Amplification and detection reagents for HIV-1

• US 20030148280A1
• Filed: 09/04/2001
• Published: 08/07/2003
• Est. Priority Date: 09/04/2001
• Status: Active Grant

• Current Assignee: Abbott Laboratories Incorporated
• Original Assignee: Abbott Laboratories Incorporated
• Inventors: Devare, Sushil G., Hackett, John R. Jr., Abravaya, Klara, Tang, Ning, Harris, Barbara J., Esping, Claudia A., Gorzowski, Jacek J., Swanson, Priscilla
• Granted Patent: US 6,852,491 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/703 Viruses associated with AIDS

Abstract

Oligonucleotide primer sets, probes, and combinations of the primer sets and probes are provided herein. These reagents are useful for amplifying and detecting HIV-1 target sequences in a test sample.

Claims

1. A primer set selected from the group consisting of:

primer set 1 (SEQ. ID. NO. 1 and SEQ. ID. NO.

     2);

primer set 2 (SEQ. ID. NO. 3 and SEQ. ID. NO.

     2);

primer set 3 (SEQ. ID. NO. 4 and SEQ. ID. NO.

     2);

primer set 4 (SEQ. ID. NO. 5 and SEQ. ID. NO.

     2);

primer set 5 (SEQ. ID. NO. 6 and SEQ. ID. NO.

     2);

primer set 6 (SEQ. ID. NO. 7 and SEQ. ID. NO.

     2);

primer set 7 (SEQ. ID. NO. 8 and SEQ. ID. NO.

     2);

primer set 8 (SEQ. ID. NO. 9 and SEQ. ID. NO.

     10);

primer set 9 (SEQ.ID. NO. 9 and SEQ.ID. NO.

     11);

primer set 10 (SEQ. ID. NO. 1 and SEQ. ID. NO.

     12);

primer set 11 (SEQ. ID. NO. 13 and SEQ. ID. NO.

     14);

primer set 12 (SEQ. ID. NO. 13 and SEQ. ID. NO.

     15);

primer set 13 (SEQ. ID. NO. 13 and SEQ. ID. NO.

     2);

primer set 14 (SEQ. ID. NO. 9 and SEQ. ID. NO.

     12);

primer set 15 (SEQ. ID. NO. 1 and SEQ. ID. NO.

     11);

primer set 16 (SEQ. ID. NO. 16 and SEQ. ID. NO.

     12);

primer set 17 (SEQ. ID. NO. 16 and SEQ. ID. NO.

     17);

primer set 18 (SEQ. ID. NO. 3 and SEQ. ID. NO.

     12);

primer set 19 (SEQ. ID. NO. 3 and SEQ. ID. NO.

     18);

primer set 20 (SEQ. ID. NO. 19 and SEQ. ID. NO.

     18);

primer set 21 (SEQ. ID. NO. 13 and SEQ. ID. NO.

     17);

primer set 22 (SEQ. ID. NO. 13 and SEQ. ID. NO.

     20);

primer set 23 (SEQ. ID. NO. 21 and SEQ. ID. NO.

     18);

primer set 24 (SEQ. ID. NO. 21 and SEQ. ID. NO.

     14);

primer set 25 (SEQ. ID. NO. 21 and SEQ. ID. NO.

     20);

primer set 26 (SEQ. ID. NO. 4 and SEQ. ID. NO.

     20);

primer set 27 (SEQ. ID. NO. 5 and SEQ. ID. NO.

     15);

primer set 28 (SEQ. ID. NO. 21 and SEQ. ID. NO.

     22);

primer set 29 (SEQ. ID. NO. 21 and SEQ. ID. NO.

     23);

primer set 30 (SEQ. ID. NO. 5 and SEQ. ID. NO.

     23);

primer set 31 (SEQ. ID. NO. 28 and SEQ. ID. NO.

     29);

primer set 32 (SEQ. ID. NO. 28 and SEQ. ID. NO.

     30);

primer set 33 (SEQ. ID. NO. 28 and SEQ. ID. NO.

     31);

primer set 38 (SEQ. ID. NO. 37 and SEQ. ID. NO.

     32);

primer set 39 (SEQ. ID. NO. 37 and SEQ. ID. NO.

     33);

primer set 40 (SEQ. ID. NO. 38 and SEQ. ID. NO.

     29);

primer set 41 (SEQ. ID. NO. 38 and SEQ. ID. NO.

     30);

primer set 42 (SEQ. ID. NO. 4 and SEQ. ID. NO.

     22);

primer set 43 (SEQ. ID. NO. 4 and SEQ. ID. NO.

     40);

primer set 44 (SEQ. ID. NO. 34 and SEQ. ID. NO.

     22);

primer set 45 (SEQ. ID. NO. 34 and SEQ. ID. NO.

     40);

primer set 46 (SEQ. ID. NO. 24 and SEQ. ID. NO.

     25); and

primer set 47 (SEQ. ID. NO. 26 and SEQ. ID. NO.

     27).

4. A method for amplifying an HIV-1 target sequence comprising the steps of:

a) contacting a test sample with amplification reagents and a primer set of claim 1 to form a reaction mixture; and

b) placing the reaction mixture under amplification conditions to amplify the HIV-1 target sequence.

