characterization of a New Coronavirus from Migratory Birds in Jiangxi Province of China. Virol Sin. 2021a. doi:10.1007/s12250-021-00402-x1-4

    29. Zhu W, Yang J, Lu S, Jin D, Wu S, Pu J, Luo XL, Liu L, Li Z, Xu J. Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses. Front Microbiol. 2021b;12:755599

    30. Zhu W, Yang J, Lu S, Lan R, Jin D, Luo XL, Pu J, Wu S, Xu J. Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China. Virol Sin. 2021c;36:402–411

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    Novel pegiviruses infecting wild birds and rodents

      Corresponding author: Mang Shi, shim23@mail.sysu.edu.cn
      Corresponding author: Jianguo Xu, xujianguo@icdc.cn
    • 1 State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China;
    • 2 Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China;
    • 3 Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, China;
    • 4 School of Medicine, Sun Yat-sen University, Shenzhen 510006, China;
    • 5 Research Institute of Public Heath, Nankai University, Tianjin 300071, China

    Abstract: Pegivirus (family Flaviviridae) is a genus of small enveloped RNA viruses that mainly causes blood infections in various mammals including human. Herein, we carried out an extensive survey of pegiviruses from a wide range of wild animals mainly sampled in the Qinghai-Tibet Plateau of China. Three novel pegiviruses, namely Passer montanus pegivirus, Leucosticte brandti pegivirus and Montifringilla taczanowskii pegivirus, were identified from different wild birds, and one new rodent pegivirus, namely Phaiomys leucurus pegivirus, was identified from Blyth’s vole. Interestingly, the pegiviruses of non-mammalian origin discovered in this study substantially broaden the host range of Pegivirus to avian species. Co-evolutionary analysis showed virus-host co-divergence over long evolutionary timescales, and indicated that pegiviruses largely followed a virus-host co-divergence relationship. Overall, this work extends the biodiversity of the Pegivirus genus to those infecting wild birds and hence revises the host range and evolutionary history of genus Pegivirus.

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