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We evaluated the new low-cost ExaVir Load (version 3) reverse transcriptase viral load assay against the Roche Cobas Amplicor assay. Results for samples tested using the reverse transcriptase assay correlated well with those obtained with the Roche assay (r = 0.85; n = 202). The version 3 reverse transcriptase assay shows improved sensitivity compared to the previous version.