AIDSWEEKLY Plus; Monday, July 26, 2004
Staff Medical Writers

According to a study from Belgium, "Since there are indications of an increasing amount of non-B subtypes in Western Europe it was decided to assess the performance of the ViroSeq HIV-1 Genotyping System on a set of samples from the AIDS Reference Laboratory at the University Hospitals Leuven, a hospital with an increasing number of patients infected with non-B subtypes.

"The set consisted of 383 samples comprising 12 different subtypes and the genotyping kit was assessed for its amplification capabilities as well as its sequencing capabilities. Amplification failed in 32 samples (8.4%)," B. Maes and coworkers reported, "and there was a tendency of a lower performance of the kit when it concerned the amplification of non-B subtypes."

Maes continued, "Regarding the sequencing performance of the HIV-1 Genotyping System, three different results could be considered. The performance of the entire set of primers (A, B, C, F, G and H) on the different subtypes showed a significant decrease of positive results for subtypes A, G and the recombinants whereas a tendency to less positive results could be detected for subtypes CRF12-BF, D, H and J.

"When looking at the performance of the individual primers for the different subtypes, only one result differed significantly: there were less positive results by applying primer F on subtype A. A tendency to less positive results was found for other combinations of primer and subtype, most of which comprised combinations with primers B, C, F and H."

"A final result was obtained by comparing the overall sequencing results of a certain primer on all the non-B subtypes with the results of the same primer on subtype B. Primer F showed significant less positive results and a tendency to less positive results was found for primer H. The other primers," said investigators, "showed comparable results.

"All of the above results regarding the sequencing primers did not include primer D since this is a back-up primer for primer A. Analysis of the results for primer D showed that less positive results were found for all the non-B subtypes, most of which were significant. The overall performance of primer D on all non-B subtypes Was only 15.7%."

"The use of primer D as a back-up primer was also investigated it generated a positive result in only 17.3% of the cases where primer A failed. Most of these positive results were subtype B (74%). As a result of sequencing problems 65 out of 351 (18.5%) samples had to be processed with ''in-house'' procedures," the authors concluded.

Maes and colleagues published the results of their research in Journal of Virological Methods (Performance of ViroSeq HIV-1 Genotyping System in routine practice at a Belgian clinical laboratory. J Virol Methods, 2004;119(1):45-49).

For additional information, contact B. Maes, Katholieke University Leuven, Rega Institute Med Research, Minderbroedersstr 10, B-3000 Louvain, Belgium.

The publisher of the Journal of Virological Methods can be contacted at: Elsevier Science BV, PO Box 211, 1000 AE Amsterdam, Netherlands.

The information in this article comes under the major subject areas of Genomics & Genetics, HIV/AIDS, Epidemiology, Diagnostics and Biotechnology.

This article was prepared by AIDS Weekly editors from staff and other reports.

Reference

Maes B, Schrooten Y, Snoeck J, et al., "Performance of ViroSeq HIV-1 Genotyping System in routine practice at a Belgian clinical laboratory.", J Virol Methods. 2004 Jul;119(1):45-9.

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