Compositions And Methods For Determining Resistance To Inhibitors Of Virus Entry Using Recombinant Virus Assays

A method for assessing a potential course of treatment with a virus entry inhibitor for a patient, comprising:

• (a) obtaining a biological sample from a patient comprising a population of human immunodeficiency virus (HIV) viral particles;
• (b) collecting data points that measure entry of the HIV population into a cell in the presence of varying concentrations of a virus entry inhibitor;
• (c) generating a log-sigmoid inhibition curve with the collected data points;
• (d) determining a baseline susceptibility value to the virus entry inhibitor for the HIV population;
• and
• (e) comparing the baseline susceptibility value of step (d) with a baseline susceptibility value for a reference population of HIV viral particles, wherein a baseline susceptibility value of step (d) that is equal to or lower than the baseline susceptibility value for the reference HIV population indicates that the potential course of treatment with the virus entry inhibitor is likely to be effective for the patient.

A method for determining whether an HIV population is resistant to an HIV entry inhibitor, comprising:

• (a) contacting a plurality of HIV viral particles with a cell in the presence of an HIV entry inhibitor, wherein the HIV entry inhibitor is an antibody or fragment thereof, wherein the cell expresses a cell surface receptor to which the viral particles bind, and wherein the cell or the viral particle comprises an indicator nucleic acid that produces a detectable signal when the viral particle enters into the cell,
• (b) collecting data points that measure entry of the HIV population into the cell by measuring the amount of the detectable signal produced by the cell in the presence of varying concentrations of the HIV entry inhibitor;
• (c) generating a log-sigmoid inhibition curve comprising the data points showing the maximum inhibition percentage for the HIV population;
• (d) comparing the maximum inhibition percentage of the inhibition curve of step (c) to the maximum inhibition percentage of a log-sigmoid inhibition curve for a reference HIV population;
• and
• (e) determining that the HIV population has reduced susceptibility to the HIV entry inhibitor if the maximum inhibition percentage observed for the HIV population is lower than the maximum inhibition percentage observed for the reference HIV population or if the entry of the HIV population cannot be completely inhibited by the HIV entry inhibitor.

A method for detecting mutations of a virus that are correlated with reduced susceptibility to a virus entry inhibitor, comprising:

• (a) obtaining individual biological samples from a subject at a plurality of different time points during infection, the samples each comprising virus molecules;
• (b) cloning a plurality of nucleic acid molecules, each comprising a gene that encodes an envelope protein for one of the virus molecules in the sample of step (a);
• (c) transfecting into a first cell:
• (i) a nucleic acid comprising one of the cloned envelope protein genes of step (b);
• and (ii) a viral expression vector which lacks the viral envelope protein gene, such that a population of identical pseudoviruses are produced by the first cell, and optionally, contacting the pseudoviruses produced by the first cell with a virus entry inhibitor;
• (d) contacting the pseudoviruses of step (c) with a second cell, wherein the second cell expresses a cell surface receptor to which the virus binds;
• (e) measuring the ability of the pseudoviruses to infect the second cell;
• (f) comparing the infectivity of the pseudoviruses of step (e) when the pseudoviruses have been exposed to the virus entry inhibitor as compared to when the pseudoviruses have not been exposed to the virus entry inhibitor, wherein a partial decrease, no change, or an increase in infectivity for the pseudoviruses exposed to the virus entry inhibitor indicates that the pseudoviruses have reduced susceptibility to the virus entry inhibitor;
• and
• (g) determining the nucleic acid sequence of at least some of the pseudoviruses of step (f) to determine whether a mutation or mutations in the gene encoding the envelope protein is correlated with the reduced susceptibility to the virus entry inhibitor.