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Interview: Exploring the flow of viruses at the human-animal-environment interface: Towards One Health Preparedness

This is the sixth interview with the PhD students of the Complex Systems & Metagenomics projects in a series of background articles. Keep following this website for the next interview in this series.


Interview with Kirsty Kwok, PhD student of the project ‘Metagenomic analysis of animal, environmental and human microbiomes in the context of excess pneumonia risk around livestock production farms in the Netherlands: flow of microorganisms’ at the Department of Viroscience, Erasmusmc.

‘During 2007-2010, there was a huge Q-fever outbreak with more than four thousand cases in the Netherlands, that was originated from dairy goat and sheep farms. Further investigation of infectious disease at animal-human interface is warranted. Follow-up epidemiological studies observed an excess pneumonia risk in residents living close to farms, however the mechanisms behind remain unknown.’

‘Advances of Next-Generation Sequencing (NGS) has opened more applications in the infectious disease field. I first learnt about Next-Generation Sequencing (NGS) when I was doing my MPhil in Hong Kong about norovirus surveillance and molecular epidemiology. I was then fascinated by the power of metagenomics sequencing (mNGS) in the context of infectious disease diagnostics, that allows pathogen detection without having prior knowledge or pre-defined targets. What’s more, mNGS also made high-throughput virome/microbiome profiling possible.’

‘Here, we aim to utilize mNGS to characterize livestock, environmental and human virome so as to untangle the mechanism of excess pneumonia risk around livestock production farms in the Netherlands. We also aim to reconstruct the virome flow between livestock, farm environments and residents who live near farms, which would potentially guide zoonotic infectious disease preparedness in a One Health context. Currently, I am conducting a systematic review on viral metagenomics study of farm animals to identify potential baseline virome profiles of farm animals to guide our project.’

PhD project: Metagenomic analysis of animal, environmental and human microbiomes in the context of excess pneumonia risk around livestock production farms in the Netherlands: flow of microorganisms.