# Patent

## Title
Enzymatic diagnostic test for SARS and other viral diseases

## Abstract

The present invention is directed towards methods, compositions and kits for testing for a virus in a sample. The methods determine the presence of a viral enzyme by contacting the sample with a peptidal compound capable of being cleaved by the viral enzyme to form peptidal compound fragments. Detection of a peptidal compound fragment confirms the presence of the virus.

## Background
RELATED APPLICATIONS
This application claims priority to U.S. Provisional Patent Application No. 60/480,605, filed Jun. 23, 2003, the entire content of which is fully incorporated herein by reference.


TECHNICAL FIELD OF THE INVENTION
The present invention provides a method, reagents and a kit for the detection of a virus in a test sample. The method involves the detection of an enzyme that is encoded by a viral nucleic acid during the replication of the virus. In one embodiment, the invention provides a method for detection of the Severe Acute Respiratory Syndrome (SARS) virus in a sample.
BACKGROUND
There is a continuing need for rapid sensitive methods for the detection of viral diseases. Rapid detection and identification of viral pathogens is essential to limit transfer and spread of viral disease and to monitor treatment methods. The need for such methods can be illustrated be the events surrounding the emergence of SARS.
SARS is a viral respiratory illness caused by the SARS-associated coronavirus (SARS-CoV). SARS was first reported in Asia in February 2003. Over the next few months, the illness spread to more than two dozen countries in North America, South America, Europe, and Asia before the SARS global outbreak of 2003 was contained. The symptoms of SARS included high fever, dry cough, and other flu like symptoms that can progress to pneumonia. Death occurred in approximately 15% of the infected patients. The contagious nature of SARS and its fast spread in several countries in Asia caused considerable concern throughout the world.
The SARS coronavirus belongs to a group of viruses similar to those causing the common cold. The SARS virus spreads by close person-to-person contact and is thought to be transmitted most readily by respiratory droplets produced when an infected person coughs or sneezes. Droplet spread can occur when droplets from an infected person are propelled a short distance (generally up to 3 feet) through the air and deposited on the mucus membranes of nearby persons. The virus also can spread when a person touches a surface contaminated with infectious droplets and then touches his or her mouth, nose, or eyes.
In most cases, symptoms of SARS first occur 2 to 5 days after exposure to the virus. However, the incubation period may be up to 2 weeks. Because of the extended incubation period, patients infected with the SARS virus may be placed in quarantine with those who are not infected. This may cause the uninfected patients and medical staff to become exposed to the SARS virus and to develop the symptoms of SARS.
Because of its ease of spread and long incubation period, it is critical to reliably determine the presence of the virus in a patient thought to be infected with SARS. Ideally, such a test should be sufficiently sensitive to detect the virus at an early stage of infection. The test should also be specific and have a low occurrence of false-positive and false-negative results.
Without a reliable test that can be used in the early stages of SARS infection, physicians and health care teams rely on a process of elimination, ruling out other known causes of the severe pneumonia before diagnosing SARS. However, a positive test result for another respiratory pathogen does not completely rule out infection with the SARS virus. Patients can be co-infected with both the SARS virus and other respiratory pathogens.
At present, two types of tests detect the presence of the SARS virus. The first of these is an enzyme immunoassay (EIA) test which detects serum antibody to SARS. The other test is a polymer chain reaction (PCR) test which detects the viral genetic material.
During the course of infection with the SARS virus, levels of specific anti-viral antibodies rise in the blood. Many of the tests currently available for the diagnosis of SARS are based on the detection of such antibodies. Such tests are typically either Enzyme Linked Immunoassays (ELISAs) or immunofluorescence assays (IFAs). With ELISAs, the antibodies cannot be detected until about 20 days after infection. IFAs can detect antibodies approximately 10 days after the initial infection. However, such assays are comparatively slow and require the growth of the virus in a cell culture.
The utility of antibody tests for detecting viruses, such as SARS, may be further limited due to the rapid mutation rate of some viruses. A Canadian study has detected the SARS virus in only 60% of those with SARS infection. Such results suggest that the virus is unstable and is mutating rapidly. This is not unexpected as coronaviruses are notorious for changing their outer surface antigens rapidly, a process termed antigenic drift.
Techniques such as the Polymer Chain Reaction (PCR) allow direct detection of the virus genetic material and, in theory, can detect infection at a very early stage. Many PCR tests use oligonucleotide microchip technology for detecting the virus with throat swabs, sputum or feces. Such tests typically take a few hours to perform and are relatively costly. In addition, currently available PCR methods give 40% of false positive and negative results, making the method ineffective.
Because of the deficiencies of presently available testing methods, there is a need for an improved test enabling the presence of viruses, such as the SARS virus, to be accurately detected at an early stage of infection. Such a test will benefit those showing symptoms of SARS by allowing for the monitoring of the course of their infection and subsequent recovery. In addition, a quick and effective test will benefit persons suspected of having the disease by allowing uninfected persons to be released from quarantine.
There is also the need for an automated test avoiding the need for manual intervention. Such a test will prevent spread of the disease due to infection during the testing process.
SUMMARY
One embodiment of the present invention provides a method for detecting a virus in a sample. The method involves contacting the sample with a peptidal compound capable of being cleaved at a cleavage point by an enzyme to form a first peptidal compound fragment and a second peptidal compound fragment. The enzyme is encoded by a nucleic acid of the virus during replication of the virus and cleaves a polyprotein encoded by the nucleic acid of the virus. A signaling moiety is linked to a portion of the peptidal compound that forms the first peptidal compound fragment. If the virus is present in the sample, the enzyme produced by the virus cleaves the peptidal compound. The virus is detected by observing the signal from the signaling moiety.
In another embodiment, a quenching moiety is linked to a portion of the peptidal compound present in the second peptidal compound fragment. The signaling moiety and the quenching moiety are linked to the peptidal compound at relative positions such that the quenching moiety quenches the signal of the signaling moiety unless the peptidal compound is cleaved at the cleavage point.
In other embodiments, the virus detected is from either the Nidovirus or the Picornavirus virus families. In one embodiment the virus is the SARS virus. In another embodiment the virus is a rhinovirus.
Another aspect of the invention provides a kit for detecting the presence of a virus in a sample. The kit includes a reagent containing a peptidal compound capable of being cleaved at a cleavage point by an enzyme encoded by the viral nucleic acid to form a first peptidal compound fragment and a second peptidal compound fragment. A signaling moiety is linked to a portion of the peptidal compound that forms the first peptidal compound fragment.
Another aspect of the invention provides a composition for detecting a virus in a sample. The composition includes a peptidal compound capable of being cleaved at a cleavage point by an enzyme encoded by the virus to form a first peptidal compound fragment and a second peptidal compound fragment. A signaling moiety is linked to a portion of the peptidal compound that forms the first peptidal compound fragment and a quenching moiety is linked to a portion of the peptidal compound that forms the second peptidal compound fragment. The signaling moiety and the quenching moiety are linked to the peptidal compound at relative positions such that the quenching moiety quenches a signal of the signaling moiety unless the peptidal compound is cleaved at the cleavage point.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic representation of a homogenous assay for the detection of a virus.
FIG. 2(A) is a Table showing polyprotein cleavage sites for selected species of Picronaviruses. HRV14: Human Rhinovirus 14; HRVb: Human Rhinovirus b; HRV16: Human Rhinovirus 16; Cxa21: Coxsackievirus A21.
FIG. 2(B) is a Table showing polyprotein cleavage sites for selected species of Picronaviruses. HRV14: Human Rhinovirus 14; HRVb: Human Rhinovirus b; HRV16: Human Rhinovirus 16; Cxa21: Coxsackievirus A21.
FIG. 2(C) is a Table showing polyprotein cleavage sites for selected species of Picronaviruses. HRV14: Human Rhinovirus 14; HRVb: Human Rhinovirus b; HRV16: Human Rhinovirus 16; Cxa21: Coxsackievirus A21.
FIG. 2(D) is a Table showing three polyprotein cleavage sites having high hydrolysis rates for selected species of picronaviruses. HRV14: Human Rhinovirus 14; HRVb: I-Human Rhinovirus b; HXV16: Human Rhinovirus 16; Cxa21: Coxsackievirus A21. A consensus peptide is also shown. SEQ ID NOS. of the cleavage sites are as follows:














