Nucleic Acid Sequences That Can Be Used as Primers and Probes in the Amplification and Detection of All Subtypes of HIV-1

• US 20140199687A1
• Filed: 03/27/2014
• Published: 07/17/2014
• Est. Priority Date: 08/08/1997
• Status: Active Grant

• Current Assignee: Biomerieux Incorporated (Compagnie Merieux Alliance SAS)
• Original Assignee: Biomerieux SA (Compagnie Merieux Alliance SAS)
• Inventors: Goudsmit, Jaap, Oudshoorn, Pieter, Jurriaans, Suzanne, Lukashov, Vladimir Vladimirovich
• Granted Patent: US 9,074,262 B2
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 1/703 Viruses associated with AIDS
• CPC Class Codes: Y10S 435/81 Packaged device or kit

Abstract

The present invention is related to nucleic acid sequences that can be used in the field of virus diagnostics, more specifically the diagnosis of infections with the AIDS causing Human Immuno-deficiency Virus (HIV). With the present invention nucleotide sequences are provided that can be used as primers and probes in the amplification and detection of HIV-1 nucleic acid. The oligonucleotide sequences provided with the present invention are located in the LTR part of the HIV viral genome. It has been found that, by using the sequences of the present invention in methods for the amplification and detection of nucleic acid a sensitive and specific detection of HIV-1 can be obtained. The benefit of the sequences of the present invention primarily resides in the fact that, with the aid of primers and probes comprising the sequences according to the invention the nucleic acid of all presently known subtypes of HIV-1 can be detected with high accuracy and sensitivity. So far no primer pairs or hybridization probes have been developed that would allow the detection of such a broad range of HIV-1 variants. The oligonucleotide sequences according to the present invention are especially useful in methods for the amplification of nucleic acid.

Claims

1-20. -20. (canceled)

21. A method for the detection of HIV-1 nucleic acid in a sample, comprising:

a) contacting the sample with a pair of oligonucleotide primers under conditions whereby nucleic acid amplification can occur; and

b) detecting the presence of amplified HIV-1 nucleic acid, thereby detecting HIV-1 nucleic acid in the sample;

wherein said pair of oligonucleotide primers consists of a first primer and a second primer,

wherein said first primer consists essentially of a first oligonucleotide that is fully complementary to a sequence of the LTR region at a first primer binding site and binds thereto under conditions whereby nucleic acid amplification can occur, said oligonucleotide being 15-26 nucleotides in length and comprising at least 15 sequential nucleotides of the nucleotide sequence of;

22. The method of claim 21, wherein said second oligonucleotide that is fully complementary to a sequence of the LTR region is 15-26 nucleotides in length and comprises at least 15 sequential nucleotides of the nucleotide sequence of:

23. The method of claim 21, wherein said first oligonucleotide comprises the nucleotide sequence of:

24. The method of claim 21, wherein detecting the presence of amplified HIV-1 nucleic acid comprises contacting the sample with one or more probe oligonucleotides selected from:

25. The method of claim 21, wherein said promoter is a T3, T7, or SP6 promoter.

26. A method for the detection of HIV-1 nucleic acid in a sample, comprising:

a) contacting the sample with a primer set under conditions whereby nucleic acid amplification can occur; and

b) detecting the presence of amplified HIV-1 nucleic acid, thereby detecting HIV-1 nucleic acid in the sample;

wherein said primer set consists of a first primer and a second primer,

wherein said first primer consists essentially of a first hybridizing oligonucleotide that is fully complementary to a sequence of the LTR region at a first primer binding site and binds thereto under conditions whereby nucleic acid amplification can occur, said oligonucleotide being 15-26 nucleotides in length and comprising at least 15 sequential nucleotides of the nucleotide sequence of;

27. The method of claim 26, wherein said second oligonucleotide that is fully complementary to a sequence of the LTR region is 15-26 nucleotides in length and comprises at least 15 sequential nucleotides of the nucleotide sequence of:

28. The method of claim 26, wherein said first oligonucleotide comprises the nucleotide sequence of:

29. The method of claim 26, wherein detecting the presence of amplified HIV-1 nucleic acid comprises contacting the sample with one or more probe oligonucleotides selected from:

30. The method of claim 26, wherein said promoter is a T3, T7, or SP6 promoter.

31. A method for the detection of HIV-1 nucleic acid in a sample, comprising:

a) contacting the sample with a pair of oligonucleotide primers under conditions whereby nucleic acid amplification can occur; and

b) detecting the presence of amplified HIV-1 nucleic acid, thereby detecting HIV-1 nucleic acid in the sample;

wherein said pair of oligonucleotide primers consists of a first primer and a second primer,

wherein said first primer consists essentially of a first hybridizing oligonucleotide that is fully complementary to a sequence of the LTR region at a first primer binding site and binds thereto under conditions whereby nucleic acid amplification can occur, said oligonucleotide being 15-26 nucleotides in length, wherein said first hybridizing oligonucleotide comprises at least 15 sequential nucleotides of the nucleotide sequence of;

32. The method of claim 31, wherein said second oligonucleotide that is fully complementary to a sequence of the LTR region is 15-26 nucleotides in length and comprises at least 15 sequential nucleotides of the nucleotide sequence of:

33. The method of claim 31, wherein said first oligonucleotide comprises the nucleotide sequence of:

34. The method of claim 31, wherein detecting the presence of amplified HIV-1 nucleic acid comprises contacting the sample with one or more probe oligonucleotides selected from:

35. The method of claim 31, wherein said promoter is a T3, T7, or SP6 promoter.