Detection of nucleic acids by quantitative polymerase chain reaction (qPCR) and quantitative reverse transcriptase PCR (qRT-PCR) remains the gold standard for supporting biodistribution, vector shedding, gene expression, and pharmacokinetics bioanalysis studies. These molecular platforms are highly valued for their sensitivity and robustness.

qPCR and RT-qPCR assays also play a central role in clinical diagnostics, where clinicians rely on them to assess levels of viral and bacterial pathogens and guide effective patient treatment. Accurate analysis of viral nucleic acids in biological matrices requires efficient extraction methods. Selecting the appropriate extraction platform is critical for successful method development, validation, and testing of any qPCR or RT-qPCR assay, and depends heavily on the unique properties of each biological matrix.

Introducing automated extraction platforms into laboratory workflows improves efficiency and consistency of results. Automated magnetic- and silica-based extraction technologies are commonly used in clinical diagnostics and bioanalysis laboratories.

In this study, we evaluated the performance of four automated platforms:

• 24-well NucliSENS® easyMag® (BioMerieux; magnetic bead-based)
• 96-well KingFisher™ Flex (Thermo Fisher Scientific; magnetic bead-based)
• 12-well QIAcube Connect (Qiagen; silica-based)
• 96-well QIAcube HT (Qiagen; silica-based)

These platforms were tested using serum, neat urine, plasma, and peripheral blood mononuclear cells (PBMCs). We assessed the detection of Epstein-Barr virus (EBV), Varicella zoster virus (VZV), Herpes simplex virus 1 (HSV-1), and Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) across these biological matrices.