Optimization of the Illumina COVIDSeq^™protocol for decentralized, cost-effective genomic surveillance

Abstract

A decentralized surveillance system to identify local outbreaks and monitor SARS-CoV-2 Variants of Concern is one of the primary strategies for the pandemic's containment. Although next-generation sequencing (NGS) is a gold standard for genomic surveillance and variant discovery, the technology is still cost-prohibitive for decentralized sequencing, particularly in small independent labs with limited resources. We have optimized the Illumina COVID-seq protocol to reduce cost without compromising accuracy. 90% of genomic coverage was achieved for 142/153 samples analyzed in this study. The lineage was correctly assigned to all samples (152/153) except for one. This modified protocol can help laboratories with constrained resources contribute to decentralized SARS-CoV-2 surveillance in the post-vaccination era.

Deciphering microbiota of acute upper respiratory infections: a comparative analysis of PCR and mNGS methods for lower respiratory trafficking potential

“…And more robust mNGS hypothesis-free techniques, although yielding a broad microbiome, pose a taxonomic-to-clinically relevant challenge. From a laboratory point of view these sequencing methods often require workflows that are technically challenging and tend to be siloed [27] because of the high capital investments needed for equipment, technology, and expertise-resulting in restricted capability for decentralized testing or application in resource-limited laboratories [14,28]. Yet from the clinical point of view, recognition of potential pathogenicity is crucial to estimate etiological relevance, to optimize treatment, and understand outbreak conditions.…”