Characterization of a Novel Betacoronavirus Related to Middle East Respiratory Syndrome Coronavirus in European Hedgehogs

ABSTRACT Bats are known to host viruses closely related to important human coronaviruses (HCoVs), such as HCoV-229E, severe-acute respiratory syndrome coronavirus (SARS-CoV), and Middle East respiratory syndrome CoV (MERS-CoV). As RNA viruses may coevolve with their hosts, we sought to investigate the closest sister taxon to bats, the Eulipotyphla, and screened European hedgehogs (Erinaceus europaeus) from Germany for CoV by nested reverse transcriptase PCR. A novel betacoronavirus species in a phylogenetic sister relationship to MERS-CoV and clade c bat CoVs was detected and characterized on the whole-genome level. A total of 58.9% of hedgehog fecal specimens were positive for the novel CoV (EriCoV) at 7.9 log10 mean RNA copies per ml. EriCoV RNA concentrations were higher in the intestine than in other solid organs, blood, or urine. Detailed analyses of the full hedgehog intestine showed the highest EriCoV concentrations in lower gastrointestinal tract specimens, compatible with viral replication in the lower intestine and fecal-oral transmission. Thirteen of 27 (48.2%) hedgehog sera contained non-neutralizing antibodies against MERS-CoV. The animal origins of this betacoronavirus clade that includes MERS-CoV may thus include both bat and nonbat hosts.

[1]  V. Corman,et al.  Close Relative of Human Middle East Respiratory Syndrome Coronavirus in Bat, South Africa , 2013, Emerging infectious diseases.

[2]  Victor M Corman,et al.  Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study , 2013, The Lancet Infectious Diseases.

[3]  Linqi Zhang,et al.  Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4 , 2013, Cell Research.

[4]  Yi Shi,et al.  Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 , 2013, Nature.

[5]  P. Woo,et al.  Genetic Characterization of Betacoronavirus Lineage C Viruses in Bats Reveals Marked Sequence Divergence in the Spike Protein of Pipistrellus Bat Coronavirus HKU5 in Japanese Pipistrelle: Implications for the Origin of the Novel Middle East Respiratory Syndrome Coronavirus , 2013, Journal of Virology.

[6]  Christian Drosten,et al.  Commentary: Middle East Respiratory Syndrome Coronavirus (MERS-CoV): Announcement of the Coronavirus Study Group , 2013, Journal of Virology.

[7]  J. Epstein,et al.  Coronaviruses in bats from Mexico , 2013, The Journal of general virology.

[8]  Herman Tse,et al.  Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests , 2013, Journal of Infection.

[9]  Christian Drosten,et al.  Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC , 2013, Nature.

[10]  Tom J. Petty,et al.  Picornavirus and enterovirus diversity with associated human diseases. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[11]  Chantal Reusken,et al.  Human Betacoronavirus 2c EMC/2012–related Viruses in Bats, Ghana and Europe , 2013, Emerging infectious diseases.

[12]  U. Buchholz,et al.  Contact investigation of a case of human novel coronavirus infection treated in a German hospital, October-November 2012. , 2013, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[13]  M. Charleston,et al.  A SIMPLE MODEL EXPLAINS THE DYNAMICS OF PREFERENTIAL HOST SWITCHING AMONG MAMMAL RNA VIRUSES , 2013, Evolution; international journal of organic evolution.

[14]  R. Geffers,et al.  Efficient Replication of the Novel Human Betacoronavirus EMC on Primary Human Epithelium Highlights Its Zoonotic Potential , 2013, mBio.

[15]  A. Debnath,et al.  A predicted receptor-binding and critical neutralizing domain in S protein of the novel human coronavirus HCoV-EMC , 2012, Journal of Infection.

[16]  M. Buchmeier,et al.  Human Coronavirus EMC Does Not Require the SARS-Coronavirus Receptor and Maintains Broad Replicative Capability in Mammalian Cell Lines , 2012, mBio.

[17]  T. Wolff,et al.  Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections. , 2012, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[18]  Alexander E. Gorbalenya,et al.  Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans , 2012, mBio.

[19]  A. Osterhaus,et al.  Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. , 2012, The New England journal of medicine.

