An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms
Rahul C. Bhoyar, Vigneshwar Senthivel, Bani Jolly, Mohamed Imran, Abhinav Jain, Mohit Kumar Divakar, Vinod Scaria, Sridhar Sivasubbu
Abstract
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 MiniSeq. For complete details on the use and execution of this protocol, please refer to Bhoyar et al. (2021).
Topics & Concepts
AmpliconDNA sequencingAmplicon sequencingComputational biologySevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Coronavirus disease 2019 (COVID-19)BiologyIllumina dye sequencingProtocol (science)GenomeComputer scienceVirologyGeneticsMedicineGenePolymerase chain reactionInfectious disease (medical specialty)16S ribosomal RNADiseasePathologyAlternative medicineSARS-CoV-2 and COVID-19 ResearchCRISPR and Genetic Engineeringvaccines and immunoinformatics approaches