Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking
2022
Donzelli, Sara | Ciuffreda, Ludovica | Pontone, Martina | Betti, Martina | Massacci, Alice | Mottini, Carla | De Nicola, Francesca | Orlandi, Giulia | Goeman, Frauke | Giuliani, Eugenia | Sperandio, Eleonora | Piaggio, Giulia | Morrone, Aldo | Ciliberto, Gennaro | Fanciulli, Maurizio | Blandino, Giovanni | Pimpinelli, Fulvia | Pallocca, Matteo
The SARS-CoV-2 Variants of Concern tracking via Whole Genome Sequencing represents a pillar of public health measures for the containment of the pandemic. The ability to track down the lineage distribution on a local and global scale leads to a better understanding of immune escape and to adopting interventions to contain novel outbreaks. This scenario poses a challenge for NGS laboratories worldwide that are pressed to have both a faster turnaround time and a high-throughput processing of swabs for sequencing and analysis. In this study, we present an optimization of the Illumina COVID-seq protocol carried out on thousands of SARS-CoV-2 samples at the wet and dry level. We discuss the unique challenges related to processing hundreds of swabs per week such as the tradeoff between ultra-high sensitivity and negative contamination levels, cost efficiency and bioinformatics quality metrics.
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