Polymerase chain reaction assays for monitoring antiviral therapy and making therapeutic decisions in the treatment of acquired immunodeficiency syndrome

• US 5,968,730 A
• Filed: 06/06/1995
• Issued: 10/19/1999
• Est. Priority Date: 05/14/1992
• Status: Expired due to Term

• Current Assignee: Leland Stanford Junior University (Stanford University)
• Original Assignee: Leland Stanford Junior University (Stanford University)
• Inventors: Holodniy, Mark, Katzenstein, David A., Merigan, Thomas C.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/470,885
• Time in Patent Office: 1,596 Days
• Field of Search: 435/5, 435/6, 435/810, 436/501, 436/63, 514/44, 536/23.1, 536/24.1, 536/24.3-33, 935/77, 935/78
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/703 Viruses associated with AIDS
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The present invention relates to methods of monitoring, via polymerase chain reaction, the clinical progression of human immunodeficiency virus infection and its response to antiretroviral therapy. According to the invention, polymerase chain reaction assays may be used to predict immunological decline and to identify, at an early stage, patients whose infection has become resistant to a particular antiretroviral drug regimen.

Claims

1. A method of evaluating the effectiveness of anti-HIV therapy of a patient comprising:

(i) collecting a plasma sample from an HIV-infected patient who is being treated with an antiretroviral agent;

(ii) amplifying the HIV-encoding nucleic acid in the plasma sample using HIV primers in about 30 cycles of PCR; and

(iii) testing for the presence of HIV-encoding nucleic acid, in the product of the PCR;

in which the absence of detectable HIV-encoding nucleic acid correlates positively with the conclusion that the antiretroviral agent is therapeutically effective.

2. The method of claim 1 in which the HIV primers are SK38 and SK39.

3. The method of claim 1 in which one HIV primer is primer NE1 (5'"'"'-TCATTGACAGTCCAGCT-3'"'"') (SEQ ID NO:

2).

4. The method of claim 1 in which one HIV primer is primer A (5'"'"'-TTCCCATTAGTCCTATT-3'"'"') (SEQ ID NO:

1).

5. The method of claim 1, 2, 3 or 4 in which the antiretroviral agent is zidovudine.

6. A method of evaluating the effectiveness of anti-HIV therapy of a patient comprising:

(i) collecting a plasma sample from an HIV-infected patient who is being treated with an antiretroviral agent;

(ii) amplifying the HIV-encoding nucleic acid in the plasma sample using HIV primers in about 30 cycles of PCR; and

(iii) testing for the presence of HIV-encoding nucleic acid in the product of the PCR;

in which the presence of detectable HIV-encoding nucleic acid correlates positively with the conclusion that the antiretroviral agent is therapeutically ineffective.

7. A method of evaluating the effectiveness of anti-HIV therapy of a patient comprising:

(i) collecting a plasma sample from an HIV-infected patient who is being treated with an antiretroviral agent;

(ii) amplifying the HIV-encoding nucleic acid in the plasma sample using HIV primers in about 30 cycles of PCR; and

(iii) testing for the presence of HIV-encoding nucleic acid in the product of the PCR;

in which the presence of detectable HIV-encoding nucleic acid correlates positively with an absolute CD4 count of less than 200 cells per cubic millimeter.

8. A method of evaluating the effectiveness of anti-HIV therapy of a patient comprising:

(i) collecting a plasma sample from an HIV-infected patient who is being treated with an antiretroviral agent;

(ii) amplifying the HIV-encoding nucleic acid in the plasma sample using HIV primers in about 30 cycles of PCR; and

(iii) testing for the presence of HIV-encoding nucleic acid sequence in the product of the PCR;

in which the absence of detectable HIV-encoding nucleic acid correlates positively with an absolute CD4 count of greater than 200 cells per cubic millimeter.

9. A method of evaluating the effectiveness of anti-HIV therapy of a patient comprising

(i) collecting a plasma sample from an HIV-infected patient who is being treated with an antiretroviral agent;

(ii) amplifying the HIV-encoding nucleic acid in the plasma sample using HIV primers in about 30 cycles of PCR; and

(iii) measuring the HIV RNA copy number using the product of the PCR, in which an HIV RNA copy number greater than about 500 per 200 ul of plasma correlates positively with the conclusion that the antiretroviral agent is therapeutically ineffective.

10. The method of claim 9 in which the HIV primers are SK38 and SK39.

11. The method of claim 9 in which one HIV primer is primer NE1 (5'"'"'-TCATTGACAGTCCAGCT-3'"'"') (SEQ ID NO:

2).

12. The method of claim 9 in which one HIV primer is primer A (5'"'"'-TTCCCATTAGTCCTATT-3'"'"') (SEQ ID NO:

1).

13. The method of claim 9, 10, 11 or 12 in which the antiretroviral agent is zidovudine.

14. A method of evaluating the effectiveness of anti-HIV therapy of a patient comprising:

(i) collecting a plasma sample from an HIV-infected patient who is being treated with an antiretroviral agent;

(ii) amplifying the HIV-encoding nucleic acid in the plasma sample using HIV primers in about 30 cycles of PCR; and

(iii) measuring the HIV RNA copy number using the product of the PCR, in which an HIV RNA copy number less than about 200 per 200 ul of plasma correlates positively with the conclusion that the anti-HIV agent is therapeutically effective.

15. The method of claim 14 in which the HIV primers are SK38 and SK39.

16. The method of claim 14 in which one HIV primer is primer NE1 (5'"'"'-TCATTGACAGTCCAGCT-3'"'"') (SEQ ID NO:

2).

17. The method of claim 14 in which one HIV primer is primer A (5'"'"'-TTCCCATTAGTCCTATT-3'"'"') (SEQ ID NO:

1).

18. The method of claim 14, 15, 16 or 17 in which the antiretroviral agent is zidovudine.

19. A method of evaluating the effectiveness of anti-HIV therapy of a patient comprising

(i) collecting one pre-treatment plasma sample from an HIV-infected patient who is about to be treated with an antiretroviral agent;

(ii) collecting a post-treatment plasma sample from the HIV-infected patient after the patient has been treated with the antiretroviral agent;

(iii) amplifying the HIV-encoding nucleic acid in the pre-treatment and post-treatment plasma samples using HIV primers in about 30 cycles of PCR;

(iv) measuring the HIV RNA copy number using the products of the PCRs of step (iii); and

(v) comparing the HIV RNA copy number in pre-treatment and post-treatment plasma samples,

in which a ratio of HIV RNA copy number in pre-treatment and post-treatment plasma samples of greater than about 4 to 1 correlates positively with the conclusion that the anti-HIV agent is therapeutically effective.

20. The method of claim 19 in which the HIV primers are SK38 and SK39.

21. The method of claim 19 in which one HIV primer is primer NE1 (5'"'"'-TCATTGACAGTCCAGCT-3'"'"') (SEQ ID NO:

2).

22. The method of claim 19 in which one HIV primer is primer A (5'"'"'-TTCCCATTAGTCCTATT-3'"'"') (SEQ ID NO:

1).

23. The method of claim 19, 20, 21 or 22 in which the antiretroviral agent is zidovudine.