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Development of a Novel Codon-Specific Polymerase Chain Reaction for the Detection of CXCR4-Utilizing HIV Type 1 Subtype B
- Source :
- AIDS Research and Human Retroviruses. 29:814-825
- Publication Year :
- 2013
- Publisher :
- Mary Ann Liebert Inc, 2013.
-
Abstract
- Insight concerning the switch in HIV-1 coreceptor use will lead to a better understanding of HIV-1 pathogenesis and host-virus dynamics. Predicting CXCR4 utilization by analyzing HIV-1 envelope consensus sequences is highly specific, but minority variants in the viral population are often missed resulting in low sensitivity. Commercial phenotypic assays are costly, and the development of sensitive in-house phenotypic assays to detect CXCR4-using HIV may not be feasible for some laboratories. A sensitive, inexpensive genotyping assay was developed to detect viral sequences associated with CXCR4-utilizing virus (X4). Codon-specific primer pairs were used to detect X4-associated codons at five positions in the HIV-1 envelope V3 loop (11, 13, 24, 25, and 32). Sixty plasma samples from HIV-1-infected individuals were analyzed by consensus sequencing and codon-specific PCR (CS-PCR). Forty-six of these were also phenotyped by Trofile or Enhanced Sensitivity Trofile (ESTA). CS-PCR detected X4 variants 17% more often than 11/24/25 consensus sequencing alone (n=60), 30% more often than Trofile (n=27), and in a limited data set, 16% more often than ESTA (n=19). CS-PCR combined with consensus sequencing had approximately 80% concordance with ESTA.
- Subjects :
- Receptors, CXCR4
Genotype
Immunology
Population
HIV Infections
Pathogenesis
V3 loop
Biology
Polymerase Chain Reaction
Virus
law.invention
law
Virology
Consensus Sequence
Consensus sequence
Humans
Codon
education
Genotyping
Polymerase chain reaction
Genetics
education.field_of_study
Phenotype
Infectious Diseases
HIV-1
Primer (molecular biology)
Subjects
Details
- ISSN :
- 19318405 and 08892229
- Volume :
- 29
- Database :
- OpenAIRE
- Journal :
- AIDS Research and Human Retroviruses
- Accession number :
- edsair.doi.dedup.....b4de9f1c45828c757913946542a2278d
- Full Text :
- https://doi.org/10.1089/aid.2012.0024