Christina Newman from the University of Wisconsin-Madison presented at the Nanopore Community Meeting in Houston on “Metagenomic sequencing of air samples to identify human viral pathogens.” Newman spoke about the loss of resolution of SARS-CoV-2 variants with the increased use of home kits. Newman noted that indoor air sampling could be used in schools to learn about viruses. A photo on a slide had a ThermoFisher air sampler. While multiplexed detection of viral nucleic acids is common, you must know what you are searching for. Sequence-independent single primer amplification (SISPA) uses a random primer for cDNA synthesis. Their workflow takes 5-6 hours, and then they use a MinION to sequence barcoded samples. The research team used this approach to sample different locations and identified several viral sequences. The Rapid SMART-9N protocol uses a DNA digest, RNA cleanup/concentration, cDNA synthesis scheme and takes only a couple of hours because it uses the Rapid PCR Barcoding Kit. This approach was used to monitor SARS-CoV-2 variants in a household outbreak! The variant they identified was one that was circulating at the time. The research team also identified Respiratory Syncytial Virus B in one individual. Newman and the team believe that unbiased metagenomic nanopore sequencing and air sampling are powerful tools to monitor and identify viruses. A challenge with this method is the presence of host and other nucleic acids.
