Performance characteristics of a modified HIV-1 drug resistance genotyping method for use in resource-limited settings

Abstract

Background: HIV-1 drug resistance (HIVDR) assays are critical components of HIV clinical management programs in the face of emerging drug resistance. However, the high costs associated with existing commercial HIVDR assays prohibit their routine usage in resource-limited settings. We present the performance characteristics of a modified commercial HIVDR testing assay. Methods: A total of 26 plasma samples were used to validate and assess the accuracy, precision, reproducibility and amplification sensitivity of a modified HIVDR assay by HIV genotyping. In addition, a cost comparison between the original and the modified assay was performed using the ingredient costing approach. Results: The performance characteristics of the modified assay were in agreement with the original assay. Accuracy, precision and reproducibility showed nucleotide sequence identity of 98.5% (confidence interval (CI), 97.9–99.1%), 98.67% (CI, 98.1–99.23) and 98.7% (CI, 98.1–99.3), respectively.  There was no difference in the type of mutations detected by the two assays (χ2 = 2.36, p = 0.26). Precision and reproducibility showed significant mutation agreement between replicates (kappa = 0.79 and 0.78), respectively (p < 0.05). The amplification sensitivity of the modified assay was 100% and 62.5% for viremia ≥1000 copies/ml and <1000 copies/ml respectively. Our assay modification translates to a 39.2% reduction in the cost of reagents. Conclusions: Our findings underscore the potential of modifying commercially available HIVDR testing assays into cost-effective, yet accurate assays for use in resource-limited settings.