Compositions and methods for determining resistance to inhibitors of virus entry using recombinant virus assays

1. A method for treating a patient with a virus entry inhibitor, comprising:

(a) obtaining or having obtained a biological sample from a patient comprising a population of human immunodeficiency virus (HIV) viral particles;

(b) contacting or having contacted a plurality of HIV viral particles from the population with a cell in the presence of varying concentrations of an entry inhibitor, wherein the cell expresses a cell surface receptor to which the HIV viral particles bind, and wherein the cell or HIV viral particle comprises an indicator nucleic acid that produces a detectable signal when the HIV viral particle enters into the cell;

(c) collecting or having collected data points that measure entry of the HIV population into the cell by measuring the detectable signal produced by the cell in the presence of varying concentrations of the virus entry inhibitor;

(d) generating or having generated a log-sigmoid inhibition curve with the collected data points;

(e) determining or having determined a baseline susceptibility value to the virus entry inhibitor for the HIV population as measured by a maximum inhibition percentage or ability to completely inhibit the HIV population;

(f) comparing or having compared the baseline susceptibility value of step (e) with a baseline susceptibility value for a reference population of HIV viral particles, wherein a baseline susceptibility value of step (e) that is equal to or higher 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; and

(g) treating the patient with the virus entry inhibitor if the baseline susceptibility value of step (e) that is equal to or higher than the baseline susceptibility value for the reference HIV population.

2. The method of claim 1 , wherein the virus entry inhibitor is SCH-C, SCH-D, UK-427857, SDFIa/b, AMD3100, TNX-355, T-20.

3. The method of claim 1 , wherein the reference HIV population is an HXB2, NL4-3, or SF2 HIV population.

4. The method of claim 1 , wherein each of the plurality of HIV viral particles comprise:

(i) a viral expression vector that lacks a nucleic acid encoding a viral envelope protein, but which comprises an indicator nucleic acid that produces a detectable signal when introduced into the cell, and

(ii) a viral envelope protein encoded by a nucleic acid of the HIV population.

5. The method of claim 1 , wherein each of the HIV viral particles comprises the same viral envelope protein.

6. The method of claim 1 , wherein the indicator nucleic acid encodes luciferase.

7. The method of claim 1 , wherein the plurality of viral particles are produced by co-transfecting into a cell (i) a plurality of nucleic acids each encoding a viral envelope protein of the HIV population, and (ii) a viral expression vector lacking a nucleic acid encoding an envelope protein, wherein the vector comprises an indicator nucleic acid that produces a detectable signal.

8. The method of claim 1 , wherein the cell surface receptor is at least one of CD4, CXCR4, and CCR5.

9. The method of claim 1 , wherein the HIV nucleic acid encodes the surface envelope glycoprotein (gp120), the transmembrane envelope glycoprotein (gp41), the envelope polyprotein (gp16), or both gp120 and gp41.

10. A method for treating a patient having an HIV population, comprising:

(a) contacting or having contacted a plurality of HIV viral particles from the HIV population 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 or having collected 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 or having generated a log-sigmoid inhibition curve comprising the data points showing the maximum inhibition percentage for the HIV population;

(d) comparing or having compared 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;

(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; and

(f) treating the patient with an effective amount of an inhibitor other than 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.

11. The method of claim 10 , wherein the reference HIV population is an HXB2, NL4-3, or SF2 population.

12. The method of claim 10 , wherein the HIV population is from a subject infected with HIV.

13. The method of claim 10 , wherein each of the plurality of viral particles comprises: (i) a viral expression vector that lacks a nucleic acid encoding a viral envelope protein, but which comprises an indicator nucleic acid that produces a detectable signal when introduced into the cell, and (ii) a viral envelope protein encoded by a nucleic acid of the HIV population.

14. The method of claim 10 , wherein the indicator nucleic acid encodes luciferase.

15. The method of claim 10 , wherein the plurality of viral particles are produced by co-transfecting into a cell: (i) a plurality of nucleic acids, each encoding a viral envelope protein of the HIV population, and (ii) a viral expression vector lacking a nucleic acid encoding an envelope protein, wherein the vector comprises an indicator nucleic acid that produces a detectable signal.

16. The method of claim 10 , wherein the cell surface receptor is at least one of CD4, CXCR4, and CCR5.

17. The method of claim 10 , wherein the HIV viral particle comprises gp160, or both gp120 and gp41.

18. The method of claim 10 , wherein the cell comprises the indicator nucleic acid that produces a detectable signal when the viral particles enter into the cell.

19. The method of claim 1 , wherein the entry inhibitor is an antibody.

20. The method of claim 19 , wherein the antibody binds to the HIV envelope surface glycoprotein (gp120).

21. The method of claim 19 , wherein the antibody binds to the CD4 binding site or the variable region 3 (V3) of the envelope surface glycoprotein.

22. The method of claim 19 , wherein the antibody binds to the HIV envelope transmembrane glycoprotein (gp41).

23. The method of claim 22 , wherein the antibody binds to the membrane proximal external region (MPER) of the HIV envelope transmembrane glycoprotein.

24. The method of claim 10 , wherein the entry inhibitor is an antibody.

25. The method of claim 24 , wherein the antibody binds to the HIV envelope surface glycoprotein (gp120).

26. The method of claim 25 , wherein the antibody binds to the CD4 binding site or the variable region 3 (V3) of the HIV envelope surface glycoprotein.

27. The method of claim 24 , wherein the antibody binds to the HIV envelope transmembrane glycoprotein (gp41).

28. The method of claim 27 , wherein the antibody binds to the membrane proximal external region (MPER) of the HIV envelope transmembrane glycoprotein.

29. The method of claim 1 , wherein the cell comprises the indicator nucleic acid that produces a detectable signal when the viral particles enter into the cell.