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.
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.


OBJECTIVE
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.


METHODS
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).
Kamat
Anupa
A
Department of Neurovirology, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India.
Ravi
V
V
Desai
Anita
A
Satishchandra
P
P
Satish
K S
KS
Borodowsky
I
I
Subbakrishna
D K
DK
Kumar
Mahendra
M
D001483:Base Sequence; D017931:DNA Primers; D015342:DNA Probes; D015750:Genes, gag; D015658:HIV Infections / Q000097:blood / Q000134:cerebrospinal fluid / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007194:India; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D012367:RNA, Viral / Q000097:blood* / Q000134:cerebrospinal fluid*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D019562:Viral Load
D017931:DNA Primers; D015342:DNA Probes; D012367:RNA, Viral