Maria Chaves from Iowa State University presented at the Nanopore Community Meeting in Houston on “Enrichment strategies for recovery of Avian influenza virus from samples using MinION.” They spoke about the current highly pathogenic avian influenza (HPAI) outbreak and the importance of timely identification and characterization. Avian influenza is a huge problem for the poultry industry. To overcome some of the challenges of metagenomic sequencing in HPAI identification, Chaves and the team created a new approach. They selected samples and used their enrichment approach. Their approach, called SASA, is semi-targeted and uses influenza primers. The team used SASA to sequence mixed infection samples, resulting in the correct identification of viruses. SISPA is a pathogen discovery approach, while the SASA method has higher sensitivity and identification of off-targets. This approach balances the identification of influenza viruses with discovery. Chaves also noted that they will refine their enrichment system and include adaptive sampling.
