An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms

Sequencing of SARS-CoV-2 genomes is crucial for understanding the genetic epidemiology of the COVID-19 pandemic. It is also critical for understanding the evolution of the virus and also for the rapid development of diagnostic tools. The present protocol is a modification of the Illumina COVIDSeq test. We describe an amplicon-based next-generation sequencing approach with short turnaround time, adapted for bench-top sequencers like MiSeq, iSeq, and Mini-Seq. For complete details on the use and execution of this protocol, please refer to Bhoyar et al. (2021).

Automated summary

Sequencing SARS-CoV-2 genomes is crucial for understanding the genetic epidemiology of the COVID-19 pandemic and evolution of the virus, as well as for rapid development of diagnostic tools. The present protocol is a modification of the Illumina COVIDSeq test, describing an amplicon-based next-generation sequencing approach with short turnaround time for bench-top sequencers like MiSeq, iSeq, and Mini-Seq.