Genetic diversity of novel circular ssDNA viruses in bats in China
Genetic diversity of novel circular ssDNA viruses in bats in China
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中国蝙蝠新型环状单链DNA病毒的遗传多样性
DOI：
10.1099/vir.0.034108-0
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发表时间：
2011-11-01
影响因子：
3.8
通讯作者：
Shi, Zhengli
中科院分区：
文献类型：
--
作者：
Ge, Xingyi;Li, Jialu;Shi, Zhengli
新的环状ssDNA基因组最近被发现在动物和环境中使用宏基因组和高通量测序方法。在这项研究中，五个全长环状ssDNA基因组回收蝙蝠粪便样品使用反向PCR与圆环病毒相关序列的基础上设计的序列从Solexa测序数据来自随机扩增方法。这五个序列与圆环病毒或最近提出的圆环病毒科的圆环病毒具有相似的基因组结构。新获得的圆环病毒/类圆环病毒基因组长度为1741 ~ 2177 bp，每个基因组都包含两个主要的ORF，即ORF 1和ORF 2，分别编码复制酶（Rep）和衣壳蛋白（Cap）。在所有5个基因组中预测了潜在的茎环区，其中3个具有典型的保守的环状病毒的九核苷酸基序。设计了一组靶向保守Rep区的引物，并用于检测个体蝙蝠中圆环病毒/环状病毒序列的流行。在检测的199份样本中，47份（23.6%）为圆环病毒基因组阳性，2份（1.0%）为圆环病毒基因组阳性。在这项研究中，总共获得了48个部分Rep序列加上5个全长基因组。详细的分析表明，这些序列与已知的圆环病毒/圆环病毒基因组有较远的关系，可能代表了属于圆环病毒科的22个新物种。
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 1 741 to 21 77 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.