Application Note

SARS-CoV-2 Sequencing with Jumpcode Genomics and AVITI™

It took 42 days from the first reported clinical case of COVID-19 until the viral genome sequence was provided to the public. This critical information release acts as the starting point for diagnostic test development and mRNA vaccine generation. The first EUA approved RT-PCR tests in the United States were made available after 70 days on February 8th, 2020.

Shotgun metagenomic NGS sequencing is the only technology capable of unbiased detection from previously unknown pathogens available on day ZERO for future pandemics. Beyond detection, meta-transcriptomic sequencing enables full genome sequence assembly, the ability to catalog co-infections, and provides valuable data on host response through host transcriptional profiling.

Sensitivity of shotgun mNGS is hindered by abundant eukaryotic (host) and prokaryotic rRNA sequences from nasal swabs. Using a guide set of over 12,500 sgRNAs targeting abundant human and bacterial ribosomal RNA sequences in the CRISPRclean® Plus workflow, we show that sequence specific...