Compositions and methods for evaluating viral receptor/co-receptor usage and inhibitors of virus entry using recombinant virus assays

Abstract

The present invention provides a method for identifying whether a compound inhibits entry of a virus into a cell which comprises: (a) obtaining nucleic acid encoding a viral envelope protein from a patient infected by the virus; (b) co-transfecting into a first cell (i) the nucleic add of step (a), and (ii) a viral expression vector which lacks a nucleic acid encoding an envelope protein, and which comprises an indicator nucleic acid which produces a detectable signal, such that the first cell produces viral particles comprising the envelope protein encoded by the nucleic acid obtained from the patient; (c) contacting the viral particles produced in step (b) with a second cell in the presence of the compound, wherein the second cell expresses a cell surface receptor to which the virus binds; (d) measuring the amount of signal produced by the second cell in order to determine the infectivity of the viral particles; and (e) comparing the amount of signal measured in step (d) with the amount of signal produced in the absence of the compound, wherein a reduced amount of signal measured in the presence of the compound indicates that the compound inhibits entry of the virus into the second cell.

1 . A method for detecting within a patient infested by a virus the development of an antibody response capable of blocking infection comprising: 
 (a) contacting a host cell with an antibody preparation from the patient, wherein the host cell comprises a nucleic acid encoding a viral protean from the patient and an indicator nucleic acid which produces a detectable signal;    (b) measuring the amount of the detectable signal produced by the host cell; and    (c) comparing the amount of signal measured in step (b) with the amount of signal produced in the absence of the antibody preparation, wherein a reduced amount of signal measured in the presence of the antibody preparation indicates that the patient has developed an antibody response to the viral protein capable of blocking infection.    
     
     
         2 . A method for detecting within a patient infected by a virus the development of an antibody response capable of blocking infection comprising: 
 (a) transfecting into a first cell 
 i) a nucleic acid encoding a viral protein from the patient, and  
 ii) a viral expression vector which lacks a nucleic acid encoding the viral protein, and which comprises an indicator nucleic acid which produces a detectable signal,  
    such that the first cell produces viral particles comprising the viral protein encoded by the nucleic acid obtained from the patient;    (b) contacting the viral particles produced in step (a) with an antibody preparation from the patient;    (c) contacting the viral particles and antibody preparation of step (b) with a second cell, wherein the second cell expresses a cell surface receptor to which the virus binds;    (d) measuring the amount of the detectable signal produced by the second cell in order to determine the infectivity of the viral particles; and    (e) comparing the amount of signal measured in step (d) with the amount of signal produced in the absence of the antibody preparation, wherein a reduced amount of signal measured in the presence of the antibody preparation indicates that the patient has developed an antibody response to the viral protein capable of blocking infection.    
     
     
         3 . A method for detecting within a patient infected by a virus the development of an antibody response capable of blocking infection comprising: 
 (a) transfecting into a first cell 
 i) a nucleic acid encoding a viral protein from the patient, and  
 ii) a viral expression vector which lacks a nucleic acid encoding the viral protein,  
    such that the first cell produces viral particles comprising the viral protein encoded by the nucleic acid obtained from the patient;    (b) contacting the viral particles produced in step (a) with an antibody preparation from the patient;    (c) contacting the viral particles and antibody preparation of step (b) with a second cell, wherein the second cell expresses a cell surface receptor to which the virus binds and wherein the second cell comprises an indicator nucleic acid which produces a detectable signal;    (d) measuring the amount of the detectable signal produced by the second cell in order to determine the infectivity of the viral particles; and    (e) comparing the amount of signal measured in step (d) with the amount of signal produced in the absence of the antibody preparation, wherein a reduced amount of signal measured in the presence of the antibody preparation indicates that the patient has developed an antibody response to the viral protein capable of blocking infection.    
     
     
         4 . The method of  claim 1 ,  2  or  3 , wherein the viral protein is an envelope protein.  
     
     
         5 . The method of  claim 1 ,  2  or  3 , wherein the viral protein is a capsid protein.  
     
     
         6 . A method for detecting within a patient infected by a virus the development of an antibody response capable of blocking infection comprising: 
 (a) incubating a first cell comprising 
 (i) a nucleic acid encoding a viral protein from the patient, and  
 (ii) a viral expression vector which lacks a nucleic acid encoding the viral protein, and which comprises an indicator nucleic acid which produces a detectable signal,  
    such that the first cell produces viral particles comprising the viral protein encoded by the nucleic acid obtained from the patient;    (b) contacting the viral particles produced in step (a) with an antibody preparation from the patient;    (c) contacting the viral particles and antibody preparation of step (b) with a second cell, wherein the second cell expresses a cell surface receptor to which the virus binds;    (d) measuring the amount of the detectable signal produced by the second cell in order to determine the infectivity of the viral particles; and    (e) comparing the amount of signal measured in step (d) with the amount of signal produced in the absence of the antibody prep on, wherein a reduced amount of signal measured in the presence of the antibody preparation indicates that the patient has developed an antibody response to the viral protein capable of blocking infection.    
     
     
         7 . The method of  claim 6  wherein the nucleic acid of (i) is part of the viral expression vector of (ii).  
     
     
         8 . The method of  claim 6  wherein the nucleic acid of (i) is integrated into the genome of the first cell.  
     
     
         9 . The method of  claim 6  wherein the viral vector of (ii) is integrated into the genome of the fast cell.  
     
     
         10 . The method of  claim 6  wherein the nucleic acid of (i) and the viral vector of (ii) a integrated into the genome of the first cell.  
     
     
         11 . The method of  claim 6  wherein the viral protein is a capsid protein.  
     
     
         12 . The method of  claim 6  wherein the viral protein is an envelope protein.  
     
     
         13 . The method of  claim 12  wherein the nucleic acid of (i) is part of the viral expression vector of (ii).  
     
     
         14 . The method of  claim 12  wherein the nucleic acid of (i) is integrated into the genome of the first cell.  
     
     
         15 . The method of  claim 12  wherein the viral vector of (ii) is integrated into the genome of the first cell.  
     
     
         16 . The method of  claim 12  wherein the nucleic acid of (i) and the viral vector of (ii) are integrated into the genome of the first cell.