Reference clones and sequences for non-subtype B isolates of human immunodeficiency virus type 1

• US 20050221301A1
• Filed: 05/23/2005
• Published: 10/06/2005
• Est. Priority Date: 11/02/1998
• Status: Active Grant

• Current Assignee: UAB Research Foundation (University of Alabama System)
• Original Assignee: UAB Research Foundation (University of Alabama System)
• Inventors: Gao, Feng, Hahn, Beatrice H., Shaw, George M.
• Granted Patent: US 7,169,396 B2
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: A61K 2800/524 Preservatives
• CPC Class Codes: A61K 8/22 Peroxides; Oxygen; Ozone
• CPC Class Codes: A61K 8/602 Glycosides, e.g. rutin
• CPC Class Codes: A61K 8/66 Enzymes
• CPC Class Codes: A61Q 11/00 Preparations for care of the teeth, of the oral cavity or of dentures; Dentifrices, e.g. toothpastes; Mouth rinses
• CPC Class Codes: A61Q 17/005 Antimicrobial preparations
• CPC Class Codes: A61Q 19/00 Preparations for care of the skin
• CPC Class Codes: A61Q 5/00 Preparations for care of the hair
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C09D 5/025 Preservatives, e.g. antimicrobial agents
• CPC Class Codes: C09D 5/14 Paints containing biocides, e.g. fungicides, insecticides or pesticides C09D5/16 takes precedence
• CPC Class Codes: C11D 3/0078 Compositions for cleaning contact lenses, spectacles or lenses
• CPC Class Codes: C11D 3/2034 aromatic
• CPC Class Codes: C11D 3/38654 containing oxidase or reductase
• CPC Class Codes: C11D 3/48 Medical, disinfecting agents, disinfecting, antibacterial, germicidal or antimicrobial compositions
• CPC Class Codes: C12N 2740/16021 Viruses as such, e.g. new isolates, mutants or their genomic sequences
• CPC Class Codes: C12N 2740/16122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 2740/16222 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 2740/16322 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12Q 1/703 : Viruses associated with AIDS

Abstract

The nucleotide sequences of the genomes of eleven molecular clones for non-subtype B isolates of human immunodeficiency virus type 1 are disclosed. The invention relates to the nucleic acids and peptides encoded by and/or derived from these sequences and their use in diagnostic methods and as immunogens.

Claims

1. A nucleic acid comprising the nucleotide sequence of the genome of a non-subtype B HIV-1 virus, wherein said nucleotide sequence is selected from sequences having SEQ ID NOS:

1 to 11 or a complementary sequence thereof.

2. The nucleic acid of claim 1, wherein said nucleic acid comprises a nucleotide sequence of at least 12 contiguous bases of said nucleic acid or a complementary sequence thereof.

3. The nucleic acid of claim 1, wherein said nucleic acid comprises a nucleotide sequence of a LTR of said nucleic acid or a complementary sequence thereof.

4. The nucleic acid of claim 1, wherein said nucleic acid encodes a polypeptide selected from the group consisting of Gag, Pol, Vif, Vpr, Env, Tat, Rev, Nef and Vpu, wherein the nucleic acid is from the genome of a non-subtype B HIV-1 virus selected from the group consisting of 92RW009.6, 92NG003.1, 92NG083.2, 93BR020.1, 93BR029.4, 90CF056.1, 94CY032.3, 94CY017.41, 96ZM651.8, 96ZM751.3, and 941N476.104 or a complementary sequence thereof.

5. A vector comprising a nucleic acid of claim 1.

6. A cell comprising a nucleic acid of claim 1.

7. A cell comprising the vector of claim 5.

8. A polypeptide encoded by a nucleic acid of claim 1.

9. The polypeptide of claim 8 comprising a contiguous sequence of at least 13 amino acids.

10. A method for producing a polypeptide of claim 8, comprising the step of growing a cell under conditions such that the encoded polypeptide is produced, said cell comprising the nucleic acid of the polypeptide of claim 8.

11. A method for producing a polypeptide of claim 8, comprising the step of growing a cell under conditions such that the encoded polypeptide is produced, said cell comprising a vector having the nucleic acid of the polypeptide of claim 8.

12. A method of inducing serum antibodies that bind at least one polypeptide of claim 8, comprising the step of administering to a mammal, in a physiologically acceptable carrier, an amount of polypeptide of claim 8 sufficient to elicit production of said antibodies.

13. A method for detecting the presence of antibodies to a non-subtype B HIV-1 virus in a sample comprising the step of contacting said sample with said polypeptide of claim 8 under conditions that allow the formation of an antibody-antigen complex and detecting the complex.

14. An antibody to a non-subtype B HIV-1 virus, said antibody binding at least one polypeptide of claim 8, wherein said antibody is made by administering to a mammal an amount of said polypeptide in a physiological carrier sufficient to elicit production of said antibody.

15. A composition comprising the antibody of claim 14, and a physiologically acceptable carrier.

16. A method for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the step of contacting said sample with the antibody of claim 14 under conditions that allow the formation of an antibody-antigen complex and detecting said complex.

17. A kit for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the antibody of claim 14.

18. A method of inducing serum antibodies that bind at least one polypeptide of claim 8, comprising the step of administering to a mammal, in a physiologically acceptable carrier, the nucleic acid which encodes said polypeptide(s) and which produces an immunologically sufficient amount of the encoded polypeptide to elicit said antibodies.

19. An antibody to a non-subtype B HIV-1 virus, said antibody binding at least one polypeptide of claim 8, wherein said antibody is made by administering to a mammal the nucleic acid encoding said polypeptide(s) in a physiologically acceptable carrier, wherein said nucleic acid produces an immunologically sufficient amount of the encoded polypeptide(s) to elicit said antibody.

20. A composition comprising the antibody of claim 19, and a physiologically acceptable carrier.

21. A method for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the step of contacting said sample with an antibody of claim 19 under conditions that allow the formation of an antibody-antigen complex and detecting said complex.

22. A kit for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the antibody of claim 19.

23. A method for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the steps of:

contacting said sample with a nucleic of claim 1;

and

detecting said nucleic acid bound to the genomic DNA, mRNA or cDNA of the non-subtype B HIV-1 virus.

24. A nucleic acid probe comprising a sequence of at least 19 contiguous nucleotides of a nucleic acid of claim 1.

25. A method of detecting the presence of a non-subtype B HIV-1 virus in a biological sample comprising the steps of:

contacting the nucleic acid of the biological sample with the nucleic acid probe of claim 24;

and

detecting the presence or absence of complexes formed between said nucleic acid of the biological sample and said nucleic acid probe.

26. A method of detecting the presence of a non-subtype B HIV-1 virus in a biological sample comprising the steps of:

contacting said biological sample with at least two nucleic acid probes of claim 24;

amplifying the RNA of the biological sample via reverse transcription-polymerase chain reaction to produce amplification products; and

detecting the presence or absence of amplification products.

27. A composition comprising the nucleic acid probe of claim 24.

28. A method for analyzing a first nucleotide sequence comprising comparing the nucleotide sequence of any one of the nucleotide sequences having SEQ ID NOS:

1 to 11 with said first sequence.

29. A method for analyzing a first amino acid sequence comprising comparing the amino acid sequence of any one of the amino acid sequences having SEQ ID NOS:

172 to 270 with said first sequence.