HIV-1 genotyping assay for global surveillance of HIV-1 drug resistance

摘要

Provided herein are new methods, primers, and kits for genotyping HIV-1, including group M viral strains. The methods can be used for HIV-1 drug resistance surveillance and monitoring, for example in resource-poor countries. The disclosed methods can detected more mixed HIV-1 population than previous methods. Given the high efficiency in genotyping diverse HIV-1 group M viral strains from plasma and dried blood spot (DBS) samples and substantial reagent cost saving, the disclosed methods can be used for HIV-1 drug resistance genotyping in both antiretroviral therapy (ART)-naive and -experienced populations for surveillance purposes and patient monitoring.

主权项

1. A method of genotyping HIV-1 in a sample, comprising:
(a) contacting a sample obtained from a subject with a first forward nucleic acid primer comprising a mixture of SEQ ID NO: 1 and 2 and a first reverse nucleic acid primer consisting of SEQ ID NO: 4, or contacting the sample obtained from a subject with a first forward nucleic acid primer consisting of SEQ ID NO: 3 and a first reverse nucleic acid primer consisting of SEQ ID NO: 4, thereby generating a first reaction mixture; (b) incubating the first reaction mixture under conditions sufficient to amplify by polymerase chain reaction (PCR) a portion of HIV-1 pol in the first reaction mixture, thereby generating a first amplification product; (c) contacting the first amplification product with a second forward nucleic acid primer consisting of SEQ ID NO: 5 and a second reverse nucleic acid primer consisting of SEQ ID NO: 6, thereby generating a second reaction mixture; (d) incubating the second reaction mixture under conditions sufficient to amplify by PCR a portion of HIV-1 pol comprising HIV-1 reverse transcriptase (RT) and HIV-1 protease (PR) in the second reaction mixture, thereby generating a second amplification product; and (e) sequencing the first amplification product and the second amplification product to determine the genotype of HIV-1, or subjecting the first amplification product and the second amplification product to allele-specific analysis to determine the genotype of HIV-1, wherein the method can detect a viral load of ≧1,000 copies/ml.