From cDNA synthesis to enrichment
The QIAseq SARS-CoV-2 Primer Panel workflow begins with converting total viral RNA into cDNA using random priming (no rRNA depletion or poly-A selection is required). This reaction is flexible with regards to input RNA used for the reverse transcription reaction. To elaborate, 5 µl viral RNA input is required as a starting point. When the viral RNA has been previously assessed using a qPCR assay, the CT value should be between 18–35. If the CT is between 12–15, then dilute the sample 100-fold in water; if it's between 15–18 then dilute 10-fold in water. This will reduce the likelihood of PCR-inhibition.
Following cDNA synthesis, primer pools (based on sequences from the ARTIC Network) are used in a high-fidelity multiplex PCR to prepare two pools of 400 bp QIAseq SARS-CoV-2 Primer Panel amplicons. The two enriched pools per sample are then combined into a single tube and then purified. This is then followed by QIAseq FX DNA library construction.
QIAseq FX DNA Library construction
Purified amplicons from a multiplex QIAseq SARS-CoV-2 Primer Panel are converted to Illumina-compatible NGS libraries using our QIAseq FX DNA Library UDI Kits, which provide a fast, fully enzymatic procedure from DNA fragmentation to NGS library.
Purified, target-enriched samples from the QIAseq SARS-CoV-2 Primer Panel are first enzymatically sheared into smaller fragments. The desired median fragment size is 250 bp. The fragmented DNA is then directly end-repaired and an "A" is added to the 3’ ends during the FX reaction, making the DNA fragments ready for adapter ligation. Following this step, Illumina platform-specific adapters are ligated to both ends of the DNA fragments. These adapters contain sequences essential for binding dual bar-coded libraries to a flow cell for sequencing.
Following adapter ligation, the reaction is purified, and any adapter-dimers are removed. This can be automated on various high-throughput automation platforms.
Whole SARS-CoV-2 genome coverage
Based on primer sequences from the ARTIC Network and this publication, the QIAseq SARS-CoV-2 Primer Panel separates 400 bp amplicons into two PCR pools that together cover the entire SARS-CoV-2 genome. Using a QIAseq FX DNA Library UDI Kit, the amplicons from the QIAseq SARS-CoV-2 Primer Panel are brought within the length requirements to perform sequencing on Illumina platforms.