Metagenomic Analysis of Viruses from Bat Fecal Samples Reveals Many Novel Viruses in Insectivorous Bats in China

Abstract

bIncreasing data indicate that bats harbor diverse viruses, some of which cause severe human diseases. In this study, sequenceindependent amplification and high-throughput sequencing (Solexa) were applied to the metagenomic analysis of viruses in bat fecal samples collected from 6 locations in China. A total of 8,746,417 reads with a length of 306,124,595 bp were obtained. Among these reads, 13,541 (0.15%) had similarity to phage sequences and 9,170 (0.1%) had similarity to eukaryotic virus sequences. A total of 129 assembled contigs (>100 nucleotides) were constructed and compared with GenBank: 32 contigs were related to phages, and 97 were related to eukaryotic viruses. The most frequent reads and contigs related to eukaryotic viruses were homologous to densoviruses, dicistroviruses, coronaviruses, parvoviruses, and tobamoviruses, a range that includes viruses from invertebrates, vertebrates, and plants. Most of the contigs had low identities to known viral genomic or protein sequences, suggesting that a large number of novel and genetically diverse insect viruses as well as putative mammalian viruses are transmitted by bats in China. This study provides the first preliminary understanding of the virome of some bat populations in China, which may guide the discovery and isolation of novel viruses in the future. Bats, the only flying mammal and the second most diverse group of mammals, are natural reservoirs of many emerging viruses (7, 38). Some bat viruses cause severe human diseases, such as lyssavirus, Hendra virus, Nipah virus, Ebola virus, and Marburg virus (16,23,29,41,47). Most of the known bat viruses have been discovered in apparently healthy bats (10,14,19,20,26,34,49). When bats are experimentally infected with henipavirus or the rabies virus, the bats shed the virus but do not produce any clinical syndrome like those observed in other animals and humans (1,17,30,40). This phenomenon may be due to the adaption of viruses to their host species, preinfection with related nonpathogenic viruses, or some unique characteristics of the bat immune system to viral infection. Considering the species richness and wide geographic distribution of bats, bats may be a source of many additional unknown viruses.The techniques for isolating viruses are straightforward but are not always successful because the majority of viruses are unable to grow in cell culture due to a lack of susceptible cell lines, a low titer of virus, or toxicity of environmental samples. PCR assays are sequence-dependent and extremely sensitive and rapid but have been complicated by the lack of a universally conserved gene or gene marker for all types of viruses. Recently, the sequence-independent amplification of viral nucleic acids followed by shotgun sequencing or pyrosequencing has been used to discover an enormous diversity of virus species and genotypes in marine and fresh water (2,6,12,37,39,45), human feces (3, 5, 43), animal tissues, and bat feces (11,13,24,32,42).In this study, six bat fecal samples were collected from six locations...

Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics

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Characterization of a Novel G3P[3] Rotavirus Isolated from a Lesser Horseshoe Bat: a Distant Relative of Feline/Canine Rotaviruses

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Investigation of hemorrhagic fever viruses inside wild populations of ticks: One of the pioneer studies in Saudi Arabia

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