[20]  T. Bestebroer,et al.  Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction. , 2012, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[21]  M. J. Adams,et al.  Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2012) , 2012, Archives of Virology.

[22]  P. Simmonds.  SSE: a nucleotide and amino acid sequence analysis platform , 2012, BMC Research Notes.

[23]  M. Knörnschild,et al.  Bats host major mammalian paramyxoviruses , 2012, Nature Communications.

[24]  T. J. Robinson,et al.  Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification , 2011, Science.

[25]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[26]  J. Drexler,et al.  Aichi Virus Shedding in High Concentrations in Patients with Acute Diarrhea , 2011, Emerging infectious diseases.

[27]  M. Müller,et al.  Amplification of Emerging Viruses in a Bat Colony , 2011, Emerging infectious diseases.

[28]  C. Reusken,et al.  Circulation of group 2 coronaviruses in a bat species common to urban areas in Western Europe. , 2010, Vector borne and zoonotic diseases.

[29]  G. Herrler,et al.  Genomic Characterization of Severe Acute Respiratory Syndrome-Related Coronavirus in European Bats and Classification of Coronaviruses Based on Partial RNA-Dependent RNA Polymerase Gene Sequences , 2010, Journal of Virology.

[30]  Yasuhiro Yoshikawa,et al.  Bat Coronaviruses and Experimental Infection of Bats, the Philippines , 2010, Emerging infectious diseases.

[31]  R. Olsthoorn,et al.  Group-specific structural features of the 5′-proximal sequences of coronavirus genomic RNAs , 2010, Virology.

[32]  N. J. Knowles,et al.  Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2015) , 2009, Archives of Virology.

[33]  P. Woo,et al.  Coronavirus Diversity, Phylogeny and Interspecies Jumping , 2009, Experimental biology and medicine.

[34]  S. Perlman,et al.  Coronaviruses post-SARS: update on replication and pathogenesis , 2009, Nature Reviews Microbiology.

[35]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[36]  Kate E. Jones,et al.  The delayed rise of present-day mammals , 1990, Nature.

[37]  L. Poon,et al.  Generic Detection of Coronaviruses and Differentiation at the Prototype Strain Level by Reverse Transcription-PCR and Nonfluorescent Low-Density Microarray , 2007, Journal of Clinical Microbiology.

[38]  Yang Liu,et al.  Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases , 2007, Emerging infectious diseases.

[39]  P. Woo,et al.  Comparative Analysis of Twelve Genomes of Three Novel Group 2c and Group 2d Coronaviruses Reveals Unique Group and Subgroup Features , 2006, Journal of Virology.

[40]  Y. Guan,et al.  Prevalence and Genetic Diversity of Coronaviruses in Bats from China , 2006, Journal of Virology.

[41]  P. Masters,et al.  The Molecular Biology of Coronaviruses , 2006, Advances in Virus Research.

[42]  E. Snijder,et al.  Nidovirus transcription: how to make sense...? , 2006, The Journal of general virology.

[43]  S. Weiss,et al.  Coronavirus Pathogenesis and the Emerging Pathogen Severe Acute Respiratory Syndrome Coronavirus , 2005, Microbiology and Molecular Biology Reviews.

[44]  Samson S. Y. Wong,et al.  Characterization and Complete Genome Sequence of a Novel Coronavirus, Coronavirus HKU1, from Patients with Pneumonia , 2005, Journal of Virology.

[45]  L. Saif.  Animal coronaviruses: what can they teach us about the severe acute respiratory syndrome? , 2004, Revue scientifique et technique.

[46]  Theo M Bestebroer,et al.  A previously undescribed coronavirus associated with respiratory disease in humans. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[47]  B. Berkhout,et al.  Identification of a new human coronavirus , 2004, Nature Medicine.

[48]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[49]  Christian Drosten,et al.  Identification of a novel coronavirus in patients with severe acute respiratory syndrome. , 2003, The New England journal of medicine.

[50]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[51]  R. Chanock,et al.  Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[52]  D. Hamre,et al.  A New Virus Isolated from the Human Respiratory Tract.∗ , 1966, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[53]  R. Baric,et al.  Coronavirus Genome Structure and Replication , 2005, Current topics in microbiology and immunology.