Citation: Cui-hong An, Juan Li, Yi-ting Wang, Shou-min Nie, Wen-hui Chang, Hong Zhou, Lin Xu, Yang-xin Sun, Wei-feng Shi, Ci-xiu Li. Identification of a novel hepacivirus in Mongolian gerbil (Meriones unguiculatus) from Shaanxi, China .VIROLOGICA SINICA, 2022, 37(2) : 307-310.  http://dx.doi.org/10.1016/j.virs.2022.01.016

Identification of a novel hepacivirus in Mongolian gerbil (Meriones unguiculatus) from Shaanxi, China

  • Highlights:
    1. The first hepacivirus detected in Mongolian gerbils from a plague zones in China.
    2. A novel hepacivirus closely related to hepacivirus E and F.
    3. Mongolian gerbils could be a potential animal model for hepacivirus pathogenicity.
    4. Extending the genetic diversity and host range of hepaciviruses.

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  • 10.1016j.virs.2022.01.016-ESM.docx
    1. Bolger, A.M., Lohse, M., Usadel, B., 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.

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

    3. Capella-Gutierrez, S., Silla-Martinez, J.M., Gabaldon, T., 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973.

    4. de Souza, W.M., Fumagalli, M.J., Sabino-Santos, G.Jr., Motta Maia, F.G., Modha, S., Teixeira Nunes, M.R., Murcia, P.R., Moraes Figueiredo, L.T., 2019. A novel hepacivirus in wild rodents from South America. Viruses 11, 297.

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

    6. Hartlage, A.S., Cullen, J.M., Kapoor, A., 2016. The strange, expanding world of animal hepaciviruses. Annu Rev Virol 3, 53–75.

    7. Hu, T., Li, J., Zhou, H., Li, C.X., Holmes, E.C., Shi, W.F., 2021. Bioinformatics resources for SARS-CoV-2 discovery and surveillance. Brief. Bioinform. 22, 631–641.

    8. Katoh, K., Misawa, K., Kuma, K., Miyata, T., 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066.

    9. Langmead, B., Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-U354.

    10. Li, W., Sun, Q., She, R., Wang, D., Duan, X., Yin, J., Ding, Y., 2009. Experimental infection of Mongolian gerbils by a genotype 4 strain of swine hepatitis E virus. J. Med. Virol. 81, 1591–1596.

    11. Li, L.L., Liu, M.M., Shen, S., Zhang, Y.J., Xu, Y.L., Deng, H.Y., Deng, F., Duan, Z.J., 2019. Detection and characterization of a novel hepacivirus in long-tailed ground squirrels(Spermophilus undulatus) in China. Arch. Virol. 164, 2401–2410.

    12. Liu, W., Wan, X., Zhong, W., 2007. Population dynamics of the Mongolian gerbils:seasonal patterns and interactions among density, reproduction and climate. J. Arid Environ. 68, 383–397.

    13. Nguyen, L.T., Schmidt, H.A., von Haeseler, A., Minh, B.Q., 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol.Biol. Evol. 32, 268–274.

    14. Riehm, J.M., Tserennorov, D., Kiefer, D., Stuermer, I.W., Tomaso, H., Zoller, L., Otgonbaatar, D., Scholz, H.C., 2011. Yersinia pestis in small rodents, Mongolia. Emerg. Infect. Dis. 17, 1320–1322.

    15. Simmonds, P., et al., 2017. ICTV virus taxonomy profile: Flaviviridae. J. Gen. Virol. 98, 2–3.

    16. Zhou, H., Ma, Z., Hu, T., Bi, Y., Mamuti, A., Yu, R., Carr, M.J., Shi, M., Li, J., Sharshov, K., Gao, G.F., Shi, W., 2019. Tamdy virus in ixodid ticks infesting bactrian camels, Xinjiang, China, 2018. Emerg. Infect. Dis. 25,

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    Identification of a novel hepacivirus in Mongolian gerbil (Meriones unguiculatus) from Shaanxi, China

      Corresponding author: Yang-xin Sun, sxpco@126.com
      Corresponding author: Wei-feng Shi, shiwf@ioz.ac.cn
      Corresponding author: Ci-xiu Li, licixiu@sdfmu.edu.cn
    • a Department of Plague and Brucellosis, Shaanxi Center for Disease Control and Prevention, Xi' An 710054, China
    • b Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
    • c Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
    • d Department of Pathogen Biology, School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China

    Abstract: Highlights:
    1. The first hepacivirus detected in Mongolian gerbils from a plague zones in China.
    2. A novel hepacivirus closely related to hepacivirus E and F.
    3. Mongolian gerbils could be a potential animal model for hepacivirus pathogenicity.
    4. Extending the genetic diversity and host range of hepaciviruses.

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