In this territory-wide molecular epidemiology study of coronaviruses (Co. Vs) in Hong Kong involving 1,541 dead wild birds, three novel Co. Vs were identified in three different bird families (bulbul CoV HKU11 [Bu. CoV HKU11], thrush CoV HKU12 [Th. CoV HKU12], and munia CoV HKU13 [Mu. CoV HKU13]). Four complete genomes of the three novel Co. Vs were sequenced. Their genomes (26,396 to 26,552 bases) represent the smallest known CoV genomes. In phylogenetic trees constructed using chymotrypsin-like protease (3CLpro), RNA-dependent RNA polymerase (Pol), helicase, spike, and nucleocapsid proteins, Bu. CoV HKU11, Th. CoV HKU12, and Mu. CoV HKU13 formed a cluster distantly related to infectious bronchitis virus and turkey CoV (group 3a Co. Vs). For helicase, spike, and nucleocapsid, they were also clustered with a CoV recently discovered in Asian leopard cats, for which the complete genome sequence was not available. The 3CLpro, Pol, helicase, and nucleocapsid of the three Co. Vs possessed higher amino acid identities to those of group 3a Co. Vs than to those of group 1 and group 2 Co. Vs. Unique genomic features distinguishing them from other group 3 Co. Vs include a distinct transcription regulatory sequence and coding potential for small open reading frames. Based on these results, we propose a novel CoV subgroup, group 3c, to describe this distinct subgroup of Co. Vs under the group 3 Co. Vs. Avian Co. Vs are genetically more diverse than previously thought and may be closely related to some newly identified mammalian Co. Vs. Further studies would be important to delineate whether the Asian leopard cat CoV was a result of interspecies jumping from birds, a situation analogous to that of bat and civet severe acute respiratory syndrome Co. Vs. Copyright © 2009, American Society for Microbiology.
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