Background: Although the finding of SARS coronavirus (SARS-CoV) in caged palm civets suggested that wild animals are the origin of SARS-CoV, subsequent studies suggested that civet may have served only as an amplification host. In 2005, we identified a coronavirus closely related to SARS-CoV (bat-SARS-CoV) in Chinese horseshoe bats. However, it remains to be determined if bat-SARS-CoV or other coronaviruses in bats are the direct progenitor of SARS-CoV.
Methods: To understand the diversity and evolution of coronaviruses in bats, a 2-year surveillance study for coronaviruses was conducted in bats from various rural areas in Hong Kong. As coronaviruses are known to have high recombination frequency, the genomes of the identified novel coronaviruses were also sequenced and analyzed to determine possible recombination events responsible for interspecies transmission.
Results: Among 1389 bats of 16 species from 24 different locations, coronaviruses were identified from anal swabs of 132 (9.5%) bats by RT-PCR. Phylogenetic analysis revealed at least seven novel coronaviruses from seven different bat species, in addition to bat-SARS-CoV. Five of them belonged to group 1 coronaviruses while two belonged to group 2 coronaviruses. Besides bat-SARS-CoV, Chinese horseshoe bats were found to harbor another novel group 1 coronavirus. The genome of this virus represents the smallest coronavirus genome and possessed a unique spike protein evolutionarily distinct from the rest of the genome and containing a 15-amino acid peptide homologous to a corresponding peptide within the RBM of spike protein of SARS-CoV, suggesting a common evolutionary origin in the spike protein of this group 1 bat coronavirus, bat-SARS-CoV, and SARS-CoV.
Conclusion: Bats are important reservoir for a huge diversity of coronaviruses, including SARS-CoV-like viruses. The finding of another group 1 coronavirus in Chinese horseshoe bats with a homologous peptide to SARS-CoV warrants further investigations on the origin of the SARS-CoV spike protein.