Cleavage Site
SEQ ID NO









HRV 2C 3A
25



HRVb 2C 3A
27



Cxa2l 2C 3a
28



HRV16 2C 3A
26



HRV14 3A 3B
29



HRVb 3A 3B
31



Cxa2l 3A 3B
32



HRVl6 3A 3B
30



HRV14 3B 3C
33



HRVb 3B 3C
35



Cxa2l 3B 3C
36



HRVl6 3B 3C
34










FIG. 3(A) is a Table showing polyprotein cleavage sites for selected species of Nidoviruses. SARS: Human Severe Acute Respiratory Syndrome Virus; BCov: Bovine Coronavirus; HCov: Human Coronavirus.
FIG. 3(B) is a Table showing polyprotein cleavage sites for selected species of Nidoviruses. SARS: Human Severe Acute Respiratory Syndrome Virus; BCov: Bovine Coronavirus; HCov: Human Coronavirus.
FIG. 3(C) is a Table showing polyprotein cleavage sites for selected species of Nidoviruses. SARS: Human Severe Acute Respiratory Syndrome Virus; BCov: Bovine Coronavirus; HCov: Human Coronavirus.
FIG. 3(D) is a Table showing polyprotein cleavage sites for selected species of nidoviruses. SARS: Human Severe Acute Respiratory Syndrome Virus; BCov: Bovine Coronavirus; HCov: Human Coronavirus. SEQ ID NOS. for the 20 residue sequences shown in alignment is as follows:














Cleavage Site
SEQ ID NO









QTSITSAVLQSGFRKM AFPS
50



VRQCSGVTFQ-GKFKKIVKG
53



KPCIKVATVQSKMSDVKCTS
56



EMLDNRATLQAIASEFSSLP
59



LRANSAVKLQNNELSPVALR
62



GSLAATVRLQAGNATEVPAN
65



CDQLREPLMQSADASTFNR
68



AMYTPHTVLQAVGACVLCNS
71



IPRRNVATLQAENVTGLFKD
74



WNTFTR--LQSLENVAYNW
77













DESCRIPTION OF THE EMBODIMENTS
One embodiment of the present invention provides a method of detecting a virus. The method is based on a proteolytic enzyme assay that indicates the presence of the virus by detecting a viral enzyme present during replication of the virus.
Cleavage of the Viral Polyprotein
During the replication of many viruses, such as the SARS virus, human immunodeficiency virus, human papilloma virus, herpes virus, rhinovirus, picomavirus, coronavirus, hepatitis C virus, and others, the viral genetic material is transcribed to form a polyprotein, which is ultimately cleaved into two or more biologically active proteins.
The cleavage of the viral polyprotein into individual proteins is a critical part of the viral life cycle. Many viruses, including those of the adenovirus, baculovirus, comovirus, picomavirus, retrovirus, and togavirus families, encode proteases which cleave the viral polyprotein at these specific cleavage positions to form the active proteins required for viral replication. For example, polyprotein processing during replication of the Cocksfoot mottle virus (genus Sobemovirus) is described in Makinen, K. et al., J. Gen. Virol. vol. 81, pp 2783-89 (2000), the contents of which are incorporated by reference.
For the purposes of this invention, a “protease” is an enzyme that catalyses the hydrolysis of a peptide bond. Proteases are part of the hydrolase class of enzymes, which are selected from the enzymatic class having the general reaction equation:

R—CONHR′+enzyme+H2O→RCOOH+R′NH2.

Some virally-encoded proteases cleave only the polyprotein of a specific virus. Others cleave the polyprotein of more than one type of virus. The specificity of protease action arises from the nature of the interaction of the protease at the cleavage region(s) of the polyprotein. A given protease will only cleave the polyprotein at a region having certain defined amino acid sequences. For example, the Rhinovirus HRV14 3C protease will cleave a polyprotein at a Glu-Gly, Glu-Ala or Glu-Gly dipeptide sequence. In addition, the rate of cleavage at these positions varies, depending on the peptide sequence of the polyprotein surrounding the cleavage position.
Thus, a virally-encoded protease can cleave the viral polyprotein at a number of different positions if the amino acid sequence at these positions is such that the cleavage reaction occurs. Similarly, if such sequences are conserved across a number of different viruses, a single protease may cleave the polyprotein of these viruses. The present method takes advantage of this specificity to provide detection methods that are specific for a single virus type or for more than one virus type.
It is believed, but not relied upon for that present invention, that during replication of certain viruses, viral-encoded proteases are autocleaved from the viral polyprotein at an early stage for the viral replication process. For example, the Picornavirus viral polyprotein is processed into the individual protein products by the viral 3C protease. This protease derives from a polypeptide sequence that is itself a part of the viral polyprotein. The mechanism by which this protease becomes cleaved from the viral polyprotein is described in Khan, A. R. et al. “Structural aspects of activation pathways of aspartic protease zymogens and viral 3C protease precursors”, Proc. Nat'l . Acad. Sci., Vol. 96, No. 20, pp. 10968-75 (1999), the contents of which are incorporated by reference. For other viruses, the viral protease responsible for cleaving the polyprotein may be encoded separately from the polyprotein.
One embodiment of the present invention provides a method of detecting a virus in a sample obtained from a patient suspected of being infected with the virus. The method is applicable to the detection of the wide range of viruses producing a virally-encoded protease that cleaves the viral polyprotein. For the purposes of this invention, a “virally-encoded protease” or “viral protease” is defined as any protease encoded from the genetic material of a virus and which cleaves a peptide bond in the viral polyprotein during replication of the virus.
Virally-encoded proteases cleave the polyprotein of a wide range of virus families, including the Nidovirus, Herpesvirus, Adenovirus, Retrovirus, Picornavirus and Potyvirus families. Rao, M. B. et al., “Molecular and Biotechnological Aspects of Microbial Proteases”, Microbiol. and Mol. Biology Rev., Vol. 62, No. 3, p. 597-635 (1998), the contents of which are incorporated by reference. Table 1 shows some examples of the proteases involved in polyprotein cleavage of viruses associated with various animal and plant diseases. Additional examples of such proteases are described in Corbalenya, A. E. and Snijder, E. J., “Viral cysteine proteinases, Perspectives in Drug Discovery and Design” 6: pp. 64-86 (1996) and Dougherby, W. G. and Semler, B. L., “Expression of virus-encoded protonases: functional and structural similarities with cellular enzymes”, Microbiol. Rev. 57, pp. 781-822 (1993), John Ziebuhr et al. “Virus-encoded proteinases and proteolytic processing in the Nidovirales”, J. Gen. Vir., Vol. 81, pp. 853-79 (2000), the contents of which are incorporated by reference.







