Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 Using the "Midnight" Panel

I will discuss the development of the “Midnight” panel for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. We show that using a multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit and nanopore sequencing we produce high-quality assembled genomes with as few as 10 000 reads (∼5 Mbp of sequence data) in as little as 9 hours from patient sampling. This method cuts the hands-on time from sample to genome by more than half compared to the more standard ARTIC ligation-based Oxford Nanopore library preparation method at considerably lower costs. It achieves even coverage and is less prone to drop-outs, especially in the context of new COVID-19 variants, like Delta. It is currently in use by over 180 institutions in 35 countries, is one of two primary methods in use by Oxford Nanopore, has been modified for use on PacBio and Illumina platforms, and the original open access protocol has been accessed over 17,000 times. This method is also amenable to modification and use for other viruses. 

Learning Objectives:
1. Identify two reasons why sequencing the genome SARS-CoV2 (the virus that causes COVID-19) is important.
2. Describe the “midnight” method for whole genome sequencing of SARS-CoV-2.
3. Explain two advantages to using the “midnight” method.