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Performance
of Two Genotyping Systems for Detection of Drug Resistance Against
HIV-1 Group M Subtypes
The use of genotyping assays for the detection and evaluation
of drug resistance mutations within the polymerase gene of HIV-1
is becoming increasingly relevant in the clinical management of
HIV-1 infection.
However, genotypic resistance assays available currently have
been optimized for genetic subtype B strains of the virus and many
clinical centers are presented with strains from subtypes A, C,
and D.
In the present report, we compare the performance of two sequence-based
commercially available kits, the ViroSeq Genotyping System
(Applied Biosystems, Foster City, CA) and the TruGene HIV-1 Genotyping
Kit (Visible Genetics, Toronto, Ontario) against a panel of
35 virus isolates from HIV-1 Group M (subtypes A-J).
Full-length consensus sequences were generated by the ViroSeq
genotyping system for 26 of 31 (83.8%) of the isolates tested, in
contrast to the TruGene genotyping system, which generated 16 of
30 (53%) usable sequences overall. Overall, subtype B isolates were
sequenced with a greater degree of success than non-subtype B isolates.
Discrepancies were found between the consensus sequences reported
by each system for each sample (mean difference 1.0%; range 0.0-3.2%),
but these appeared to be random and did not affect interpretation
of the major resistance codons.
In addition, both systems were able to amplify template RNA
from low copy viral load plasma samples (102-103
RNA copies/ml) taken from a random selection of patient samples
encompassing subtypes A-C.
The authors conclude, “While the availability of these genotyping
systems should facilitate studies of HIV-1 drug resistance in countries
in which these subtypes are prevalent, the performance against subtypes
other than B needs to be improved.”
06/13/03
Reference
S
Beddows and others. Performance of two commercially available sequence-based HIV-1
genotyping systems for the detection of drug resistance against
HIV type 1 group M subtypes. Journal of Medical Virology
70(3): 337-342. July 2003 (May 6, 2003 online).
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