Automated nucleic acid isolation methods for HDV viral load quantification can lead to viral load underestimation.

BACKGROUND: HDV infection is a cause of severe liver disease. Diagnosis and monitoring of HDV RNA are important to patient management. Since 2012, a WHO standard for HDV RNA quantification has been available; however, the impact of RNA extraction methods on HDV viral load quantification has never been evaluated.

METHODS: The aim of this study was to compare four commonly used automated nucleic acid (NA) extraction methods (AmpliPrep, MagNA Pure, QIAcube QBK and QIAcube VRK) with a manual RNA extraction method (Instant Virus RNA/DNA kit) and evaluate the possible effect of each method on HDV RNA yield with subsequent amplification with the Robogene HDV assay. Serum samples from HDV-positive patients taken before treatment with pegylated interferon-α2a and at treatment weeks 12 and 48 were studied.

RESULTS: The automated extraction methods MagNA Pure, Ampliprep and QIAcube VRK extraction led to about 10-fold lower HDV RNA values compared with the manual method of NA extraction, while the difference was smaller with QIAcube QBK (about 6-fold lower). The median viral load was 10,665 IU/ml for the manual method, 445 IU/ml for AmpliPrep, 3,209 IU/ml for MagNA Pure, 2,060 IU/ml for QIAcube QBK and 3,568 IU/ml for QIAcube VRK. Use of MagNA Pure led to misclassification of two on-treatment samples with low viral load as being false negative.

CONCLUSIONS: The NA extraction method had a significant impact on the measured HDV viral loads determined by the commonly used Robogene assay, with the manual RNA method yielding consistently higher values of viral load. ClinicalTrials.gov Identifier: NCT00932971.