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Open AccessArticle

Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China

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Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
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State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China
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Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong 999077, China
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Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China
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Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
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Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this manuscript.
Viruses 2019, 11(11), 980; https://doi.org/10.3390/v11110980
Received: 28 August 2019 / Revised: 11 October 2019 / Accepted: 22 October 2019 / Published: 24 October 2019
(This article belongs to the Section Animal Viruses)
While dromedaries are the immediate animal source of Middle East Respiratory Syndrome (MERS) epidemic, viruses related to MERS coronavirus (MERS-CoV) have also been found in bats as well as hedgehogs. To elucidate the evolution of MERS-CoV-related viruses and their interspecies transmission pathway, samples were collected from different mammals in China. A novel coronavirus related to MERS-CoV, Erinaceus amurensis hedgehog coronavirus HKU31 (Ea-HedCoV HKU31), was identified from two Amur hedgehogs. Genome analysis supported that Ea-HedCoV HKU31 represents a novel species under Merbecovirus, being most closely related to Erinaceus CoV from European hedgehogs in Germany, with 79.6% genome sequence identity. Compared to other members of Merbecovirus, Ea-HedCoV HKU31 possessed unique non-structural proteins and putative cleavage sites at ORF1ab. Phylogenetic analysis showed that Ea-HedCoV HKU31 and BetaCoV Erinaceus/VMC/DEU/2012 were closely related to NeoCoV and BatCoV PREDICT from African bats in the spike region, suggesting that the latter bat viruses have arisen from recombination between CoVs from hedgehogs and bats. The predicted HKU31 receptor-binding domain (RBD) possessed only one out of 12 critical amino acid residues for binding to human dipeptidyl peptidase 4 (hDPP4), the MERS-CoV receptor. The structural modeling of the HKU31-RBD-hDPP4 binding interphase compared to that of MERS-CoV and Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) suggested that HKU31-RBD is unlikely to bind to hDPP4. Our findings support that hedgehogs are an important reservoir of Merbecovirus, with evidence of recombination with viruses from bats. Further investigations in bats, hedgehogs and related animals are warranted to understand the evolution of MERS-CoV-related viruses. View Full-Text
Keywords: hedgehog; Merbecovirus; coronavirus; novel species; China hedgehog; Merbecovirus; coronavirus; novel species; China
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Lau, S.K.P.; Luk, H.K.H.; Wong, A.C.P.; Fan, R.Y.Y.; Lam, C.S.F.; Li, K.S.M.; Ahmed, S.S.; Chow, F.W.; Cai, J.-P.; Zhu, X.; Chan, J.F.W.; Lau, T.C.K.; Cao, K.; Li, M.; Woo, P.C.Y.; Yuen, K.-Y. Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China. Viruses 2019, 11, 980.

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