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Journal of Virology, January 2009, p. 908-917, Vol. 83, No. 2
0022-538X/09/$08.00+0     doi:10.1128/JVI.01977-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Comparative Analysis of Complete Genome Sequences of Three Avian Coronaviruses Reveals a Novel Group 3c Coronavirus

Patrick C. Y. Woo,^1,2,3,4, Susanna K. P. Lau,^1,2,3,4, Carol S. F. Lam,⁴ Kenneth K. Y. Lai,⁴ Yi Huang,⁴ Paul Lee,⁴ Geraldine S. M. Luk,⁵ Kitman C. Dyrting,⁵ Kwok-Hung Chan,⁴ and Kwok-Yung Yuen^1,2,3,4*

State Key Laboratory of Emerging Infectious Diseases,¹ Research Centre of Infection and Immunology,² Carol Yu Centre for Infection,³ Department of Microbiology, The University of Hong Kong,⁴ Agriculture, Fisheries, and Conservation Department, Hong Kong⁵

Received 18 September 2008/ Accepted 20 October 2008

In this territory-wide molecular epidemiology study of coronaviruses (CoVs) in Hong Kong involving 1,541 dead wild birds, three novel CoVs were identified in three different bird families (bulbul CoV HKU11 [BuCoV HKU11], thrush CoV HKU12 [ThCoV HKU12], and munia CoV HKU13 [MuCoV HKU13]). Four complete genomes of the three novel CoVs were sequenced. Their genomes (26,396 to 26,552 bases) represent the smallest known CoV genomes. In phylogenetic trees constructed using chymotrypsin-like protease (3CL^pro), RNA-dependent RNA polymerase (Pol), helicase, spike, and nucleocapsid proteins, BuCoV HKU11, ThCoV HKU12, and MuCoV HKU13 formed a cluster distantly related to infectious bronchitis virus and turkey CoV (group 3a CoVs). 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 3CL^pro, Pol, helicase, and nucleocapsid of the three CoVs possessed higher amino acid identities to those of group 3a CoVs than to those of group 1 and group 2 CoVs. Unique genomic features distinguishing them from other group 3 CoVs 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 CoVs under the group 3 CoVs. Avian CoVs are genetically more diverse than previously thought and may be closely related to some newly identified mammalian CoVs. 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 CoVs.

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* Corresponding author. Mailing address: State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong. Phone: (852) 28554892. Fax: (852) 28551241. E-mail: hkumicro{at}hkucc.hku.hk

Published ahead of print on 29 October 2008.

P. C. Y. Woo and S. K. P. Lau contributed equally to the manuscript.

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Journal of Virology, January 2009, p. 908-917, Vol. 83, No. 2
0022-538X/09/$08.00+0     doi:10.1128/JVI.01977-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

This article has been cited by other articles:

• Woo, P. C. Y., Lau, S. K. P., Huang, Y., Yuen, K.-Y. (2009). Coronavirus Diversity, Phylogeny and Interspecies Jumping. Exp. Biol. Med. 234: 1117-1127 [Abstract] [Full Text]