Julie Karl & Robert Maddox from the University of Wisconsin-Madison presented at the Nanopore Community Meeting 2021 about “SARS-CoV-2 sequencing: on the midnight train to throughput.” They started with statistics from November 11, 2021 about global COVID-19 cases, including data from GISAID. The GISAID graph showed which countries had contributed to the database. Karl shared data from the Wisconsin Department of Health Sciences and the state’s SARS-CoV-2 sequencing efforts. Karl then shared what the University of Wisconsin HIV Vaccine Research lab activity had been. They sequenced the 12th case of SARS-CoV-2 in the United States in early February of 2020. In another study, they evaluated persistent SARS-CoV-2 infection in an immunocompromised patient. The team sequenced and quantified viral load, detecting mutations of interest in persistent infections. The lab has a CDC contract for SARS-CoV-2 sequencing an routinely performs animal experiments. The lab is switching to the Midnight workflow for SARS-CoV-2 sequencing. Maddox explained that the samples they obtain are nasal swab samples and are stored at a testing facility for variable times. The team also aimed to sequence ~192 samples for surveillance. The ARTIC workflow (from Josh Quick) is a tiled primer amplification with two primer pools. The prep includes an SPRI clean-up and normalization. One key difference between the Midnight and ARTIC protocols is the number of amplicons: 29 vs 98 for the ARTIC. Midnight uses the Rapid library prep and can do 96 samples and does not require normalization. Maddox noted that they prep samples in a 96-well plate. Maddox shared data comparing 639 Midnight samples and 343 ARTIC samples… with more samples being eligible for GISAID submission when prepared using the Midnight protocol. Maddox noted that they are considering use of the Bonito basecaller, which is more computationally intensive and may also help investigate samples with less than 20X coverage. This session explained the key differences between these two protocols for sequencing SARS-CoV-2 samples. I thought it was interesting that the Rapid sample prep kit!
