Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses

Abstract

Bats are hosts to a variety of viruses capable of zoonotic transmissions. Because of increased contact between bats, humans, and other animal species, the possibility exists for further cross-species transmissions and ensuing disease outbreaks. We describe here full and partial viral genomes identified using metagenomics in the guano of bats from California and Texas. A total of 34% and 58% of 390,000 sequence reads from bat guano in California and Texas, respectively, were related to eukaryotic viruses, and the largest proportion of those infect insects, reflecting the diet of these insectivorous bats, including members of the viral families Dicistroviridae, Iflaviridae, Tetraviridae, and Nodaviridae and the subfamily Densovirinae. The second largest proportion of virus-related sequences infects plants and fungi, likely reflecting the diet of ingested insects, including members of the viral families Luteoviridae, Secoviridae, Tymoviridae, and Partitiviridae and the genus Sobemovirus. Bat guano viruses related to those infecting mammals comprised the third largest group, including members of the viral families Parvoviridae, Circoviridae, Picornaviridae, Adenoviridae, Poxviridae, Astroviridae, and Coronaviridae. No close relative of known human viral pathogens was identified in these bat populations. Phylogenetic analysis was used to clarify the relationship to known viral taxa of novel sequences detected in bat guano samples, showing that some guano viral sequences fall outside existing taxonomic groups. This initial characterization of the bat guano virome, the first metagenomic analysis of viruses in wild mammals using second-generation sequencing, therefore showed the presence of previously unidentified viral species, genera, and possibly families. Viral metagenomics is a useful tool for genetically characterizing viruses present in animals with the known capability of direct or indirect viral zoonosis to humans.

FIG. 1.

Sequence classification for California and Texas bat guano-derived sequences based on BLASTx (E value < 0.001). (A) Percentages of sequences with similarity to those of eukaryotes, bacteria, phages, and eukaryotic virus in GenBank and to unclassifiable sequences. (B) Percentages of most abundant eukaryotic viral matches classified by viral families. Plant viruses are highlighted in green, insect viruses are highlighted in red, and mammalian viruses are not highlighted. (C) Eukaryotic viral families in California roost GF-3 to -7 and in one Texas roost at two collection time points (TM1-4 and TM5-8).

FIG. 2.

Phylogenetic analysis of bat guano-associated nodavirus GF-4 based on its 950-aa RNA-dependent RNA polymerase (RdRp) region. RNA1 of nodaviruses encodes the RdRp protein of ∼1,000 aa.

FIG. 3.

(A) Genome organization of bat cyclovirus GF-4; (B) genome organization of bat circovirus-like virus TM6; (C) phylogenetic analysis of bat cyclovirus GF-4 and circovirus-like virus TM6 based on the complete amino acid sequence of the Rep protein (∼280 aa).

FIG. 4.

Phylogenetic analysis of bat kobuvirus based on its 660-aa partial P1 region. The P1 region of kobuviruses encodes structural proteins of ∼870 aa.

FIG. 5.

Phylogenetic analysis of bat astrovirus based on its 225-aa partial ORF1a region. ORF1a of astroviruses encodes nonstructural protein proteases of ∼900 aa.

FIG. 6.

Phylogenetic analysis of bat parvovirus based on its 210-aa partial nonstructural (NS) ORF. The NS ORF of parvoviruses encodes replication-associated protein REP of ∼700 aa.

FIG. 7.

Phylogenetic analysis of bat AAV based on its 160-aa partial capsid protein VP1 region. The VP1 protein of AAVs is ∼700 aa.

FIG. 8.

Phylogenetic analysis of bat CoV based on its 110-aa partial replicase region. Nonstructural proteins 8 and 9 of CoV are ∼300 aa.