Archives of Virology

, Volume 164, Issue 10, pp 2613–2616 | Cite as

Molecular characterization of a new badnavirus infecting green Sichuan pepper (Zanthoxylum schinifolium)

  • Min Xu
  • Song Zhang
  • Zhiyou Xuan
  • Jiaxing Wu
  • Peng Dong
  • Yan Zhou
  • Ruhui Li
  • Mengji CaoEmail author
Annotated Sequence Record


A new virus with a circular double-stranded DNA genome was discovered in green Sichuan pepper with vein clearing symptoms. Its complete genome of 8,014 bp contains three open reading frames (ORF) on the plus strand, which is typical of members of the genus Badnavirus in the family Caulimoviridae. Sequence comparisons revealed that the new virus has the highest nucleotide sequence identity with grapevine vein-clearing virus (GVCV). In particular, the identity of the two viruses in the ORF3 RT-RNase H region is 71.9%, which is below the species demarcation cutoff of 80% for badnaviruses. Phylogenetic analysis also placed the new virus with GVCV in a cluster. The virus was tentatively named “green Sichuan pepper vein clearing-associated virus” (GSPVCaV). The geographical distribution and genetic diversity of GSPVCaV were studied. Another isolate was found to be highly divergent.



This research was supported by the Intergovernmental International Science, Technology and Innovation (STI) Collaboration Key Project of China’s National Key R&D Programme (NKP) (2017YFE0110900), Fundamental Research Funds for the Central Universities (XDJK2018AA002), Chongqing Research Program of Basic Research and Frontier Technology (cstc2017jcyjBX0016), and Overseas Expertise Introduction Project for Discipline Innovation (111 Center) (B18044). We thank the editor and two anonymous reviewers for their constructive comments and suggestions.

Compliance with ethical standards

I have read and abided by the statement of ethical standards for manuscripts submitted to Archives of Virology.

Conflict of interest

All authors declare they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

705_2019_4357_MOESM1_ESM.jpg (182 kb)
Supplementary Fig. S1 Detection of viral mRNAs by RT-PCR and HTS (transcriptome read mapping). M, DL2000 DNA marker; 1 and 2, ORF1; 3 and 4, ORF2; 4 and 5, ORF3 (JPEG 182 kb)
705_2019_4357_MOESM2_ESM.docx (21 kb)
Supplementary material 2 (DOCX 21 kb)


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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.National Citrus Engineering Research Center, Citrus Research InstituteSouthwest UniversityChongqingChina
  2. 2.Academy of Agricultural SciencesSouthwest UniversityChongqingChina
  3. 3.Chongqing Agricultural Technology Extension StationChongqingChina
  4. 4.National Germplasm Resources LaboratoryUSDA-ARSBeltsvilleUSA

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