TABLE 1







EXAMPLES OF VIRAL-CODED PROTEASES INVOLVED IN


POLYPROTEIN PROCESSING









Virus
Protease
Associated Disease










Picornaviridae









Enterovirus
3C (CSL), 2A(CSL)
Meningitis, gastro-




intestinal infections


Coxsackievirus
3C
Common cold


Echovirus
3C
Summer flu, hand-foot-and




mouth


Poliovirus
3C
Poliomyelitis


Rhinovirus
3C (CSL), 2A(CSL)
Common cold, asthma




exacerbation in allergies


Aphthovirus
3C (CSL), L (Cys)
Foot and mouth disease


Cardiovirus
3C (CSL)
Encephalitis, heart disease




(mainly murine, affects




other mammals)


Hepatovirus
3C (CSL)
Hepatitis A (chronic




jaundice)







Togoviridae









Alphaviruses
Cys and Ser
Equine encephalitis


Poxyviruses
Ser
Smallpox


Rubiviruses
Cys
Rubella (German measles)







Paramyxoviridae









Parainfluenza
Ser
Respiratory infection


RSV
Ser
Infant bronchiolitis, viral




pneumonia


Coronaviridae
Cys, 3C-like CSL, Ser
Infant bronchiolitis, viral




pneumonia


SARS
Cys, 3C like, PL1 PL2
Acute respiratory




syndrome


Arterivirus
Cys
Pig disease







Flaviviridae









Flavivirus
NS3 (Ser, unique), NS2B




(Ser, unique)


Yellow-fever
NS3 (Ser, unique)
Yellow-fever


virus


HepC virus
NS3 (Ser, unique)
Hepatitis C


Pestivirus
Cys, Ser
Pigs, cattle and sheep




disease


Adenoviridae

Acute upper respiratory,




eye and intestinal tract,




infant death


Herpesviridae
Herpesviridae
Herpes (systemic and




topical)







Retroviridae









HIV
Asp
AIDS


Caliciviridae
3C-like (CSL)
Rabbit hemorrhagic




disease







Potyviridae









Potyvirus
NIa (3C-like CSL), HCpro
Potato disease



(Cys)


Bymovirus
3C-like (CSL), Cys
Plant disease







Comoviridae









Comovirus
p24 (3C-like CSL)
Plant disease


Nepovirus
p23 (3C-like CSL)
Plant disease









Sources

    
    
        1) Gorbalenya, A. E. and Snijder, E. J., Viral cysteine proteinases, Perspectives in Drug Discovery and Design 6: pp. 64-86 (1996)
        2) Dougherby, W. G. and Semler, B. L., Expression of virus-encoded protonases: functional and structural similarities with cellular enzymes, Microbiol. Rev., Vol. 57, pp. 781-822 (1993)
    
    


Proteases are subdivided into two major groups, depending on their site of action. Exopeptidases cleave the peptide bond proximal to the amino or carboxy termini of the substrate, whereas endopeptidases cleave peptide bonds distant from the termini of the substrate. Based on the functional group present at the active site, proteases are further classified into four prominent sub-groups. These are serine proteases, aspartic proteases, cysteine proteases, and metalloproteases.
Viruses produce many different proteases, including members of the above classes. For example, the Hepatitis C virus genome encodes a specific serine protease and a metallo-protease (NS2 and NS3) and the Rhinovirus genome encodes cysteine proteases (3C and 2A). The SARS genome encodes a cysteine protease (3CL). Anand K. et al., Coronavirus Main Protease (3CLpro) Structure: Basis of Design of Anti-SARS Drugs” Science, Vol. 30, pp. 1763-67 (2003), the contents of which are incorporated by reference. In addition, the SARS genome encodes the PL1 and PL2 main proteases. Each member of the herpesvirus family encodes a unique serine protease. Adenoviruses code for a serine-centered, neutral protease specific for selected Gly-Ala bonds in several virus-encoded precursor proteins. Retroviruses encode an aspartyl protease, which is responsible for processing the gag and pol polyprotein precursors into the structural proteins of the mature virus.
Viral-encoded Enzymes
The cleavage of the polyprotein to produce functional viral proteins is a key step in the virus maturation process. The cleavage step occurs at an early stage of viral replication cycle. This requires that the viral-encoded proteases responsible for this process are themselves present at an early stage of replication. Because the proteases are present early in the cycle of infection, their detection allows viral infection to be confirmed at an early stage.
Tissue infected by a virus contains fully assembled virus particles as well as components of the viral particles. These components include the active proteases. See Sosnovtsev, S. V., et al., “Cleavage of the feline calicivirus capsid precursor is mediated by a virus-encoded proteinase”, J. Virol., Vol. 72, pp. 3051-59 (1998), the contents of which are incorporated by reference. It is also known that certain viruses, for example the Influenza types A and B viruses, produce surface glyco-proteins with neuraminidase activity whose presence confirms infection with the virus. ZSTATFLU® Product Package Insert (ZymeTx, Inc., Oklahoma City, Okla. 73104)
Detection of Polyprotein Cleaving Proteases
In one embodiment of the present invention, the presence of a viral-encoded protease associated with a virus is detected by observing the cleavage of a peptidal compound having a specific cleavage site for the protease. The specificity of the cleavage reaction depends upon the amino acid sequence at the cleavage site. Specific cleavage sites for many viral-encoded proteases have been identified. See, for example, John Ziebuhr et al. “Virus-encoded proteinases and proteolytic processing in the Nidovirales”, J. Gen. Vir., 81, pp. 853-79 (2000), the contents of which is incorporated by reference. The viral cleavage sites are chosen such that their cleavage is specific for the type of virus to be detected. Table 2 shows examples of some viral proteases along with peptides that are specifically cleaved by them.








TABLE 2







EXAMPLES OF SPECIFIC CLEAVAGE PEPTIDES









Protease
Specific Cleavage Peptides












Rhinovirus 3CL
Arg-Pro-Val-Val-Val-Gln-Gly-Pro-Asn




SEQ ID NO: 83


 


Coronavirus
Ser-Thr-Leu-Gln-Ser-Gly-Leu-Arg-Lys


TGEV 3CL
SEQ ID NO: 84


 


SARS COV 3CL
Ala-Thr-Val-Arg-Leu-Gln-Ala-Gly-Phe



SEQ ID NO: 85


 



