Genetic diversity of novel circular ssDNA viruses in bats in China

J Gen Virol. 2011 Nov;92(Pt 11):2646-2653. doi: 10.1099/vir.0.034108-0. Epub 2011 Jul 27.

Abstract

Novel circular ssDNA genomes have recently been detected in animals and in the environment using metagenomic and high-throughput sequencing approaches. In this study, five full-length circular ssDNA genomes were recovered from bat faecal samples using inverse PCR with sequences designed based on circovirus-related sequences obtained from Solexa sequencing data derived from a random amplification method. These five sequences shared a similar genomic organization to circovirus or the recently proposed cyclovirus of the family Circoviridae. The newly obtained circovirus/cyclovirus-like genomes ranged from 1741 to 2177 bp, and each consisted of two major ORFs, ORF1 and ORF2, encoding putative replicase (Rep) and capsid (Cap) proteins, respectively. The potential stem-loop region was predicted in all five genomes, and three of them had the typical conserved nonanucleotide motif of cycloviruses. A set of primers targeting the conserved Rep region was designed and used to detect the prevalence of circovirus/cyclovirus sequences in individual bats. Among 199 samples tested, 47 were positive (23.6%) for the circovirus genome and two (1.0%) were positive for the cyclovirus genome. In total, 48 partial Rep sequences plus the five full-length genomes were obtained in this study. Detailed analysis indicated that these sequences are distantly related to known circovirus/cyclovirus genomes and may represent 22 novel species that belong to the family Circoviridae.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • China
  • Chiroptera
  • Circoviridae / classification*
  • Circoviridae / genetics*
  • Circoviridae / isolation & purification
  • Circoviridae Infections / veterinary*
  • Circoviridae Infections / virology
  • DNA, Viral / chemistry
  • DNA, Viral / genetics*
  • Feces / virology
  • Genetic Variation*
  • Molecular Sequence Data
  • Open Reading Frames
  • Sequence Analysis, DNA

Substances

  • DNA, Viral

Associated data

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