Comparative quantification of diverse serotypes of HIV-1 in plasma from a diverse population of patients

Abstract

HIV-1 is characterised by extensive genetic variability encompassing at least 10 different phylogenetically related clades within the major group of HIV-1 subtypes. Most commercially available HIV-1 RNA plasma viral load assays have been optimised with clade B viruses and may yield misleadingly low RNA levels for nonclade B viruses that are increasingly found in Europe. In this study we compare the most recent versions of the Roche Amplicor HIV Monitor and the Chiron Quantiplex for ability to detect viraemia in a population of patients infected with a range of HIV-1 subtypes. EDTA-treated plasma was obtained from 206 patients. The Amplicor and Quantiplex assays were carried out in accordance with manufacturers' instructions. Results from 53/206 (25.7%) samples differed by >0.4 log between Amplicor 1.5 and Quantiplex 3.0. A >0.5 log and 1.0 log difference was detected between Amplicor 1.5 and Quantiplex 3.0 in 37/206 (17.9%) and 7/206 (3.4%) of samples, respectively. Overall, Amplicor 1.5 gave a median value of 0.22 log higher than Quantiplex 3.0. Discordant results were detected in 53 out of 206 (25.7%) samples. Of these 22 out of 123 (17.9%) samples were of UK origin, 18 out of 43 (41.9%) African, 1 out of 8 (12.5%) South American, 1 out of 6 (16.7%) North American, 4 out of 9 (44.4%) North European, 3 out of 11 (23.7%) South European and 3 out of 7 (42.3%) Asian samples, respectively. Serotyping revealed that discordant viral load results between Amplicor 1.5 and Quantiplex 3.0 occurred within samples from all subtypes (A-E). Despite the improvements made to both the Roche Amplicor and the Chiron Quantiplex assays discordant results were detected between the two assays in 25.7% of cases. In a substantial minority of patients there were major discrepancies between the two assays that were not explained by HIV subtype differences.

Impact of Human Immunodeficiency Virus Type 1 (HIV-1) Genetic Diversity on Performance of Four Commercial Viral Load Assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT

“…Overall, viral load values in the Monitor v1.5 and LCx assays tended to run slightly higher (0.2 to 0.3 log 10 ) than those in the bDNA assay. Similar results have been observed in previous studies (6,8,31,47).…”

“…The somewhat reduced correlations observed in the present study likely reflect the genetically diverse panel. In studies where performance with non-subtype B virus isolates was examined, correlations and agreement between assays were reduced, comparable with our results (6,8,12,42,43,47). Overall, viral load values in the Monitor v1.5 and LCx assays tended to run slightly higher (0.2 to 0.3 log 10 ) than those in the bDNA assay.…”

“…However, cases of failed detection or significant levels of underquantification by bDNA have been noted. For example, Clarke et al reported one sample that was below the 50-copies/ml LLD of bDNA but was quantified at 4.1 log 10 copies/ml by Monitor v1.5 (subtype designation was not reported) (8). Others have demonstrated underquantitation of specific CRF02_AG strains and some subtype F strains (1,23,15,43).…”

“…Significant underquantification of virus has the potential to lead to an inappropriate strategy for patient management (20). Genetic heterogeneity of HIV-1 is one important factor with potential to jeopardize reliability of viral load measurements (1,8,12,23,24,29,42,46).…”

Sequencing Assays for Failed Genotyping with the Versant Hepatitis C Virus Genotype Assay (LiPA), Version 2.0

“…More recently, two cases of amplifiable samples giving uninterpretable LiPA results were observed in the Netherlands, and the authors underlined the close resemblance of these two viral strains to viruses of genotypes 2 and 3 originating from non-Western countries (21). The failure of some quantitative RT-PCR assays to detect or to amplify correctly African strains of HCV or HIV has been reported frequently (22)(23)(24), and the LiPA may suffer from the same type of bias.…”