QIAseq DIRECT SARS-CoV-2 Kit A

QIAGEN's QIAseq DIRECT SARS-CoV-2 Kit A is a single-box targeted NGS library preparation solution for whole genome amplification and sequencing of the SARS-CoV-2 viral genome. Designed for genomic surveillance and variant detection research, the kit supports direct conversion of viral RNA into sequencing-ready libraries in a streamlined 4-hour workflow that begins with random-primed cDNA synthesis — no rRNA depletion or poly-A selection required.

The panel consists of approximately 550 primers that generate 425 amplicons covering the entire SARS-CoV-2 viral genome using an overlapping and redundant targeting approach intended to reduce drop-outs caused by novel viral mutations. Following cDNA synthesis, multiplexed primer pools are used in a high-fidelity PCR to prepare two pools of approximately 250 bp amplicons, which are combined, bead-purified, and then amplified and indexed using Unique Dual Indices (UDIs) that mitigate read mis-assignment due to index hopping. The protocol requires 5 µl of viral RNA as starting volume, regardless of titer, and produces libraries that are compatible with Illumina platforms including iSeq 100, MiniSeq, MiSeq, NextSeq 500/550, HiSeq 2500, HiSeq 3000/4000 and NovaSeq 6000.

The shorter, similar-sized amplicons eliminate the need for fragmentation and improve sequence uniformity and read depth. Multiplexing supports up to 384 samples per lane on instruments such as the NovaSeq, enabling laboratories to scale up sequencing throughput for surveillance efforts. When paired with QIAGEN CLC Genomics Workbench, the panel delivers data that can be used to identify variants across samples and compare against reference or uploaded SARS-CoV-2 genomes.