Background: Improved viral detections by the real time PCR over the manual assays have
been reported by various manufacturers. However, discrepancies and discordance between different
platforms targeting the same pathogen have also been observed at different settings.
Methods: We used an analytical study design to compare the performance of the Cobas Taqman
/Cobas Ampliprep version 2.0 against the standard Amplicor Monitor 1.5 using 200 routine clinical samples, in Abuja-
Results: Taqman and Amplicor detected 118/200 (59%) and 83/200 (41.5%) samples respectively. Two of 83 samples
(2.4%) undetectable by Cobas Taqman, were detectable by Roche Amplicor, while 5 of 37 samples (13.5%) which were
undetectable by Amplicor using Taqman. Among the 81 detectable samples by both assays 4 samples (4.9%) had a log10
difference > 0.5 log copies, while 9 samples (11.1%) showed a wider discrepancy of >1 log10. Bland and Altman’s
comparison shows no significant difference between the two methods (p=0.2825) and CI-0.06171 to 0.2087.
Conclusion: We observed a remarkable improvement in the performance of COBAS AmpliPrep/COBAS TaqMan version
2.0 Assay over Amplicor Monitor version 1.5 in the quantification of HIV1 RNA viral load. Discrepancies of clinical
significance, in the viral load between the two platforms were also recorded. The implications of the inability of the
automated Taqman 2.0 to detect 2.4% of samples detectable by the Amplicor need to be considered by programs,
clinicians and the manufacturers. Periodic evaluation of platforms to detect new circulating HIV subtypes within each
locality is also recommended.