Human Betacoronavirus Lineage C and Identification of N-Terminal Dipeptidyl Peptidase As Its Virus Receptor

Abstract

The invention provides an isolated essentially mammalian positive-sense single stranded RNA virus classifiable as belonging to the Order: Nidovirales; Family: Coronaviridae; Subfamily: Coronavirinae; Genus: Betacoronavirus; and non-Lineage A, non-Lineage B or non-Lineage D, human betacoronavirus. The invention also provides a human virus having a receptor binding domain (RBD) capable of binding to a dipeptidyl peptidase 4. The invention also provides diagnostic means and methods, prophylactic means and methods and therapeutic means and methods to be employed in the diagnosis, prevention and/or treatment of disease, in particular of respiratory disease, in particular of mammals, more in particular in humans.

37 . A method for the treatment or prevention of a MERS-CoV infection, comprising providing a mammal with a therapeutically effective amount of:
 a) a sequence that is at least 95% identical with the sequence of any one of SEQ ID NOs: 4-13 or an immunogenic fragment thereof,   b) a sequence that is at least 95% identical with a nucleic acid sequence encoding an amino acid sequence selected from the sequences of SEQ ID NOs: 5-13 or an immunogenic fragment thereof,   c) a mammalian positive-sense single stranded RNA virus which is a human  betacoronavirus  comprising a sequence that is at least 95% identical with the sequence of any one of SEQ ID NOs: 4-13 or comprising a nucleic acid encoding an amino acid sequence selected from the sequences of SEQ ID NOs: 5-13.   
     
     
         38 . The method of  claim 37 , wherein said mammalian positive-sense single stranded RNA virus comprises a nucleic acid or amino acid sequence selected from:
 a) a sequence that is at least 95% identical with the sequences of SEQ ID NOs: 14, 16, 16, 490 or 654, and   b) a sequence that is at least 95% identical with a nucleic acid sequence encoding an amino acid sequence selected from the sequences of SEQ ID NOs: 16, 490 and 654.   
     
     
         39 . The method of  claim 37 , wherein said mammal is provided with an inactivated whole virus. 
     
     
         40 . The method of  claim 37 , wherein said mammal is provided with a Spike protein having at least 95% sequence identity with a sequence of SEQ ID NO: 12 or an immunogenic fragment thereof and/or a N protein having at least 95% sequence identity with a sequence of SEQ ID NO: 5 or an immunogenic fragment thereof. 
     
     
         41 . The method of  claim 37 , wherein said mammal is a human. 
     
     
         42 . The method of  claim 37  for the treatment or prevention of atypical pneumonia and/or renal failure. 
     
     
         43 . The method of  claim 37 , wherein said mammal is a rabbit. 
     
     
         44 . A method of identifying a candidate modulator as an agent that modulates the function of a dipeptidyl peptidase, said method comprising:
 a) providing a proteinaceous substance comprising an amino acid sequence selected from the sequences of SEQ ID NOs: 5-13 or an immunogenic fragment thereof, and additionally comprising at least a fragment of an N-terminal dipeptidyl peptidase protein in the presence and absence of said candidate modulator under conditions permitting binding of a first fragment derived from a virus with a second fragment derived from a peptidase protein,   b) measuring binding of said first fragment to said second fragment, wherein a decrease or increase in binding in the presence of said candidate modulator, relative to binding in the absence of said candidate modulator, identifies said candidate modulator as an agent that modulates the function of a dipeptidyl peptidase.   
     
     
         45 . The method of  claim 44 , wherein said first and/or said second fragment is detectably labeled, preferably with a moiety selected from the group consisting of a radioisotope, a fluorophore, a quencher of fluorescence, an enzyme, and an affinity tag. 
     
     
         46 . A method of identifying a candidate antiviral agent as an agent that modulates the binding of a virus to dipeptidyl peptidase, said method comprising:
 a) providing a proteinaceous substance comprising an amino acid sequence selected from the sequences of SEQ ID NOs: 5-13 or an immunogenic fragment thereof, and additionally comprising at least a fragment of an N-terminal dipeptidyl peptidase protein in the presence and absence of said candidate antiviral agent under conditions permitting binding of a first fragment derived from a virus with a second fragment derived from a peptidase protein,   b) measuring binding of said first fragment to said second fragment, wherein a decrease or increase in binding in the presence of said antiviral agent, relative to binding in the absence of said candidate modulator, identifies said antiviral agent as an agent that modulates the function of a dipeptidyl peptidase.   
     
     
         47 . The method of  claim 46 , wherein said first and/or said second fragment is detectably labeled, preferably with a moiety selected from the group consisting of a radioisotope, a fluorophore, a quencher of fluorescence, an enzyme, and an affinity tag.