Combatting outbreaks: rapid avian influenza genomic surveillance at the source

Webinar overview

During this webinar, we heard from Dr. Peter Thielen and Dr. Erik Karlsson, who recently led the team at the Institut Pasteur du Cambodge that rapidly decoded the full genome sequence from a human infection with avian influenza A (H5N1) virus in under 24 hours using nanopore sequencing. Dr. Karlsson discussed the challenges of detecting and monitoring avian influenza, and how advanced sequencing technologies can help to improve our understanding of the virus and its transmission dynamics.

We also explored the importance of expanding capacity for genomic surveillance efforts, both in terms of monitoring the spread of avian influenza among bird populations and in detecting potential spillover events into humans. Our third speaker, Ellen de Vries, PhD student, Agriculture Victoria and La Trobe University, discussed in-field nanopore sequencing of avian influenza, its impacts on wildlife, and the inherent implications on farmed poultry. With the threat of another pandemic looming, it is critical that we take action now to better understand and control the spread of this serious pathogen.

Meet the speakers

Dr. Erik Karlsson serves as Acting Head of the Virology Unit at Institut Pasteur du Cambodge (IPC) in Phnom Penh, Cambodia. He is the Director of the National Influenza Center and the Regional WHO H5 Reference Laboratory, and is integral to the ongoing global response to the COVID-19 pandemic as the Coordinator of the WHO COVID-19 Global Reference Laboratory. Dr Karlsson is an Internationally recognised expert in respiratory viruses and surveillance, especially those with zoonotic and pandemic potential. He is also the founder of the Consortium of Animal market Networks to Assess Risk of emerging Infectious diseases through Enhanced Surveillance (CANARIES).

Ellen de Vries is currently a PhD student with Agriculture Victoria and La Trobe University. She is also working for the Defence, Science and Technology Group in the biological agent detection area as a defence research scientist. Her PhD has focused on utilising MinION for the rapid characterisation and detection of viruses with human and agricultural importance, such as avian influenza, Ross River virus and emerging orthobunyaviruses.

Peter Thielen is a Senior Scientist at Johns Hopkins University Applied Physics Laboratory. Peter's research focuses on advancing DNA and RNA sequencing to support rapid decision-making in clinical, environmental, and national security domains. He leads multiple programs that focus on transitioning basic research approaches to operational environments, including viral genomic surveillance (e.g., influenza virus, SARS-CoV-2), characterisation of genetically modified plant species, and the use of aquatic environmental DNA for ecological species monitoring. These projects focus across domains of molecular biology, bioinformatics, and laboratory hardware development, with the ultimate goals of enabling specialised, long-duration genomic analysis capabilities outside traditional laboratory environments.