Val-Ser-Val-Asn-Ser-Thr-Leu-Gln-Ser-



Gly-Leu-Arg-Lys-Met-Ala-Cys



SEQ ID NO: 86









In the present invention, a region of the viral polyprotein containing a cleavage site for the protease to be detected is mimicked by a peptidal compound. For the purposes of this invention, the term “peptidal compound” is any compound containing a cleavage site for a protease encoded by the virus or viruses that are to be detected. Under appropriate conditions, the protease will cleave the peptidal compound to form a “first peptidal compound fragment” and a “second peptidal compound fragment”. The conditions required for performing such enzyme cleavage reactions are well known for those skilled in the art.
A region of the peptidal compound that forms one of the peptidal compound fragments is tagged by directly or indirectly attaching a signaling moiety that allows that fragment to be detected. For the purposes of the invention, the “signaling moiety” can be any label that produces a detectable signal. For example, the signaling moiety can be a detectable label that produces a fluorescencent, a chemiluminescent or a calorimetric signal.
In one embodiment, the cleavage site is specific for a single virus. This allows for a specific test that detects this virus and shows low cross-reactivity for other viruses. In another embodiment, the cleavage site that conserved across more than one virus. This allows for a single test that will detect more than one virus.
It is believed, but not relied upon for the present invention, that since polyprotein-cleaving proteases are not present on the viral surface, they are less subject to mutation than are viral-coat proteins. Also, since these proteases have an important role in the virus life cycle, significant mutation is unlikely.
The method of the present invention can be used to test for the presence of a virus in a sample contaminated with the virus. In one embodiment, the sample is taken from an organism. For example, the method can test for a virus in a sample taken from an animal or plant host. In one embodiment, the method tests for a virus in a sample taken from a human patient. The sample can be mucus, saliva, throat wash, blood, serum, plasma, urine, spinal fluid, sputum, tissue biopsy, broncheoalveolar fluid, vaginal fluid, tear fluid or another biological sample. For example, the SARS virus is known to be present in saliva. Wang, W-K “Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis” Emerg Infect Dis [serial on the Internet] (June 2004). Available from: http://www.cdc.gov/ncidod/EID/vol10no7/03-1113.htm. The invention includes methods where the sample is treated to disrupt cells to release viral components, including the protease, e.g. by using sonification. The presence of a virus is confirmed by detecting a viral protease produced by the virus. In one embodiment, the protease level is correlated with the level of viral replication or viral load.
In one embodiment of the invention, the peptidal compound includes a sequence of at least four amino acids residues from the sequence in the region of a polyprotein cleavage site, including the protease cleavage site. In another embodiment, the peptidal compound includes at least seven amino acids residues from the protease cleavage site. In another embodiment, the peptidal compound includes at least ten amino acids residues from the protease cleavage site. In yet another embodiment, the peptidal compound includes at least four amino acids from a sequence that is a consensus sequence of the sequences at the cleavage sites of two or more viruses. In other embodiments, the peptidal compound contains at least seven, or at least ten, amino acids from a consensus sequence of the cleavage sites of two or more viruses.
In another embodiment, the one or more amino acids present in the peptidal compound are modified or replaced by an analog. Analogs are amino acids that have a structure similar to the native compound but differ from it in respect to certain components or side chains.
Alternatively, one or more amino acids may be replaced by similar amino acids without altering the cleavage properties of the mimic peptidal compound. Useful conservative substitutions are shown in Table 3, “Preferred substitutions.” Conservative substitutions whereby an amino acid of one class is replaced with another amino acid of the same type fall within the scope of the invention so long as the substitution does not materially alter the cleavage properties of the peptidal compound. Such substitutions can be tested using a method such as that described in Example 5 to determine whether the substitution alters the cleavage properties.







