NCM 2023 Singapore: Advances in rapid, accurate, field-forward sequencing to respond to avian influenza virus at the animal-human interface

Every second counts between detection and response. The total cost of an outbreak grows exponentially from time of detection, making identification critical at emergence or early stages of spread. Cambodia is a hotspot of emerging and endemic viruses and the Virology Unit at Institut Pasteur du Cambodge has been performing One Health surveillance at the human-livestock-wildlife interface for 25 years. Improving our ability to monitor multiple pathogens at high-risk interfaces using Oxford Nanopore technology built up during the COVID-19 pandemic sequencing will facilitate response, help develop key biosecurity practices/guidelines to reduce risk, and enable Early Warning. Avian influenza virus (AIV) is causing major global challenges, including spillover into mammalian species and occasionally into humans. Therefore, it is critical to quickly sequence AIV strains to assess risk. We have successfully employed a rapid, integrated barcode, multi-segment protocol for AIV with field-forward bioinformatics to perform surveillance in animal and environmental samples from live bird markets and from human AIV cases in Cambodia. In addition, benchmarking R9 versus R10 chemistry for AIV reveals significant improvement in speed, coverage, and accuracy – with major reductions in indel rates in vitally important low-complexity regions of the virus such as the multibasic cleavage site. Taken together, nanopore sequencing provides a fast and accurate way to quickly respond and assess AIV both in the laboratory and the field, in both endemic and emerging environments.