HIV-1 genotyping and coreceptor tropism assay

1. A method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance and HIV tropism, comprising:

generating a plurality of cDNA species from a plurality of RNA molecules in an HIV sample population,

clonally amplifying a plurality of first amplicons and second amplicons from the cDNA species, wherein the first amplicons are amplified using first pairs of primers that amplify a HIV genomic region of the cDNA species encoding the Gag proteins p2, p7, p1 and p6, and the protease, reverse transcriptase, and integrase enzymes and the second amplicons are amplified using second pairs of primers that amplify a HIV genomic encoding region of the cDNA species encoding the env-C2V3 region;

determining the nucleic acid sequence compositions of the clonally amplified first amplicons and second amplicons;

selecting a guide sequence with minimal divergence from the determined nucleic acid sequence compositions for mapping variants of the determined nucleic acid sequence compositions by comparing the determined nucleic acid sequence compositions to reference sequences;

identifying variants occurring at least 1% in the determined nucleic acid sequence compositions by comparing the determined nucleic acid sequence compositions to the guide sequence; and

correlating the determined variants with variants of HIV drug resistance and HIV tropism.

2. The method of claim 1 , wherein the first amplicons include first and second overlapping fragments corresponding to the genomic region encoding p2 to 5′ region of reverse transcriptase enzyme and the genomic region encoding 3′ region of reverse transcriptase enzyme to integrase enzyme.

3. The method of claim 1 , wherein the variation associated with HIV tropism is known to be associated with a coreceptor.

4. The method of claim 3 , wherein the coreceptor is known to be associated with CCR5 and CXCR4.

5. The method of claim 1 , wherein the variation associated with HIV drug resistance is known to be associated with a particular drug class or drug.

6. The method of claim 5 , wherein the HIV drug class is selected from the group consisting of protease inhibitors, integrase inhibitors, nucleotide/nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, and maturation inhibitors.

7. The method of claim 1 , wherein the HIV sample population is derived from a single patient.

8. The method of claim 7 , wherein the single patient is drug naive.

9. The method of claim 7 , wherein the single patient was previously exposed to HIV anti-retroviral drug therapy.

10. The method of claim 1 , further comprising administering an HIV drug based on the determined HIV drug resistance and HIV tropism.

11. A method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance and HIV tropism, comprising:

generating a plurality of cDNA species from a plurality of RNA molecules in an HIV sample population,

clonally amplifying a plurality of first amplicons and second amplicons from the cDNA species, wherein the first amplicons are amplified using first pairs of primers that amplify a HIV genomic region of the cDNA species encoding the Gag proteins p2, p7, p1 and p6, and the protease, reverse transcriptase, and integrase enzymes and the second amplicons are amplified using second pairs of primers that amplify a HIV genomic encoding region of the cDNA species encoding the env-C2V3 region, wherein the first amplicons include first and second overlapping fragments corresponding to the genomic region encoding p2 to 5′ region of reverse transcriptase enzyme and the genomic region encoding 3′ region of reverse transcriptase enzyme to integrase enzyme;

determining the nucleic acid sequence compositions of the clonally amplified first amplicons and second amplicons;

selecting a guide sequence with minimal divergence from the determined nucleic acid sequence compositions for mapping variants of the determined nucleic acid sequence compositions by comparing the determined nucleic acid sequence compositions to reference sequences;

identifying variants occurring at least 1% in the determined nucleic acid sequence compositions by comparing the determined nucleic acid sequence compositions to the guide sequence; and

correlating the determined variants with variants of HIV drug resistance and HIV tropism.

12. The method of claim 11 , wherein the variation associated with HIV tropism is known to be associated with a coreceptor.

13. The method of claim 12 , wherein the coreceptor is known to be associated with CCR5 and CXCR4.

14. The method of claim 11 , wherein the variation associated with HIV drug resistance is known to be associated with a particular drug class or drug.

15. The method of claim 11 , wherein the HIV drug class is selected from the group consisting of protease inhibitors, integrase inhibitors, nucleotide/nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, and maturation inhibitors.

16. The method of claim 11 , wherein the HIV sample population is derived from a single patient.

17. The method of claim 16 , wherein the single patient is drug naive.

18. The method of claim 16 , wherein the single patient was previously exposed to HIV anti-retroviral drug therapy.

19. The method of claim 11 , further comprising administering an HIV drug based on the determined HIV drug resistance and HIV tropism.

20. A method of treating HIV in a subject in need thereof, comprising:

generating a plurality of cDNA species from a plurality of RNA molecules in an HIV sample population obtained from the subject,

clonally amplifying a plurality of first amplicons and second amplicons from the cDNA species, wherein the first amplicons are amplified using first pairs of primers that amplify a HIV genomic region of the cDNA species encoding the Gag proteins p2, p7, p1 and p6, and the protease, reverse transcriptase, and integrase enzymes and the second amplicons are amplified using second pairs of primers that amplify a HIV genomic encoding region of the cDNA species encoding the env-C2V3 region;

determining the nucleic acid sequence compositions of the clonally amplified first amplicons and second amplicons;

selecting a guide sequence with minimal divergence from the determined nucleic acid sequence compositions for mapping variants of the determined nucleic acid sequence compositions by comparing the determined nucleic acid sequence compositions to reference sequences;

identifying variants occurring at least 1% in the determined nucleic acid sequence compositions by comparing the determined nucleic acid sequence compositions to the guide sequence;

correlating the determined variants with variants of HIV drug resistance and HIV tropism; and

administering an HIV drug or combination of HIV drugs based on the determined HIV drug resistance and HIV tropism.

21. The method of claim 1 , wherein the method detects both minority drug-resistant viruses and non-R5 HIV-1 variants.

22. The method of claim 11 , wherein the method detects both minority drug-resistant viruses and non-R5 HIV-1 variants.

23. The method of claim 20 , wherein the method detects both minority drug-resistant viruses and non-R5 HIV-1 variants.