TABLE 3







Preferred substitutions









Original residue
Exemplary substitutions
Preferred substitutions





Ala (A)
Val, Leu, Ile
Val


Arg (R)
Lys, Gln, Asn
Lys


Asn (N)
Gln, His, Lys, Arg
Gln


Asp (D)
Glu
Glu


Cys (C)
Ser
Ser


Gln (Q)
Asn
Asn


Glu (E)
Asp
Asp


Gly (G)
Pro, Ala
Ala


His (H)
Asn, Gln, Lys, Arg
Arg


Ile (I)
Leu, Val, Met, Ala, Phe,
Leu



Norleucine


Leu (L)
Norleucine, Ile, Val, Met,
Ile



Ala, Phe


Lys (K)
Arg, Gln, Asn
Arg


Met (M)
Leu, Phe, Ile
Leu


Phe (F)
Leu, Val, Ile, Ala, Tyr
Leu


Pro (P)
Ala
Ala


Ser (S)
Thr
Thr


Thr (T)
Ser
Ser


Trp (W)
Tyr, Phe
Tyr


Tyr (Y)
Trp, Phe, Thr, Ser
Phe


Val (V)
Ile, Leu, Met, Phe, Ala,
Leu



Norleucine









By selecting a peptidal compound to mimic a particular polyprotein cleavage site, the method of the present invention can be used to test for a wide range of viruses. In one embodiment, the virus detected is from the picornavirus family. This family of viruses includes the human rhinoviruses and the coxsackieviruses. FIGS. 2A-D show the sequences around known cleavage positions in the polyproteins encoded by some such viruses. The viruses shown are Human Rhinovirus 14 (HRV14), Human Rhinovirus b (HRVb), Human Rhinovirus 16 (HRV16) and Coxsackievirus A21 (Cxa21). The figures also show sequence alignment between the cleavage sites of the viruses and consensus peptide sequences. Sequence alignment was performed using the CLUSTAL W (1.82) general purpose sequence analysis program. (European Bioinformatics Institute, available at www.ebi.ac.uk/clustalw).
In the test method for a particular virus, protease cleavage of a peptidal compound containing an amino acid sequence including one of the polypeptide cleavage regions is detected. By selecting a peptidal compound that shows low homology to sequences present in similar viruses, a specific test for the virus can be performed. The invention also includes methods where two or more peptidal compounds are cleaved, either by a single protease or by different proteases.
In another embodiment, the virus detected is a Nidovirus. This class of viruses includes the SARS virus, Bovine Coronavirus and Human Coronavirus. The SARS genome is available at: M. Marra et al., http://www.bcgsc.ca/bioinfo/SARS. The genome shows more than a 44% homology with the coronavirus genome and, like the coronavirus genome, encodes a 3CL protease (Sequence homology performed using the software packages available at EMBL (European Bioinformatics Institute, http://www.ebi.ac.uk/embl/index.html)).
FIGS. 3A-D show the amino acid sequences around known cleavage positions in the polyproteins encoded by these viruses. Sequence alignments between the cleavage sites of the three viruses and consensus sequences are also shown. Sequence alignment was again performed using the CLUSTAL W (1.82) sequence analysis program. FIG. 3(A) shows that the cleavage regions centered at, for example, positions 180 or 818 of the SARS polyprotein shows little homology with the Human or Bovine Coronavirus polyprotein. By choosing peptide sequence mimicking the sequence of one of these cleavage positions, a specific test for the SARS virus can be performed. Similarly, by choosing a Human Coronavirus polyprotein sequence showing low homology to either the SARS or Bovine Coronavirus polyprotein, a specific test for Human Coronavirus can be performed.
Assays for Protease Cleaving Activity
One embodiment of the present invention provides a homogenous assay for the detection of a virus. The chosen peptidal compound is synthesized and linked to a signaling moiety at one side of the cleavage region and to a quencher moiety at the other side of the cleavage region. A “homogeneous assay” is an assay not requiring separation of signaling moiety from other assay components.
For the purposes of the invention, a “quencher moiety” is any substance that is capable of reducing or eliminating the signal emitted by the signaling moiety. For example, the quencher moiety may act by absorption of the signal emitted by the signaling moiety or by an energy transfer mechanism. The distance between the signaling moiety and the quencher moiety is such that presence of the quencher moiety substantially reduces or eliminates the signal emitted from the signaling moiety unless the peptidal compound is cleaved at a position resulting in separation of the signaling and quencher moieties.
In one embodiment, the signaling moiety and quencher moiety are separated by no more than 5 amino acid residues. In another embodiment, the signaling moiety and quencher moiety are separated by no more than 10 amino acid residues. In yet another embodiment, the signaling moiety and quencher moiety are separated by no more than 15 amino acid residues. In yet another embodiment, the signaling moiety and quencher moiety are separated by no more than 20 amino acid residues.
The peptidal compound is contacted with the sample being tested for the presence of a virus. If the virus is present in the sample, the viral protease is also present. This protease cleaves the peptidal compound and a change in the signal from the signaling moiety can be observed. FIG. 1 shows a representation of the cleavage reaction. Such homogenous fluorescent and colorimetric assays are known to those skilled in the art. See, for example: Biochemistry, Allinger, Wang Q. M. et al., “A continuous calorimetric assay for rhinovirus-14 3C protease using peptide p-nitroanilides as substrates” Anal. Biochem. Vol. 252, pp. 238-45 (1997), and Basak S. et al. “In vitro elucidation of substrate specificity and bioassay of proprotein convertase 4 using intramolecularly quenched fluorogenic peptides” Biochem. J. Vol. 380, pp. 505-14 (2004) the contents of which are incorporated by reference. However, it is believed that such methods have not previously been utilized for the diagnosis of viral disease.
In another embodiment of the present invention, the signaling moiety is a chemiluminescent signaling moiety. The chemiluminescent signaling moiety is attached to one side of the cleavage region of the peptidal compound and a fluorescent accepting quencher moiety is attached at the other side of the cleavage region. U.S Pat. No. 6,243,980, the contents of which are incorporated by reference, describes such a detection system, involving the use of a chemiluminescent 1,2-dioxetane compound as the signaling moiety. If the viral protease is not present in the sample, cleavage of the peptidal compound does not occur. The energy from the 1,2-dioxetane decomposition is transferred to the fluorescent accepting moiety and released at a wavelength distinct from the emission spectrum of the 1,2-dioxetane. If the peptidal compound is cleaved, the fluorescent accepting moiety is separated from the 1,2-dioxetane and a chemiluminescent emission from the dioxetane compound is observed.
In another embodiment, the signaling moiety is a fluorescent compound and the quencher moiety is a fluorescent compound having an excitation spectrum that overlaps the emission spectrum of the signaling moiety . Here, the two moieties are separated apart at a distance consistent with fluorescent resonance energy transfer so that the fluorescent moiety is capable of acting as a resonance energy donor.
In another embodiment, a quenching group, such as a non-fluorescent absorbing dye is used in place of the fluorescent accepting quenching moiety. Suitable quenching groups are described in U.S. Pat. No. 6,243,980, the contents of which are incorporated by reference.
In such a test method, the test sample is contacted with the peptidal compound under conditions that allow cleavage of the peptidal compound by the protease if the virus is present in the sample. In one embodiment, the temperature is controlled. For example, the temperature can be controlled at 37 deg C. to provide optimal conditions for the enzyme reaction. The signal from the cleaved peptidal compound fragment is then detected using a detection device appropriate to the label used.
Another embodiment of the present invention provides a heterogeneous assay for the detection of a virus. In one embodiment of the heterogeneous method, a first member of a first binding pair is linked to one side of the cleavage region of the peptidal compound. A first member of a second binding pair, or a signaling moiety, is linked to the other side of the cleavage region of the peptidal compound. A second member of the first binding pair is linked to a solid-phase. Alternatively, one side of the peptide can be linked directly to the solid-phase. A “heterogeneous assay” is an assay in which the solid-phase is separated from another assay component during the assay.
The peptidal compound is incubated with the solid-phase and a sample being tested for the presence of a virus. The incubation conditions are such that binding occurs between the first and second members of the first binding pair. If a protease having the ability to cleave the peptidal compound at the cleavage site is present in the patient sample, the peptidal compound is cleaved causing the peptidal compound fragment linked to the first member of a second binding pair, or the signaling moiety, to become detached from the solid phase.
The solid-phase and liquid phase are then separated. If a signaling moiety is linked to the peptidal compound, the amount of signaling moiety in either the solid phase or the liquid phase is measured to determine the presence of the protease, and hence the virus, in the sample. If a first member of a second binding pair is linked to the peptidal compound, a second member of the second binding pair linked to a signaling moiety is incubated with the peptidal compound under conditions such that binding occurs between the first and second members of the second binding pair. The presence of the virus is then detected as above.
The above steps may be varied or combined without departing from the method of the present invention. For example, those skilled in the art will recognize that, in the heterogeneous assay method, the second member of the second binding pair linked to the signaling moiety can be contacted with the peptidal compound before or at the same time as the solid-phase is contacted with the peptidal compound.
Many different binding pairs may be used for the first and second binding pairs. However, the binding pairs must be chosen such that that the first binding pair does not interact with the second binding pair. Examples of such binding pairs are well known in the art and include biotin/avidin, biotin/strephavidin, antibody/antigen, antibody/hapten, binding protein/bound molecule and complementary nucleic acid sequences. The first member of each binding pair, or the signaling moiety, can be directly linked to the peptide by a covalent bond or indirectly via a spacer molecule having coupling functional groups at each end. Examples of such linkers include an alkyl, a glycol, an ether, a polyether, a polynucleotide and a polypeptide molecule.
Solid-phases suitable for use in the heterogeneous assay include, but are not limited to test tubes, microtiter plates, microtiter wells, beads, dipsticks, polymer microparticles, magnetic microparticles, nitrocellulose, chip arrays and other solid phases familiar to those skilled in the art. The signaling moiety used in the heterogeneous assay may be any label known to those skilled in the art. Such labels include radioactive, calorimetric, fluorescent and luminescent labels.
A heterogeneous chemiluminescent assay for the detection of proteases is described in U.S. Pat. No. 56,243,980, the contents of which are incorporated by reference. Here, the second member of the second binding pair is conjugated with an enzyme, such as alkaline phosphatase, which triggers 1,2-dioxetane to emit a chemiluminescent signal.
In one embodiment, the homogeneous or heterogeneous assay method of the present invention is automated so that a result can be obtained without the need for medical staff to be exposed to a patient thought to be infected by the viral disease under test. For example, the patient can be tested in a clean room (for example, but not limited to P3 type room). The patient can pick up, or get before entering the room, a diagnostic kit, which can include a solid phase coated with a labeled peptide of the type discussed above. For example, the solid phase can be a tissue which was previously immersed with peptide, or a test stick that can be from the type used to test pregnancy. The patient can supply a sample, such as a saliva sample, at a pre-prepared spot on the solid phase.
The solid phase containing the sample is then incubated to allow the enzymatic reaction to occur. In one embodiment, the reaction temperature in controlled at 37° C. to provide optimal conditions for the enzyme reaction. When the incubation is complete, the sample to be tested can be measured on a spectrophotometer, using a remote control, or a mechanical system operated manually from outside the room. The sample can be tested for a qualitative color or UV detection. After the test the sample can be discarded by an automated system, or a remote operated handle that trashes the sample.
Detection of New Emerging Viral Diseases
In another embodiment, the present invention provides a method for developing an assay for the detection of a newly emergent virus. Once the genome of the emergent virus is identified and its reproduction system known, viral proteases and those regions of the viral polyprotein that are cleaved by such proteases can be determined by examining the sequence homology between the sequence of the emergent virus and that of known viruses. Specific mimic peptide compounds bridging the regions cleaved by the protease are then prepared and tested to determine the activity of the polyprotein cleaving protease against each peptide. In one embodiment, the peptide showing the highest rate of cleavage is chosen and used in the preparation of the test for the virus. The cleavage rates of such compounds may be determined using a method such as that described in Orr D.C. et al. “Hydrolysis of a series of synthetic peptide substrates by the human rhinovirus 14 3C proteinase, cloned and expressed in E. coli”, J. Gen. Vir. Vol. 70, pp. 2931-42 (1989), the contents of which are incorporated by reference.
The reason for the effectiveness of the method for new emerging viral diseases is that the basic function of the proteolytic activity is maintained in the overall mechanism of the virus maturation. Specific proteases can be rapidly analyzed once the genome of the new virus has been identified. Thus, a new protease from a new emerging virus is constructed based on the template of a protease from a similar known virus from the same family. For each virus family, a library of peptides can be synthesized and the rate of cleavage by the protease measured. Based on there results, a consensus peptide is chosen, as is shown in Example 5 for rhinovirus.
The proteolytic class of the enzyme can be classified using data in the literature. Several databases exist that include an extensive amount of information about enzymes as they relate to their designated class. For example, Swiss-Prot Enzyme nomenclature database at http://kr.expasy.org/enzyme or classification of enzymes at http://www-biol.paisley.ac.uk/marco/enzyme_electrode/Chapter1/page 1a.htm. The enzyme can be further classified upon sequencing the enzyme and comparing its homology to other enzymes. Often times, the sequence for the enzyme has already been determined and can thus be found in the literature or a database (e.g. Genbank)http://www.ncbi.nlm.nih.gov/Genbank/) or UniProt/Swiss-Prot Protein Knowledgebase (European Bioinformatics Institute at http://www.ebi.ac.uk/swissprot/ or GOR IV Secondary Structure Prediction Method (e.g. http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.p1?page=/NPSA/npsa_server.html). If the enzyme sequence has not been identified, the enzyme can be isolated according to a variety of techniques known to those skilled in the art. Additionally, the enzyme can be synthesized using recombinant DNA techniques that are commonly known to scientists practicing in the field of molecular biology (See Short Protocols in Molecular Biology, 2d. ed., John Wiley & Sons (1992), which is incorporated herein by reference.
Sequencing of the target protein can be performed at the amino acid level and/or the DNA level using techniques known to those skilled in such an art. To determine the DNA sequence of the target protein, the method discussed in Wilhelm Arrange, DNA sequencing strategies, Automated and Advanced Approaches, 15 BN 0971136832 (S. Zimmerman, ed.), which is also incorporated herein by reference, can be used. The determined sequence of the enzyme can be compared for homology to other known sequences of classified enzymes having an identified tertiary, or preferably quaternary structure. Information regarding such enzymes are located databases, such as the Brookhaven Crystallographic Data Bank (http://pdb.pdb.bnl.gov).
After categorizing the chemical reactions the enzymes undergo, the specific peptide sequence at the cleavage regions of the viral polyprotein is determined by comparing the genome sequence to a homologous genome. Mimic peptidal compounds are then prepared as described above. In one embodiment, the peptidal compounds contain peptides having 6-15 amino acids from the cleavage regions. A library of such compounds is prepared and the cleavage rate determined for each compound determined. Peptidal compounds having high cleavage rates are then selected for use in viral tests. Kits, Compositions and Reagents for the Detection of Viral Disease
The present invention also provides for kits for detecting a viral disease. In one embodiment, the kit contains at least a reagent comprising one the mimic peptidal compounds described above and a buffer in a package or container. In one embodiment, a signaling moiety is linked to a portion of the peptidal compound present in one peptidal compound fragment. In another embodiment, a quencher moiety linked to a portion of the peptidal compound present in the other peptidal compound fragment. The signaling moiety and the quencher moiety are linked to the peptidal compound at relative positions such that the quencher molecule quenches the signal of the reporter molecule unless the peptidal compound is cleaved at the cleavage point.
In another embodiment, the kit contains the following in one or more packages or containers: (a) a construct reagent comprising (i) a peptidal compound capable of being cleaved by the enzyme to form two peptidal compound fragments, (ii) a first member of a first binding pair linked to a portion of the peptidal compound present in one peptide fragment, and (iii) a first member of a second binding pair linked to a portion of the peptidal compound present in the other peptidal compound fragment, (b) a solid-phase reagent comprising a second member of the first binding pair is linked to a solid-phase, and (c) a signaling reagent comprising a second member of the second binding pair linked to a signaling moiety.
In yet another embodiment, the kit contains the following in one or more packages or containers: (a) a construct reagent comprising (i) a peptidal compound capable of being cleaved by the enzyme to form two peptidal compound fragments, (ii) a first member of a first binding pair linked to a portion of the peptidal compound present in one peptidal compound fragment, and (iii) a signaling moiety linked to a portion of the peptidal compound present in the other peptidal compound fragment and (b) a solid-phase reagent comprising a second member of the first binding pair is linked to a solid-phase.
When a kit is supplied, the different components may be packaged in separate containers and admixed immediately before use. Such packaging of the components separately may permit long-term storage without losing the active components' functions. Embodiments in which two or more of components (a)-(c) are found in the same container are also contemplated.
In another embodiment, the above kits further comprise one or more of the following reagents:

