OmniVira

Highly diversified coronaviruses in neotropical bats.

Victor Max Corman1 Andrea Rasche2,1 Thierno Diawo Diallo1 Veronika M Cottontail3 Andreas Stöcker4 Breno Frederico de Carvalho Dominguez Souza4 Jefferson Ivan Corrêa4 Aroldo José Borges Carneiro5 Carlos Roberto Franke5 Martina Nagy6 Markus Metz7 Mirjam Knörnschild3 Elisabeth K V Kalko8,3 Simon J Ghanem9 Karen D Sibaja Morales10 Egoitz Salsamendi11,3 Manuel Spínola10 Georg Herrler2 Christian C Voigt9 Marco Tschapka8,3 Christian Drosten1 Jan Felix Drexler1
Affiliations 11 institutions
  1. Institute of Virology, University of Bonn Medical Centre, Bonn, Germany.
  2. University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.
  3. Institute of Experimental Ecology, University of Ulm, Ulm, Germany.
  4. Infectious Diseases Research Laboratory, University Hospital Professor Edgard Santos, Federal University of Bahia, Salvador, Brazil.
  5. School of Veterinary Medicine, Federal University of Bahia, Salvador, Brazil.
  6. Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany.
  7. Fondazione Edmund Mach, Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, S. Michele all'Adige, Italy.
  8. Smithsonian Tropical Research Institute, Balboa, Panama.
  9. Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
  10. Instituto Internacional en Conservación y Manejo de Vida Silvestre, Universidad Nacional, Heredia, Costa Rica.
  11. Department of Zoology and Animal Cell Biology, University of the Basque Country, Bilbao, The Basque Country.
PMID23761408 DOI10.1099/vir.0.054841-0 Year2013 Journal The Journal of general virology J Gen Virol Languageeng Statusppublish

Abstract

Bats host a broad diversity of coronaviruses (CoVs), including close relatives of human pathogens. There is only limited data on neotropical bat CoVs. We analysed faecal, blood and intestine specimens from 1562 bats sampled in Costa Rica, Panama, Ecuador and Brazil for CoVs by broad-range PCR. CoV RNA was detected in 50 bats representing nine different species, both frugivorous and insectivorous. These bat CoVs were unrelated to known human or animal pathogens, indicating an absence of recent zoonotic spill-over events. Based on RNA-dependent RNA polymerase (RdRp)-based grouping units (RGUs) as a surrogate for CoV species identification, the 50 viruses represented five different alphacoronavirus RGUs and two betacoronavirus RGUs. Closely related alphacoronaviruses were detected in Carollia perspicillata and C. brevicauda across a geographical distance exceeding 5600 km. Our study expands the knowledge on CoV diversity in neotropical bats and emphasizes the association of distinct CoVs and bat host genera.

Supporting text Virus Host Location
Genetic Variation 127 Americas 3 Animals 1948 Blood 1 Chiroptera 371 Cluster Analysis 31 Coronavirus 92 Feces 113 Intestines 7 Molecular Sequence Data 160 Phylogeography 30 RNA, Viral 193 RNA-Dependent RNA Polymerase 49 Sequence Analysis, DNA 113

Evidence records

4 total
Zoonotic Surveillance
3 records · 2 evidence types
Evidence type Viral Detection
2 records
OVE1461 Viral Detection
Key finding

Coronavirus RNA was detected by broad-range PCR in 50 bats sampled in Costa Rica, Panama, Ecuador and Brazil.

Virus
Clitocybe odora virus Coronaviridae
Host
bats Chiroptera Natural host
Location
Costa Rica Panama Ecuador Brazil
Supporting text

We analysed faecal, blood and intestine specimens from 1562 bats sampled in Costa Rica, Panama, Ecuador and Brazil for CoVs by broad-range PCR. CoV RNA was detected in 50 bats representing nine different species, both frugivorous and insectivorous.

Method
broad-range PCR
Sample type
faecal specimens | blood specimens | intestine specimens
Geographic raw
Costa Rica | Panama | Ecuador | Brazil
Country inferred
CRI | PAN | ECU | BRA
OVE1463 Viral Detection
Key finding

Closely related alphacoronaviruses were found in two different bat species, Carollia perspicillata and C. brevicauda, suggesting cross-species viral transmission among neotropical bats.

Virus
Alphacoronavirus
Host
Seba's short-tailed bat Carollia perspicillata Natural host Carollia brevicauda Natural host
Location
Costa Rica Panama Ecuador Brazil
Supporting text

Closely related alphacoronaviruses were detected in Carollia perspicillata and C. brevicauda across a geographical distance exceeding 5600 km.

Method
broad-range PCR | RNA-dependent RNA polymerase (RdRp) sequence comparison
Geographic raw
neotropical region (Costa Rica, Panama, Ecuador, and Brazil)
Evidence type Reservoir Ecology
1 records
OVE1464 Reservoir Ecology
Key finding

Distinct coronaviruses were associated with particular bat host genera in neotropical regions, indicating host genus-specific ecological maintenance.

Virus
Coronaviridae Clitocybe odora virus
Host
bats Chiroptera Natural host
Location
neotropical regions
Supporting text

Our study expands the knowledge on CoV diversity in neotropical bats and emphasizes the association of distinct CoVs and bat host genera.

Method
broad-range PCR | RdRp-based grouping units analysis
Sample type
faecal specimens | blood specimens | intestine specimens
Geographic raw
neotropical regions
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE1462 Phylogenetic Evolution
Key finding

Phylogenetic analysis of bat coronavirus RdRp sequences showed five distinct alphacoronavirus and two betacoronavirus lineages that were genetically distinct from known human or animal coronaviruses.

Virus
Alphacoronavirus Betacoronavirus
Host
bats Chiroptera Natural host
Location
Not specified
Supporting text

Based on RNA-dependent RNA polymerase (RdRp)-based grouping units (RGUs) as a surrogate for CoV species identification, the 50 viruses represented five different alphacoronavirus RGUs and two betacoronavirus RGUs.

Genes or proteins
RNA-dependent RNA polymerase (RdRp)
Analysis methods
RdRp-based grouping units | phylogenetic classification