5. The method of claim 4 further comprising the step of detecting the amplified HIV-1 target sequence.

8. A kit for amplifying HIV-1 comprising:

(a) a primer set of claim 1;

and

(b) amplification reagents.

2. An oligonucleotide set for comprising a primer set and detection probe, wherein the oligonucleotide set is selected from the group consisting of:

oligo set 1 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     41);

oligo set 2 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     42);

oligo set 3 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     43);

oligo set 4 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     44);

oligo set 5 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     45);

oligo set 7 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     47);

oligo set 8 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     48);

oligo set 9 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     49);

oligo set 10 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     50);

oligo set 11 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     51);

oligo set 12 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     52);

oligo set 13 (SEQ. ID. NO. 28, SEQ. ID. NO. 29, and SEQ. ID. NO.

     53);

oligo set 14 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     41);

oligo set 15 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     42);

oligo set 16 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     43);

oligo set 17 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     44);

oligo set 18 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     45);

oligo set 20 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     47);

oligo set 21 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     48);

oligo set 22 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     49);

oligo set 23 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     50);

oligo set 24 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     51);

oligo set 25 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     52);

oligo set 26 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     53);

oligo set 27 (SEQ. ID. NO. 28, SEQ. ID. NO. 31, and SEQ. ID. NO.

     41);

oligo set 28 (SEQ. ID. NO. 28, SEQ. ID. NO. 31, and SEQ. ID. NO.

     42);

oligo set 29 (SEQ. ID. NO. 28, SEQ. ID. NO. 31, and SEQ. ID. NO.

     43);

oligo set 30 (SEQ. ID. NO. 28, SEQ. ID. NO. 31, and SEQ. ID. NO.

     44);

oligo set 31 (SEQ. ID. NO. 28, SEQ. ID. NO. 31, and SEQ. ID. NO.

     45);

oligo set 33 (SEQ. ID. NO. 28, SEQ. ID. NO. 31, and SEQ. ID. NO.

     47);

oligo set 34 (SEQ. ID. NO. 28, SEQ. ID. NO. 31, and SEQ. ID. NO.

     48);

oligo set 35 (SEQ. ID. NO. 37, SEQ. ID. NO. 32, and SEQ. ID. NO.

     55);

oligo set 36 (SEQ. ID. NO. 37, SEQ. ID. NO. 33, and SEQ. ID. NO.

     55);

oligo set 38 (SEQ. ID. NO. 37, SEQ. ID. NO. 33, and SEQ. ID. NO.

     57);

oligo set 39 (SEQ. ID. NO. 38, SEQ. ID. NO. 29, and SEQ. ID. NO.

     50);

oligo set 40 (SEQ. ID. NO. 38 , SEQ. ID. NO. 29, and SEQ. ID. NO.

     51);

oligo set 41 (SEQ. ID. NO. 38, SEQ. ID. NO. 29, and SEQ. ID. NO.

     52);

oligo set 42 (SEQ. ID. NO. 38, SEQ. ID. NO. 29, and SEQ. ID. NO.

     53);

oligo set 43 (SEQ. ID. NO. 38, SEQ. ID. NO. 30, and SEQ. ID. NO.

     50);

oligo set 44 (SEQ. ID. NO. 38, SEQ. ID. NO. 30, and SEQ. ID. NO.

     51);

oligo set 45 (SEQ. ID. NO. 38, SEQ. ID. NO. 30, and SEQ. ID. NO.

     52);

oligo set 46 (SEQ. ID. NO. 38, SEQ. ID. NO. 30, and SEQ. ID. NO.

     53);

oligo set 47 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     58);

oligo set 48 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     59);

oligo set 49 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     60);

oligo set 50 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     61);

oligo set 51 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     62);

oligo set 52 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     63);

oligo set 53 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     64); and

oligo set 54 (SEQ. ID. NO. 28, SEQ. ID. NO. 30, and SEQ. ID. NO.

     65).

6. A method for detecting the presence of HIV-1 in a test sample comprising:

a) contacting a test sample with amplification reagents and an oligonucleotide set of claim 2 to form a reaction mixture;

b) placing the reaction mixture under amplification conditions to form an amplification product;

c) forming an amplification product/probe hybrid; and

d) detecting the hybrid as an indication of the presence of HIV-1 in the test sample.

7. The method of claim 6 wherein the amplification product/probe hybrid is formed while the reaction mixture is under amplification conditions.

9. A kit for detecting HIV-1 comprising:

(a) an oligonucleotide set of claim 2;

and

(b) amplification reagents.

3. A probe selected from the group consisting of:

SEQ. ID. NO. 41;

SEQ. ID. NO. 42;

SEQ. ID. NO. 43;

SEQ. ID. NO. 44;

SEQ. ID. NO. 45;

SEQ. ID. NO. 47;

SEQ. ID. NO. 48;

SEQ. ID. NO. 49;

SEQ. ID. NO. 50;

SEQ. ID. NO. 51;

SEQ. ID. NO. 52;

SEQ. ID. NO. 53;

SEQ. ID. NO. 55;

SEQ. ID. NO. 57;

SEQ. ID. NO. 58;

SEQ. ID. NO. 59;

SEQ. ID. NO. 60;

SEQ. ID. NO. 61;

SEQ. ID. NO. 62;

SEQ. ID. NO. 63;

SEQ. ID. NO. 64; and

SEQ. ID. NO. 65.