    
    
        (a) a wash buffer reagent for use using heterogeneous assays;
        (b) a negative control reagent free of a protease capable of cleaving the construct reagent;
        (c) a positive control containing a protease capable of cleaving the construct reagent;
        (d) a signal generation reagent for development of a detectable signal from the signaling moiety; and
        (d) a sample collection means such as a syringe, throat swab, or other sample collection device.
    
    


The reagents included in the kits can be supplied in containers of any sort such that the life of the different components are preserved and are not adsorbed or altered by the materials of the container. For example, sealed glass ampules may contain lyophilized reagents, or buffers that have been packaged under a neutral, non-reacting gas, such as nitrogen. Ampules may consist of any suitable material, such as glass, organic polymers, such as polycarbonate, polystyrene, etc.; ceramic, metal or any other material typically employed to hold similar reagents. Other examples of suitable containers include simple bottles that may be fabricated from similar substances as ampules, and envelopes, that may comprise foil-lined interiors, such as aluminum or an alloy. Other containers include test tubes, vials, flasks, bottles, syringes, or the like. Containers may have a sterile access port, such as a bottle having a stopper that can be pierced by a hypodermic injection needle. Other containers may have two compartments that are separated by a readily removable membrane that upon removal permits the components to be mixed. Removable membranes may be glass, plastic, rubber, etc.
Kits may also be supplied with instructional materials. Instructions may be printed on paper or other substrate, and/or may be supplied as an electronic-readable medium, such as a floppy disc, CD-ROM, DVD-ROM, Zip disc, videotape, audiotape, etc. Detailed instructions may not be physically associated with the kit; instead, a user may be directed to an internet web site specified by the manufacturer or distributor of the kit, or supplied as electronic mail.
In another embodiment, the invention provides a composition for detecting a virus in a sample. The composition includes a buffer and a mimic peptidal compound capable of being cleaved at a cleavage point by a protease produced by the virus to form a first peptidal compound fragment and a second peptidal compound fragment. A signaling moiety is linked to a portion of the peptidal compound present in the first peptidal compound fragment and a quenching moiety is linked to a portion of the peptidal compound present in the second peptidal compound fragment. The signaling moiety and the quenching moiety are linked to the peptidal compound at relative positions such that the quenching moiety quenches a signal of the signaling moiety.
In one embodiment, the virus is a Rhinovirus. In this embodiment, the composition can include a peptidal compound containing an amino acid sequence present one of the cleavage sites on the Rhinovirus polyprotein. For example, the amino acid sequence can be one of the Rhinovirus sequences listed in Table 2.
In another embodiment, the virus is the SARS virus. In this embodiment, can include a peptidal compound can containing an amino acid sequence present one of the cleavage sites on the SARS virus polyprotein. For example, the amino acid sequence can be one of the Rhinovirus sequences listed in Table 3.
A more complete understanding of the present invention can be obtained by reference to the following specific Examples. The Examples are described solely for purposes of illustration and are not intended to limit the scope of the invention. Changes in form and substitution of equivalents are contemplated as circumstances may suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitations. Modifications and variations of the invention as hereinbefore set forth can be made without departing from the spirit and scope thereof, and, therefore, only such limitations should be imposed as are indicated by the appended claims.
EXAMPLES
Example 1
Detection of Protease Activity
Enzymatic activity for 3C protease can be detected using chromogenic substrates as described in: Wang, Q. M. et al. “A continuous colorimetric assay for rhinovirus-14 3C protease using peptide p-nitroanilides as substrates” Anal. Biochem. Vol. 252, pp. 238-45 (1997), the contents of which are incorporated by reference. Tagged substrates are used to determine the ability of the protease to cleave. The first peptide substrate used is tagged using p-nitroaniline. When p-nitroaniline is cleaved from the peptide, a signal is produced. The cleavage causes an aromatic pi-electron system to form, the presence of which absorbs in the 405 nm range of the electromagnetic spectrum. The nanomolar extinction coefficient of the cleaved p-nitroaniline is 104 mole−1cm31 1.
Alternatively, a substrate is constructed having a florescent tag attached to one end and a quencher attached to the other end. When the peptide is cleaved fluorescence is detected. Other tags use a similar principle using color reactions.
Example 2
Homogenous Fluorescence Resonance Energy Transfer Assay for 3C Protease
Human Rhinovirus serotype 1A (ATCC) is used to clone the 3C Protease into the expression vector pET16-b and transformed for production into the E. coli strain BL21-DE3-pLys-S. 3C Protease expression is induced with 1 mM IPTG at 25° C. and purified from the soluble protein extract by chromatography on a SourceQ (Pharmacia) followed by gel filtration. HRV 3CP activity was measured by fluorescence resonance energy transfer using a dimodified decapeptide substrate MOC-Arg-Ala-Glu-Leu-Gln-Gly-Pro-Tyr-Asp-Lys-DNP-NH2 (SEQ ID NO: 113) (7-methoxy coumarin-4-acetic acid fluorochrome and dinitrophenol quencher) with a Km value of 16.8 μM. Inhibition was measured as a change in initial velocity (V0) as a function of inhibitor (I) concentration and substrate (S) concentration.
Assays are performed in 100 uL volumes in a 96 well format at 30° C. containing 25 mM Tris HCl pH 8.0, 150 mM NaCl, 1 mM EDTA pH 8.0, 6 mM DTT, 2-6 uM substrate, 2% DMSO, 416 nM 3CP and inhibitor as needed. Fluorescence is monitored by excitation at 328 nm and emission at 393 nm with 10 nm cutoffs. Data are analyzed with the nonlinear regression analysis program EnzFitter (BioSoft) with the equation:

