The Chinese rufous horseshoe bat () has been suggested to carry the direct ancestor of severe acute respiratory syndrome (SARS) coronavirus (SCoV), and the diversity of SARS-like CoVs (SLCoV) within this species is therefore worth investigating. Here, we demonstrate the remarkable diversity of SLCoVs in and identify a strain with the same pattern of phylogenetic incongruence (i.e. an indication of recombination) as reported previously in another SLCoV strain. Moreover, this strain possesses a distinctive 579 nt deletion in the region that was also found in a human SCoV from the late-phase epidemic. Phylogenetic analysis of the region suggested that the human SCoVs are phylogenetically closer to SLCoVs in than to SLCoVs in other species. These findings reveal a closer evolutionary linkage between SCoV in humans and SLCoVs in , defining the scope of surveillance to search for the direct ancestor of human SCoVs.


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