Metagenomic Analysis of the Viromes of Three North American Bat Species: Viral Diversity among Different Bat Species That Share a Common Habitat

Abstract

Effective prediction of future viral zoonoses requires an in-depth understanding of the heterologous viral population in key animal species that will likely serve as reservoir hosts or intermediates during the next viral epidemic. The importance of bats as natural hosts for several important viral zoonoses, including Ebola, Marburg, Nipah, Hendra, and rabies viruses and severe acute respiratory syndrome-coronavirus (SARS-CoV), has been established; however, the large viral population diversity (virome) of bats has been partially determined for only a few of the ϳ1,200 bat species. To assess the virome of North American bats, we collected fecal, oral, urine, and tissue samples from individual bats captured at an abandoned railroad tunnel in Maryland that is cohabitated by 7 to 10 different bat species. Here, we present preliminary characterization of the virome of three common North American bat species, including big brown bats (Eptesicus fuscus), tricolored bats (Perimyotis subflavus), and little brown myotis (Myotis lucifugus). In samples derived from these bats, we identified viral sequences that were similar to at least three novel group 1 CoVs, large numbers of insect and plant virus sequences, and nearly full-length genomic sequences of two novel bacteriophages. These observations suggest that bats encounter and disseminate a large assortment of viruses capable of infecting many different animals, insects, and plants in nature.

The Fecal Viral Flora of California Sea Lions

“…For example, feces from insectivorous bats contain a significant fraction of insect viruses and plant viruses (19,35), and porcine circovirus and plant viruses can be detected in human feces (34,67). Densoviruses, known to infect insects and crustaceans, were found exclusively in 6/14 sea lions in rehabilitation, which may be attributable to differences in the diet of captive versus wild sea lions, with the former being fed frozen herring (at times contaminated with nematode larvae and insects) rather than a variety of prey.…”

Gut Virome Sequencing in Children With Early Islet Autoimmunity

“…The contaminating ribosomal fraction was reduced by partial digestion of unprotected nucleic acids by a nuclease cocktail. A sequence-independent single-primer amplification of all nucleic acids followed, as adapted from previous studies (3,4). Each sample was processed in duplicate (i.e., with two different tag sequences).…”

Highly diversified coronaviruses in neotropical bats

“…There are only two studies on bat CoVs from the Neotropics, one from Trinidad and Tobago yielding two highly diversified alphacoronaviruses (Carrington et al, 2008) and a recently published second one from Mexico yielding alpha and betacoronaviruses summarized in 13 different clades (Anthony et al, 2013). From the neighbouring temperate northern American areas, additional bat alphacoronavirus clades have been described (Dominguez et al, 2007;Donaldson et al, 2010;Huynh et al, 2012;Misra et al, 2009;Osborne et al, 2011).…”