Ki=(I/((VmaxxS)/V0)/Ks)−I−S 

Substrate concentrations used are lower than the Km of the substrate (16.8 uM) so no corrections for an S/Km term were used.

Example 3
Using the CELLSCAN® Cytometer to Detect Protease Activity
The CELLSCAN® (Medis Technologies Ltd., New York, N.Y.) is a cytometer that can monitor the fluorescence intensity and polarization by using fluorescence probes within individual, non-adherent living cells and can also be used to detect protease activity. The heart of the CELLSCAN is a Cell carrier that contains up to 10,000 wells. A description of the CELLSCAN cytometer and its other uses for diagnosis of cancer and autoimmune diseases is available at: www.medisel.com.
A CELLSCAN probe is loaded with a specific peptidal compound. For example, the peptidal compound can contain a peptide that is specific for SARS. The peptidal compound is tagged with a fluorescent group on one side of the cleavage region and a quencher on the other. The sample under test, e.g. saliva or mucus, is loaded on the probe
If active protease exists, the CELLSCAN will detect fluorescence caused by the cleaved peptide. The presence of active protease and its concentration in the saliva is an indication of an active virus and serves as an indication for the contagious status of the patient.
Example 4
Paper-tissue-Based Automated System for the Detection of SARS
A solution of a color-tagged peptidal compound specific for 3Cl-SARS protease is prepared. The peptide is prepared in a pH 7.0 buffer solution in a millimolar concentration. A tissue (wet-wipes tissues) is immersed in the peptidal compound solution and is kept moist. The saliva or mucus specimen suspected of containing the SARS virus is put in contact with the tissue. If the SARS virus is present, the 3CL SARS protease cleaves the tagged peptide sequence and a color reaction occurs.
Several possibilities exist for detection of the colored reaction product. For a qualitative analysis, a color reaction may be detected visually. For a qualitative analysis, the tissue is transferred to spectrophotometric analyzer for either fluorescence or color detection. The process can be automated so as to protect those performing the assay from infection.
Example 5
Determining an Optimal Peptide Sequence for a Rhinovirus Assay
The cleavage sites of the Rhinovirus HRV14 3C protease are aligned as shown in Table 4. Table 4 also shows the QG dipeptides that appear in the HRV14 primary sequence, showing the six sites that are cleaved. The QA and EG dipeptide sites are also shown. One of each of these sites is known to be cleaved.








TABLE 4







QG DIPEPTIDES THAT APPEAR IN THE



HRV14 PRIMARY SEQUENCE












Cleavage



Location on polyprotein
Sequence
Site














QG Site




331
SEQ ID NO: 87
IB1C



KSIVPQGLPTTT


 


1,002
SEQ ID NO: 88
2A2B



CIAEEQGLSDYI


 


1,429
SEQ ID NO: 89
2C3A



LETLFQGPVYKD


 


1,514
SEQ ID NO: 90
3A3B



LFAQTQGPYSGN


 


1,537
SEQ ID NO: 91
3B3C



RPVVVQGPNTEF


 


1,704
SEQ ID NO: 92



GGNGRQGFSAQL


 


1,719
SEQ ID NO: 93
3C3D



YFVEKQGQVIAR


 



QA Site


716
SEQ ID NO: 94



SNLVVQAMYVPH


 


950
SEQ ID NO: 95



YPSRFQAGVMKG


 


1,099
SEQ ID NO: 96
2B2C



PYIERQANDGWF


 


1,139
SEQ ID NO: 97



NKVLPQAKEKLE


 


1,485
SEQ ID NO: 98



ERAMNQASMIIN


 



EG Site


205
SEQ ID NO: 99



QLASH EGGNVSV


 


567
SEQ ID NO: 100
IC1D



TVALTEGLGDEL


 


940
SEQ ID NO: 101



TNIWIEGSPYYP


 


982
SEQ ID NO: 102



GLLTAEGSGYVC


 


1,632
SEQ ID NO: 103



ISEDLEGVDATL


 


2,001
SEQ ID NO: 104



EIYVVEGGMPSG









The cleavage peptides that mimic the cleavage sites for rhinovirus HRV14 are constructed and presented in Table 5.








TABLE 5







CLEAVAGE PEPTIDES












Cleavage





site


Cleavage Peptide
Mimicked
Peptide





SEQ ID NO: 105 DSLETLFQGPVYK
2C/3A
I



 


SEQ ID NO: 106 EAIAEEQGLSDYIT
2A/2B
II


 


SEQ ID NO: 107 VPYIERQANDGWFRK
2B/2C
III


 


SEQ ID NO: 108 RSKSIVPQGLPTTTY
1B/1C
IV


 


SEQ ID NO: 109 SQTVALTEGLGDELEEY
1C/1D
V


 


SEQ ID NO: 110 KLFAQTQGPYSGNP
3A/3B
VI


 


SEQ ID NO: 111 YRPVVVQGPNTEF
3B/3C
VII


 


SEQ ID NO: 112 KQYFVEKQGQVIAR
3C/3D
VIII









Next, the rate of hydrolysis for each of the peptidal compounds is determined. The assay used is a fluorometric, or HPLC based or UV based assay. Such assays are well known to those skilled in the art. One such method is described in Orr D. C. et al. “Hydrolysis of a series of synthetic peptide substrates by the human rhinovirus 14 3C proteinase, cloned and expressed in E. coli”, J. Gen. Vir. Vol. 70, pp. 2931-42 (1989). Table 6 shows the relative rate of hydrolysis for the cleavage of synthetic peptides that mimic the HRV14 3C cleavage sites.







