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Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample

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Abstract

Metagenomic analysis through high-throughput sequencing is a tool for detecting both known and novel viruses. Using this technique, a novel circular single-stranded DNA (ssDNA) virus genome was discovered in respiratory secretions from a febrile traveler. The virus, named human respiratory-associated PSCV-5-like virus (HRAPLV), has a genome comprising 3,018 bases, with two major putative ORFs inversely encoding capsid (Cap) and replicase (Rep) protein and separated by two intergenic regions. One stem-loop structure was predicted in the larger intergenic region (LIR). The predicted amino acid sequences of the Cap and Rep proteins of HRAPLV showed highest identity to those of porcine stool-associated circular virus 5 isolate CP3 (PoSCV 5) (53.0% and 48.9%, respectively). The host tropism of the virus is unknown, and further study is warranted to determine whether this novel virus is associated with human disease.

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Authors and Affiliations

  1. Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China

    Lunbiao Cui, Xiaojuan Zhu, Xiling Guo, Yiyue Ge, Kangchen Zhao, Xian Qi, Zhiyang Shi, Fengcai Zhu & Minghao Zhou

  2. Jiangsu International Travel Healthcare Center, Nanjing, China

    Binyao Wu & Lixin Sun

Authors
  1. Lunbiao Cui
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  2. Binyao Wu
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  3. Xiaojuan Zhu
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  4. Xiling Guo
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  5. Yiyue Ge
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  6. Kangchen Zhao
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  7. Xian Qi
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  8. Zhiyang Shi
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  9. Fengcai Zhu
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  10. Lixin Sun
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  11. Minghao Zhou
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Corresponding authors

Correspondence to Lixin Sun or Minghao Zhou.

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Funding

This study was funded in part by Science and Technology Support Program of Jiangsu Province for Emerging Infectious Diseases Control and Prevention (No. BE2015714), Key Medical Discipline of Jiangsu Province (ZDXKA2016008), the National Natural Science Foundation of China (81501785), the Natural Science Foundation of Jiangsu Province (BK20141030, BK20161583), and the “333” Projects of Jiangsu Province.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of Jiangsu Provincial Center for Disease Control and Prevention and Jiangsu International Travel Healthcare Center.

Informed consent

Informed consent was obtained from all individual participants included in the study.

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705_2017_3481_MOESM1_ESM.tif

Fig. S1 NeighborNet networks based on the complete genome sequence of HRAPLV and other circular single-stranded DNA viruses. A filled diamond indicates the sample obtained in this study (TIFF 274 kb)

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Cite this article

Cui, L., Wu, B., Zhu, X. et al. Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample. Arch Virol 162, 3305–3312 (2017). https://doi.org/10.1007/s00705-017-3481-3

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  • DOI: https://doi.org/10.1007/s00705-017-3481-3

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