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Background In resource-limited settings, viral load monitoring of HIV-infected patients receiving antiretroviral therapy (ART) is not readily available due to high costs. Here, we compared the accuracy and costs of quantitative and qualitative pooled methods to standard viral load testing. Methods Blood was collected prospectively from 461 patients receiving first-line ART in Mozambique who had not been evaluated previously with viral load testing. Screening for virologic failure of ART was performed quantitatively (i.e. standard viral loads) and qualitatively (one and two rounds of polymerase chain reaction; PCR). Individual samples and minipools of 5 samples were then analyzed using both methods. The relative efficiency, accuracy and costs of each method were calculated based on viral load thresholds for ART failure. Results Standard viral load testing of individual samples revealed a high rate of ART failure (19-23%) across all virologic failure thresholds, and the vast majority of the patients (93%) with viral loads >1,500 copies/ml had genotypic resistance to drugs in their ART regimen. Pooled quantitative screening and deconvolution testing had positive and negative predictive values exceeding 95% with cost savings of $11,250 compared to quantitative testing of each sample individually. Pooled qualitative screening and deconvolution testing had a higher cost savings of $30,147 for one PCR round and $25,535 for two PCR rounds compared to quantitative testing each sample individually. Both pooled qualitative PCR methods had positive and negative predictive values ≥90%, but the pooled one-round PCR method had a sensitivity of 64%. Conclusions Given the high rate of undiagnosed ART failure and drug resistance in this cohort, it is clear that virologic monitoring is urgently needed in this population. Here, we compared alternative methods of virologic monitoring to standard viral load testing of individual samples and found these methods to be cost saving and accurate. The test characteristics of each method will likely need to be considered for each local population before it is adopted.

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