Amy Klink: Nanopore (MinION) sequencing to detect and sequence full genomes of emerging RNA viruses in avian and marine mammal species

Lightning talk: Amy Klink, of the University of Alaska Anchorage, described how she and her team used nanopore cDNA sequencing to rapidly genotype emerging avian and marine mammal viruses throughout regions of Alaska. Amy noted that RNA viruses are of particular interest: they are able to rapidly mutate, and can jump between species and between host cells. She described how viral outbreaks of two Paramyxoviruses - Newcastle disease virus (NDV) & phocine distemper virus (PDV) - and influenza had resulted in the deaths of over 1,500 harbour and grey seals off the Anchorage coast. Amy and her team first adapted an MS-RTPCR protocol for avian and mammalian influenza to generate sequencing libraries from primary preserved influenza samples. The paramyxoviruses NDV and PDV were amplified via a Zibra project tiling RT-PCR method. The resulting partial- and full-genome amplicons were prepared for sequencing using the 1D^2 (SQK-LSK308) and 1D (SQK-LSK108) kits and sequenced on the MinION. Reads were basecalled via Albacore, trimmed with Porechop/ Filtlong and mapped via Minimap2. Amy displayed how the NDV 1D^2 library provided initial proof of concept, producing a pairwise identity with the LaSota strain of 74.4%. As the team generated more sequencing data for the genomes, they were able to map where the viruses were evolving from: analysis of the segmented genomes of influenza isolates demonstrated reassortment of segments from very different areas, enabling the mapping of potential outbreak hotspots.