Evaluation of an optimized protocol and Illumina ARTIC V4 primer pool for sequencing of SARS-CoV-2 using COVIDSeq™ and DRAGEN™ COVID Lineage App workflow

Next-Generation Sequencing based genomic surveillance has been widely implemented for identification and tracking of emerging SARS-CoV-2 variants to guide the Public Health response to the COVID-19 pandemic. Amplicon-based assays, such as the Illumina^® COVIDSeq™ Test (RUO) and COVIDSeq Assay (RUO), enable scalable sequencing of SARS-CoV-2, leveraging V3 and V4 primer designs from the ARTIC community and DRAGEN™ COVID Lineage App analysis available on Illumina BaseSpace™. We report here a comparison of COVIDSeq performance for SARS-CoV-2 genome reporting using the ARTIC V3 based primer pool (including primers for human control genes) that is provided with the COVIDSeq kit versus the ARTIC V4 based Illumina COVIDSeq V4 primer pool, using an optimized protocol and DRAGEN COVID Lineage App analysis. The data indicates that both primer pools enable robust reporting of SARS-CoV-2 variants. The Illumina COVIDSeq V4 primer pool has superior performance for SARS-CoV-2 genome reporting, particularly in samples with low virus load, and is therefore the recommended primer pool for genomic surveillance of SARS-CoV-2 for research use using COVIDSeq.