A likely animal reservoir for SARS-CoV was identified in rhinolophid bats (4,5).
Detection of genetically related betacoronaviruses in bats from Africa and Eurasia parallels detection of SARS-CoV in rhinolophid bats from Eurasia and related betacoronaviruses in hipposiderid bats from Africa (9).
Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during 20022003.
Rhinolophid bats and their viruses were analyzed at a different taxonomic scale (within genus).
Lack of concordance between phylogenies of rhinolophid bats and their CoVs can be interpreted as evidence for host shifts between bats of the genus Rhinolophus.
First, SARS-like CoVs and other rhinolophid CoVs (RfV1 and RpV1) show evidence of interspecies transmission.
Although we acknowledge that this interpretation may be limited by sample size, it may also indicate that rhinolophid bats, the hosts of a cluster of SARS-like CoVs within which human and civet SARS CoV nestle phylogenetically (6, 7), are more likely to foster the host shifts of CoVs than are other bat species.
We compared the genetic diversity of CoVs isolated from rhinolophids and vespertilionids and the corresponding diversity among bat taxa by using the index of nucleotide diversity 0t) described by Nei (28) in Arlequin version 3.
Verspertilionids and their CoVs showed phylogenetic congruence, and rhinolophids and their CoVs showed incongruous phylogenies (Figure 4).
Genetic diversity of CoVs harbored by rhinolophids and vespertilionids was similar (vespertilionids [pi] = 0.