Redefining Virus Ecology and Evolution Using Metagenomics

Title:  REDEFINING VIRUS ECOLOGY AND EVOLUTION USING METAGENOMICS

Speaker:  Prof Eddie Holmes, University of Sydney

Abstract:  RNA viruses are diverse components of global ecosystems. Bulk RNA shotgun sequencing – metatranscriptomics – has transformed our understanding of the virosphere, providing a uniquely powerful means to describe the viral composition of any sample, and helping to reveal how viruses move across the human-animal interface and eventually emerge as new infectious diseases. However, the metagenomic identification of RNA viruses has traditionally been limited to those with sequence similarity to known viruses, such that highly divergent viruses that comprise the “dark matter” of the virosphere remain challenging to detect. Herein, I will show how metatranscriptomics, combined with advances in artificial intelligence (AI) technology that can integrate primary sequence and structural information to accurately and efficiently detect viral sequences, is providing new insights into fundamental aspects of virus evolution, ecology and emergence. I will use metatranscriptomics to identify the fundamental drivers of virus diversity and evolution at the scale of individual ecosystems, revealing the impact of host barriers to cross-species virus transmission. I will also show how a combination of metatranscriptomics and AI has led to the discovery of tens of thousands of novel RNA viruses, redefining our knowledge of the scale and composition of the virosphere. The RNA viruses newly identified were far more divergent than those described previously, and present in diverse ecological niches, including the air, hot springs and hydrothermal vents, varying dramatically in abundance between ecological types.

Bio: Eddie Holmes is an NHMRC Leadership Fellow and Professor of Virology in the School of Medical Sciences, University of Sydney, Australia, which he joined in 2012. Eddie received his undergraduate degree from the University of London (1986) and his Ph.D. from the University of Cambridge (1990). Between 1993-2004 he held various positions at the University of Oxford, including University Lecturer in Evolutionary Biology and Fellow of New College. He was elected a Fellow of the Australian Academy of Science (FAA) in 2015 and of the Royal Society (FRS) in 2017. In 2017 he won the New South Wales Premier’s Prize for Science and Engineering – Biological Sciences and in 2020 he won the overall New South Wales Premier’s Prize for Science and Engineering. In 2021 he received the Prime Minister’s Prize for Science.