HIV-1 genotyping assay for global surveillance of HIV-1 drug resistance
Inventors
Yang, Chunfu • Zhou, Zhiyong • Wagar, Nicholas • DeVos, Joshua R.
Assignees
Centers of Disease Control and Prevention CDC • US Department of Health and Human Services
Publication Number
US-10053741-B2
Publication Date
2018-08-21
Expiration Date
2032-07-05
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Abstract
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.
Core Innovation
The invention provides new methods, primers, and kits specifically designed for genotyping HIV-1, including diverse group M viral strains and subtypes such as A, B, C, D, F, G, H, J, K, CRFs, and URFs. These methods focus on detection of HIV-1 protease and reverse transcriptase gene resistance mutations within the pol gene region, enabling surveillance of HIV-1 drug resistance and patient monitoring, particularly in resource-poor settings.
The problem addressed by the invention arises from the global challenge of emerging drug-resistant HIV-1 strains due to antiretroviral therapy, especially in resource-limited countries where access to laboratory monitoring is scarce or absent. Existing FDA-approved genotyping assays like ViroSeq and TRUGENE are expensive and primarily designed for subtype B, limiting their use in regions where non-B subtypes and recombinant forms predominate. There was a need for a broadly sensitive, cost-effective, and accurate genotyping assay capable of detecting multiple HIV-1 group M subtypes and mixtures of viral populations.
The disclosed methods improve upon prior in-house assays by overcoming limitations such as incomplete coverage of protease gene regions and reduced sensitivity to mixture detection caused by sequencing primer issues. The invention features primers designed to amplify and sequence relevant HIV-1 pol regions, enabling high specificity (at least 99%) and sensitivity (at least 95%) for genotyping diverse HIV-1 strains from plasma and dried blood spot samples. The methods support use with both RNA and DNA templates, including nested PCR approaches, and can incorporate comparisons with established surveillance drug resistance mutation lists to guide therapeutic decisions.
Claims Coverage
The patent includes multiple independent claims focusing on degenerate oligonucleotide primers and kits incorporating such primers, covering compositions and methods for HIV-1 genotyping.
Degenerate oligonucleotides with attached labels
The presence of degenerate oligonucleotides consisting of sequences from SEQ ID NOS: 1, 2, 3, 5, 7, 8, or 9 with an attached label selected from radioactive isotopes, ligands, chemiluminescent agents, fluorophores, haptens, enzymes, or combinations thereof.
Kits comprising degenerate oligonucleotides and reagents for RNA isolation, reverse transcription, PCR, and sequencing
Kits containing one or more degenerate oligonucleotides of the disclosed sequences along with reagents for isolating RNA, performing reverse transcription, RT-PCR, and nucleic acid sequencing; optionally including oligonucleotides SEQ ID NOS: 4, 6, and/or 10, and materials for blood sample collection and HIV-1 viral load determination.
Specific combinations of primers within kits
Kits comprising specific primer combinations such as degenerate oligonucleotides SEQ ID NOS: 1-3 with SEQ ID NO: 4, nested PCR primers SEQ ID NOS: 5 and 6, and sequencing primers SEQ ID NOS: 7-10 in various arrangements to optimize amplification and sequencing of HIV-1 pol gene regions.
Inclusion of enzymes and nucleotides in kits
Kits may include DNA polymerase enzymes, dNTPs, or both to facilitate PCR amplification within the genotyping assay.
The independent claims collectively cover degenerate labeled oligonucleotide primers specific for HIV-1 group M genotyping, kits incorporating these primers with amplification and sequencing reagents, multiple primer combinations optimized for nested PCR and sequencing, and inclusion of essential enzymes and reagents enabling comprehensive HIV-1 drug resistance genotyping.
Stated Advantages
Broad sensitivity in genotyping multiple HIV-1 group M subtypes and CRFs from plasma and dried blood spots, enhancing utility in diverse geographic regions.
High specificity (≥99%) and sensitivity (≥95%) for detecting HIV-1 drug resistance mutations, including mixed viral populations.
Substantial reagent cost savings compared to commercial assays, reducing costs by approximately 75%, facilitating accessibility in resource-poor settings.
Improved detection of nucleotide mixtures due to optimized primer design and reduced sequencing background noise.
Capability to genotype samples even after prolonged storage of dried blood spots at ambient temperature, supporting practical surveillance and monitoring.
Documented Applications
Population-based surveillance of HIV-1 drug resistance in resource-limited settings.
Monitoring HIV-1 drug resistance development in patients receiving antiretroviral therapy, including both ART-naïve and ART-experienced populations.
Detection of HIV-1 drug resistance mutations in protease and reverse transcriptase genes to guide therapeutic regimen choices.
Use of dried blood spot samples for HIV-1 viral load measurement and genotyping, enabling sample collection and transport in remote or resource-poor environments.
Implementation in public health programs in multiple countries including Vietnam, Malawi, Nigeria, Cameroon, Zambia, Thailand, and others for HIVDR surveillance.
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