Quantitation of HIV-1 RNA levels in plasma and CSF of asymptomatic HIV-1 infected patients from South India using a TaqMan real time PCR assay

Abstract Background Most of the quantitation assays for HIV-1 RNA used currently are designed and optimized for HIV-1 subtype B viruses and hence may not be suitable for India, where the predominant subtype is HIV-1 subtype C. Objectives Development and standardization of HIV-1 TaqMan real time PCR...

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Bibliographic Details
Published in:Journal of clinical virology 2007-05, Vol.39 (1), p.9-15
Main Authors: Kamat, Anupa, Ravi, V, Desai, Anita, Satishchandra, P, Satish, K.S, Borodowsky, I, Subbakrishna, D.K, Kumar, Mahendra
Format: Article
Language:English
Subjects:
Allergy and Immunology
Base Sequence
Biological and medical sciences
DNA Primers
DNA Probes
Fundamental and applied biological sciences. Psychology
Genes, gag
HIV infection in South India
HIV Infections - blood
HIV Infections - cerebrospinal fluid
HIV Infections - virology
HIV-1 - genetics
HIV-1 - isolation & purification
HIV-1 TaqMan viral load assay
Human immunodeficiency virus 1
Human viral diseases
Humans
India
Infectious Disease
Infectious diseases
Medical sciences
Microbiology
Miscellaneous
Molecular Sequence Data
Plasma and CSF viral loads
Polymerase Chain Reaction - methods
Reproducibility of Results
RNA, Viral - blood
RNA, Viral - cerebrospinal fluid
Sensitivity and Specificity
Viral diseases
Viral diseases of the lymphoid tissue and the blood. Aids
Viral Load
Virology
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Summary:Abstract Background Most of the quantitation assays for HIV-1 RNA used currently are designed and optimized for HIV-1 subtype B viruses and hence may not be suitable for India, where the predominant subtype is HIV-1 subtype C. Objectives Development and standardization of HIV-1 TaqMan real time PCR assay suitable for measuring plasma and CSF viral RNA levels in HIV subtype C infected individuals. Study design A TaqMan real time PCR was developed using primers and probes selected in the gag region for detection of Indian HIV-1 subtype C strain. Plasma ( n = 120) and CSF samples ( n = 46) obtained from HIV infected subjects were used to evaluate the sensitivity and specificity of the assay. A comparative evaluation was carried out with a commercially available quantitative HIV viral load assay (Roche Amplicor Version 1.5). Results The TaqMan assay was able to amplify all HIV-1 group M subtypes except subtype E. Viral loads could be estimated in all the plasma ( n = 120) and 40/46 CSF samples obtained from HIV positive subjects. Sensitivity of this assay was found to be 180 copies/ml. Correlation with the commercially available viral load assay was very good ( r = 0.885). Conclusions A TaqMan real time PCR was standardized for HIV-1 subtype C and it was more sensitive (180 copies/ml) than standard Amplicor monitor assay, Version 1.5 (400 copies/ml).
ISSN:1386-6532
1873-5967
DOI:10.1016/j.jcv.2006.12.026