TABLE 6







RELATIVE RATE OF HYDROLYSIS FOR THE CLEAVAGE


OF SYNTHETIC PEPTIDES THAT MIMIC THE HRV14 3C


CLEAVAGE SITES (From Orr D. C. et al.)












Relative
Hydrolysis





Hydrolysis rate
rate
Cleavage
Peptide
















1.00
355
2C/3A
I



0.024
8
2A/2B
II



0.0005
0
2B/2C
III



0.0005
0
1C/1D
V



0.44
147
3A/3B
VI



0.11
37
3B/3C
VII



0.003
1
3C/3D
VIII










The best substrate is chosen based on the reaction rates. Based on the results, a library of different sized peptides is constructed and the analyzed by the same assay. For Rhinovirus 14 the best peptide is: Arg-Pro-Val-Val-Val-Gln-Gly-Pro-Asn.
Example 6
Choosing a Cleavage Peptide from Picornaviruses and Coxaciviruses.
Table 7 shows an alignment of the amino acid sequences at the 2A.1C cleavage site for different Picornaviruses and Coxaciviruses. The cleavage site is at the QG dipeptide. The sequences show a high degree of homogeneity. Such homogeneity can be used to identify a cleavage site in a particular virus if cleavage sites for other member of the virus family have been identified.
Once a cleavage site showing a high cleavage rate is identified for certain member of a virus family, a sequence at the cleavage site can be identified in a related virus on the basis of the homogeneity of the sequences.







TABLE 7





ALINGMENT OF CLEAVAGE SITES FOR DIFFERENT


CORNA VIRUSES AND COXACIVIRUSES



































HUMAN
i
g
n
c
m
e
a
l
F
Q
G
p
l
r
y
k
d
l
k
i


COXACIVIRUS


COXA2


SED ID NO: 118


HUMAN
i
g
n
c
m
e
a
l
F
Q
G
p
i
q
y
r
d
v
m
i


COXACIVIRUS


COXA4


SED ID NO: 119


BOVINE
i
g
n
v
l
e
a
l
F
Q
G
p
v
c
y
k
p
l
r
i


ENTEROVIRUS


BOVEV


SED ID NO: 120


HUMAN
v
g
a
t
l
e
a
l
F
Q
G
p
p
i
y
r
e
i
k
i


COXACIVIRUS


COXA9


SED ID NO: 121


HUMAN
v
g
a
t
l
e
a
l
F
Q
G
p
p
i
y
r
e
i
k
i


COXACIVIRUS


COXB1


SED ID NO: 122


HUMAN
v
g
a
t
l
e
a
l
F
Q
G
p
p
i
y
r
e
i
k
i


COXACIVIRUS


COXB5


SED ID NO: 123


HUMAN
v
g
a
t
l
e
a
l
F
Q
G
p
p
i
y
r
e
i
k
i


ECHOVIRUS


EC11G


SED ID NO: 124


HUMAN
v
g
a
t
l
e
a
l
F
Q
G
p
p
v
y
r
e
i
k
i


COXACIVIRUS


COXB4


SED ID NO: 125


SWINE
v
g
a
t
l
e
a
l
F
Q
G
p
p
v
y
r
e
i
k
i


VESICULAR


DISEASE VIRUS


SVDVH


SED ID NO: 126


SWINE
v
g
a
t
l
e
a
l
F
Q
G
p
p
v
y
r
e
i
k
i


VESICULAR


DISEASE VIRUS


SVDVU


SED ID NO: 127


HUMAN
v
g
t
t
l
e
a
l
F
Q
G
p
p
v
y
r
e
i
k
i


COXACIVIRUS


COXB3


SED ID NO: 128


HUMAN
t
q
d
k
l
e
a
l
F
Q
G
p
p
t
f
k
e
i
k
i


ENTEROVIRUS


HUEV7


SED ID NO: 129


HUMAN
v
v
d
v
m
s
a
i
F
Q
G
p
i
s
l
d
a
p
p
p


RHINOVIRUS


HRV1B


SED ID NO: 130


HUMAN
v
v
d
v
m
t
a
i
F
Q
G
p
i
d
m
k
n
p
p
p


RHINOVIRUS


HRV2


SED ID NO: 131


HUMAN
a
a
q
a
m
e
a
i
F
Q
G
i
d
l
q
s
p
p
p
p


RHINOVIRUS


HRV89


SED ID NO: 132


HUMAN
i
t
d
s
l
e
t
l
F
Q
G
p
v
y
k
d
l
e
i
d


RHINOVIRUS


HRV14


SED ID NO: 133

## Claims

1. A method for determining the presence of a Nidovirus or Picornavirus virus in a sample suspected of containing said virus, the method comprising:
Contacting a sample with a substrate peptide comprising at least four amino acid residues and capable of being cleaved at a cleavage point by an enzyme to form a cleaved first peptide fragment and a second peptide fragment; and
detecting the virus by observing the signal from a signaling moiety linked to the substrate peptide;
wherein the enzyme is encoded by nucleic acid of the virus and is present in the sample;
wherein said substrate peptide comprises an amino acid sequence identical to a sequence of a polyprotein cleavage region of said enzyme and including said cleavage point;
wherein said peptide cleavage fragments are peptide fragments of the substrate peptide;
wherein a signaling moiety is linked to a portion of the peptide present in the first peptide fragment; and
wherein said method is a heterogeneous assay method.

2. The method of claim 1, wherein a quenching moiety is linked to a portion of the peptide present in the second peptide fragment and wherein the signaling moiety and the quenching moiety are linked to the peptide at relative positions such that the quenching moiety quenches the a signal of the signaling moiety unless the peptide is cleaved at the cleavage point.

3. The method of claim 1, further comprising contacting the sample with a second peptide comprising at least four amino acid residues and capable of being cleaved at a cleavage point by a second enzyme, wherein the second enzyme is encoded by the viral nucleic acid, and wherein said second peptide comprises an amino acid sequence identical to a sequence of a polyprotein cleavage region of said second enzyme and including said cleavage point.

4. The method of claim 1, wherein the enzyme is a protease.

5. The method of claim 1, wherein the signal of the signaling moiety is selected from a group consisting of a moiety emitting a fluorescent signal, a colorimetric signal, and a chemiluminescent signal.

6. The method of claim 5, wherein the signal of the signaling moiety emits a fluorescent signal.

7. The method of claim 1, wherein the virus is detected in a sample taken from an animal thought to be infected by the virus.

8. The method of claim 7, wherein the animal is human.

9. The method of claim 8, wherein the sample is selected from a group consisting of mucus, saliva, blood, serum, plasma, urine, spinal fluid, sputum, tissue biopsy, broncheoalveolar fluid, and tears.

10. The method of claim 1, wherein the virus is a Rhinovirus.

11. The method of claim 1, wherein said peptide comprises at least seven amino acid residues.

12. The method of claim 1, wherein said peptide comprises at least ten amino acid residues.