SeqCenter uses the latest set of primers (NEB VarSkip Short v2) to enrich your SARS-CoV-2 sample for viral reads. These primers, specifically designed to enhance coverage across Omicron variants, leverage a tiled amplicon approach. The resulting amplicons undergo sequencing via our standard whole genome sequencing pipeline, aiming for 150Mbps of reads per sample. This service includes assembling reads using the SARS-CoV-2 reference genome as a scaffold, and we provide both fastq and genome fasta files.
The ARTIC enrichment method effectively generates >70% coverage across genomes, even for samples with Ct values as high as 35. However, as we do not measure viral load before library preparation, we suggest using samples with Ct values below 35. We also accept raw samples in VTM media, which will be processed using Qiagen’s Viral RNA kits.