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Detection and characterization of a novel hepacivirus in long-tailed ground squirrels (Spermophilus undulatus) in China

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Abstract

Rodent populations are known to be reservoirs of viruses with the potential to infect humans. However, a large number of such viruses remain undiscovered. In this study, we investigated the shedding of unknown viruses in long-tailed ground squirrel (Spermophilus undulatus) feces by high-throughput sequencing. A novel and highly divergent virus related to members of the genus Hepacivirus was identified in ground squirrel liver. This virus, tentatively named RHV-GS2015, was found to have a genome organization that is typical of hepaciviruses, including a long open reading frame encoding a polyprotein of 2763 aa. Sequence alignment of RHV-GS2015 with the most closely related hepaciviruses yielded p-distances of the NS3 and NS5B regions of 0.546 and 0.476, respectively, supporting the conclusion that RHV-GS2015 is a member of a new hepacivirus species, which we propose to be named “Hepacivirus P”. Phylogenetic analysis of the NS3 and NS5B regions indicated that RHV-GS2015 shares common ancestry with other rodent hepaciviruses (species Hepacivirus E, and species Hepacivirus F), Norway rat hepacivirus 1 (species Hepacivirus G), and Norway rat hepacivirus 2 (species Hepacivirus H). A phylogenetic tree including the seven previously identified rodent hepaciviruses revealed extreme genetic heterogeneity among these viruses. RHV-GS2015 was detected in 7 out of 12 ground squirrel pools and was present in liver, lung, and spleen tissues. Furthermore, livers showed extremely high viral loads of RHV-GS2015, ranging from 2.5 × 106 to 2.0 × 108 copies/g. It is reasonable to assume that this novel virus is hepatotropic, like hepatitis C virus. The discovery of RHV-GS2015 extends our knowledge of the genetic diversity and host range of hepaciviruses, helping to elucidate their origins and evolution.

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    Authors and Affiliations

    1. Key Laboratory of Medical Virology and Viral Disease, Ministry of Health of the People’s Republic of China, Beijing, 102206, China

      Li-li Li, Meng-meng Liu, Ya-long Xu, Hong-yan Deng & Zhao-jun Duan

    2. National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-cheng District, Beijing, 100052, China

      Li-li Li, Meng-meng Liu, Ya-long Xu, Hong-yan Deng & Zhao-jun Duan

    3. Department of Medical Microbiology, Qingdao University Medical College, Qingdao, 266021, China

      Meng-meng Liu & Hong-yan Deng

    4. State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China

      Shu Shen & Fei Deng

    5. Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, 830001, China

      Yu-jiang Zhang

    6. Shaanxi University of Chinese Medicine, Xi’an, 712046, China

      Ya-long Xu

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    Correspondence to Fei Deng or Zhao-jun Duan.

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    The authors declare that there are no conflicts of interest.

    Funding

    This work was supported by grants from the National Key R&D Program of China (2016YFC1201904), the National Science and Technology Major Project of China (No. 2018ZX10305409-004-002) and the Science and Technology Basic Work Program (2013FY113500), from the Ministry of Science and Technology of China.

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    The study protocol was approved by the Ethics Committee of China CDC and adhered to Chinese ethics laws and regulations.

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    The GenBank [/EMBL/DDBJ] accession number for the complete genome nucleotide sequence of the novel hepacivirus found in this study is MG211815.

    Li-li Li and Meng-meng Liu contributed equally to the manuscript.

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    Li, Ll., Liu, Mm., Shen, S. et al. Detection and characterization of a novel hepacivirus in long-tailed ground squirrels (Spermophilus undulatus) in China. Arch Virol 164, 2401–2410 (2019). https://doi.org/10.1007/s00705-019-04303-z

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