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. 2016 Mar;10(3):609-20.
doi: 10.1038/ismej.2015.138. Epub 2015 Aug 11.

Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases

Zhiqiang Wu  1 , Li Yang  1 , Xianwen Ren  1 , Guimei He  2 , Junpeng Zhang  2 , Jian Yang  1 , Zhaohui Qian  1 , Jie Dong  1 , Lilian Sun  1 , Yafang Zhu  1 , Jiang Du  1 , Fan Yang  1 , Shuyi Zhang  2   3 , Qi Jin  1   4
Affiliations

Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases

Zhiqiang Wu et al. ISME J. 2016 Mar.

Abstract

Studies have demonstrated that ~60%-80% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs.

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Figures

Figure 1
Figure 1
Numbers of bat samples from various provinces. The numbers of the 4440 bat samples belonging to the 40 bat species identified are indicated by a pie chart for each province. The numbers of samples from the 40 bat species and the provinces and dates of collection are detailed in Supplementary Table S1.
Figure 2
Figure 2
Overall view of the reads from 19 families of mammalian viruses in each pooled sample. (a) Heatmap based on the normalized sequence reads of 19 families of mammalian viruses in each pooled sample. The bat species are listed in the left text column. Location information is provided in the right text column. The names of the mammalian viral families are presented in the top text row. The boxes colored from blue to red represent the metagenomic sequencing reads observed (reads varied between 8283 and 2 919 423, respectively). (b) Overview of classifications from family to genus of the viruses of the 19 families identified in the bats in this study. Different families are labeled in different colors. The viruses that could not be assigned to any known genus are labeled in red font.
Figure 3
Figure 3
Phylogenetic analysis of bat main single-stranded RNA (ssRNA) viruses. (a) Phylogenetic tree based on the complete RNA-dependent RNA polymerase (RdRp, NSP12) proteins of CoVs. (b) Phylogenetic tree based on the complete Spike (S) proteins of CoVs. (c) Phylogenetic tree based on the L proteins of ParaVs. (d) Phylogenetic tree based on the complete RNA-dependent RNA polymerase proteins of PicoVs.
Figure 4
Figure 4
Phylogenetic analysis of bat main DNA viruses. (a) Phylogenetic tree based on the complete replicase (Rep) proteins of CVs. (b) Phylogenetic tree based on the VP1 proteins of members of the subfamily Parvovirinae. The bat viruses identified in this study are labeled in red.
Figure 5
Figure 5
Phylogenetic analysis of sporadically identified viruses from bats. (a) Phylogenetic tree based on the polyproteins of CalVs. (b) Phylogenetic tree based on the large T proteins of polyomaviruses (PyVs). (c) Phylogenetic tree based on the complete ORF1 and ORF2 sequences of hepatitis E viruses (HEVs). (d) Phylogenetic tree based on the partial L (RNA-dependent RNA polymerase (RdRp)) proteins of rhabdoviruses (RhaVs). (e) Phylogenetic tree based on the partial L proteins of bunyaviruses (BunyaVs). The bat viruses identified in this study are labeled in red.
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