Virome Analysis for Identification of Novel Mammalian Viruses in Bat Species from Chinese Provinces

Abstract

bBats are natural hosts for a large variety of zoonotic viruses. This study aimed to describe the range of bat viromes, including viruses from mammals, insects, fungi, plants, and phages, in 11 insectivorous bat species (216 bats in total) common in six provinces of China. To analyze viromes, we used sequence-independent PCR amplification and next-generation sequencing technology (Solexa Genome Analyzer II; Illumina). The viromes were identified by sequence similarity comparisons to known viruses. The mammalian viruses included those of the Adenoviridae, Herpesviridae, Papillomaviridae, Retroviridae, Circoviridae, Rhabdoviridae, Astroviridae, Flaviridae, Coronaviridae, Picornaviridae, and Parvovirinae; insect viruses included those of the Baculoviridae, Iflaviridae, Dicistroviridae, Tetraviridae, and Densovirinae; fungal viruses included those of the Chrysoviridae, Hypoviridae, Partitiviridae, and Totiviridae; and phages included those of the Caudovirales, Inoviridae, and Microviridae and unclassified phages. In addition to the viruses and phages associated with the insects, plants, and bacterial flora related to the diet and habitation of bats, we identified the complete or partial genome sequences of 13 novel mammalian viruses. These included herpesviruses, papillomaviruses, a circovirus, a bocavirus, picornaviruses, a pestivirus, and a foamy virus. Pairwise alignments and phylogenetic analyses indicated that these novel viruses showed little genetic similarity with previously reported viruses. This study also revealed a high prevalence and diversity of bat astroviruses and coronaviruses in some provinces. These findings have expanded our understanding of the viromes of bats in China and hinted at the presence of a large variety of unknown mammalian viruses in many common bat species of mainland China.

Experimental Inoculation of Artibeus jamaicensis Bats with Dengue Virus Serotypes 1 or 4 Showed No Evidence of Sustained Replication

“…Recent metagenomic analyses have identified viruses belonging to the Retroviridae, Herpesviridae, Poxviridae, Flaviviridae, Reoviridae, Picobirnaviridae families, among others, as part of the bat viromes. [30][31][32][33][34] Moreover, the existence of several yet unknown mammalian viruses in bats is indicated by these studies. Dengue is the most important viral disease transmitted by mosquitoes to humans.…”

Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens

“…In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution. R ecent metatranscriptomic and metagenomic studies of animals, fungi, insects, plants, and environmental samples have shown that mycoviruses are ubiquitous in nature (1)(2)(3)(4)(5)(6)(7)(8)(9)(10). Analyses of viral metagenomes (i.e., viromes) of environmental samples suggest that the field of virology has discovered less than 1% of the existing viral diversity, and the rate of discovery by metagenomics is higher than those of all other methods combined (11).…”

Genetic characterization of a novel picornavirus detected in Miniopterus schreibersii bats

“…Among bat viruses, members of the Picornaviridae family remain a neglected group. Although the zoonotic potential of several picornaviruses (PV) had been described, only two studies have reported complete genomic sequence and characterization of bat picornaviruses (BatPV) (Lau et al, 2011;Wu et al, 2012). Picornaviruses are found in humans and a wide variety of animals, in which they have the ability to cause respiratory, cardiac, hepatic, neurological, mucocutaneus and systematic diseases with different levels of severity (Tracy et al, 2006).…”