OmniVira

Alphacoronaviruses in New World bats: prevalence, persistence, phylogeny, and potential for interaction with humans.

Christina Osborne1 Paul M Cryan Thomas J O'Shea Lauren M Oko Christina Ndaluka Charles H Calisher Andrew D Berglund Mead L Klavetter Richard A Bowen Kathryn V Holmes Samuel R Dominguez
Affiliations 1 institutions
  1. Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.
PMID21589915 DOI10.1371/journal.pone.0019156 Year2011 Journal PloS one PLoS One Languageeng Statusepublish

Abstract

Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.

Supporting text Virus Host Location
Animals 1948 Chiroptera 371 Coronaviridae 13 Humans 1440 Phylogeny 805 Reverse Transcriptase Polymerase Chain Reaction 35

Evidence records

9 total
Zoonotic Surveillance
7 records · 2 evidence types
Evidence type Viral Detection
5 records
OVE973 Viral Detection
Key finding

Alphacoronavirus RNA was detected in big brown bats (Eptesicus fuscus) sampled in Colorado with a reported prevalence of 10%.

Virus
Alphacoronavirus
Host
big brown bat Eptesicus fuscus Natural host
Location
United States
Supporting text

We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence.

Method
RT-PCR | RNA detection
Sample type
feces | anal swabs
Geographic raw
Colorado
Country inferred
USA
OVE974 Viral Detection
Key finding

Alphacoronavirus RNA was detected in long-legged bats (Myotis volans) sampled in Colorado with a reported prevalence of 8%.

Virus
Alphacoronavirus
Host
Myotis volans Natural host
Location
United States
Supporting text

We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence.

Method
RT-PCR | RNA detection
Sample type
feces | anal swabs
Geographic raw
Colorado
Country inferred
USA
OVE975 Viral Detection
Key finding

Alphacoronavirus RNA was detected in little brown bats (Myotis lucifugus) sampled in Colorado with a reported prevalence of 3%.

Virus
Alphacoronavirus
Host
little brown bat Myotis lucifugus Natural host
Location
United States
Supporting text

We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence.

Method
RT-PCR | RNA detection
Sample type
feces | anal swabs
Geographic raw
Colorado
Country inferred
USA
OVE976 Viral Detection
Key finding

Alphacoronavirus RNA was detected in western long-eared bats (Myotis evotis) sampled in Colorado with a reported prevalence of 2%.

Virus
Alphacoronavirus
Host
long-eared Myotis Myotis evotis Natural host
Location
United States
Supporting text

We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence.

Method
RT-PCR | RNA detection
Sample type
feces | anal swabs
Geographic raw
Colorado
Country inferred
USA
OVE982 Viral Detection
Key finding

High prevalence of alphacoronavirus RNA in big brown bats roosting near humans suggests potential animal-to-human spillover opportunities.

Virus
Alphacoronavirus
Host
big brown bat Eptesicus fuscus Natural host human Homo sapiens Natural host
Location
Not specified
Supporting text

Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses.

Method
RT-PCR detection of viral RNA
Evidence type Reservoir Ecology
2 records
OVE977 Reservoir Ecology
Key finding

Repeated detection of alphacoronavirus RNA across sequential summers in big brown and long-legged bats indicates maintenance of the virus within bat populations at rural sites.

Virus
Clitocybe odora virus Alphacoronavirus
Host
big brown bat Eptesicus fuscus Natural host Myotis volans Natural host
Location
rural sampling sites
Supporting text

At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study.

Method
field sampling | RNA detection
Sample type
feces | anal swabs
Geographic raw
rural sampling sites
OVE978 Reservoir Ecology
Key finding

Consistent presence of CoV RNA in big brown bats across all sampled urban maternity roosts suggests local ecological maintenance of the virus in urban bat populations.

Virus
Clitocybe odora virus Alphacoronavirus
Host
big brown bat Eptesicus fuscus Natural host
Location
urban maternity roosts
Supporting text

CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested.

Method
field sampling | RNA detection
Sample type
feces | anal swabs
Geographic raw
urban maternity roosts
Genomic Evolution
2 records · 1 evidence types
Evidence type Phylogenetic Evolution
2 records
OVE979 Phylogenetic Evolution
Key finding

RdRp gene sequences from Colorado bat alphacoronaviruses formed three clusters distinct from Old World bat coronaviruses, indicating divergent evolutionary lineages in New World bats.

Virus
Alphacoronavirus Clitocybe odora virus
Host
bats Chiroptera Natural host
Location
Not specified
Supporting text

Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats.

Genes or proteins
RdRp gene
Analysis methods
phylogenetic clustering | sequence comparison
OVE981 Phylogenetic Evolution
Key finding

Similar nucleotide sequences of a CoV were detected in big brown bats and long-legged bats, supporting infection across different bat genera.

Virus
Clitocybe odora virus Alphacoronavirus
Host
big brown bat Eptesicus fuscus Natural host Myotis volans Natural host
Location
Not specified
Supporting text

Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera.

Analysis methods
RT-PCR | amplicon sequencing | phylogenetic comparison