Phyloseminar
The Platinum Age of Virus Discovery: Why the next 5 years will define the next 5 decades of virology
Transcriptomic/metatranscriptomic sequencing is revolutionizing the exploration of Earth’s virome. Yet analysis methods are inefficient and don’t scale to the available data. The global biology community has freely shared more than 30 petabases (3x10^16 nt) of sequence data from 10+ million biological samples. Painstakingly collected over 15 years, public data encompass all continents, oceans, thousands of animals, plant, and fungal species, and valued at ~$3.6-14.9 billion dollars in direct sequencing cost.
To uncover the total diversity of RNA viruses we developed a cloud-based sequence alignment platform called Serratus (www.serratus.io), with which we analyzed 7.4 million public sequencing datasets for the RNA viral hallmark gene, RNA-dependent RNA polymerase. We identified the equivalent of over 500,000 novel RNA viruses which is over an order of magnitude increase of known virus diversity; including at least nine new species of Coronaviruses (CoV).
Planetary-scale informatics provides us with unprecedented depth of insights with which to describe virus evolution and ecology. Seven of the novel CoV identified are encoded on segmented genomes (of monophyletic origin). The majority of novel nidoviruses were identified in samples from aquatic vertebrates (axolotl, leopard frog, seahorse, fugu fish, etc…) supporting that there is a vast uncharacterized reservoir of marine nidoviruses. With a high-sensitivity search, we detect genome-fragments from over 40 distinct uncharacterized nidoviruses. For both novel and known nidoviruses, we expand virus host-ranges, geographic distributions, ecological niches and identify potential hidden reservoirs in an unbiased manner which at times, challenge our preconceptions about nidovirales.
Explosive growth in data volumes and the breadth of Earth’s biodiversity captured by global biological sequencing, will change bioinformatics in the near future. The next decade of virology will be illuminated by computational advances and requires a shift in our conceptualization of virus discovery and it's applications to pandemic surveillance. What can be learned today (with scalable methods) from Nidovirales lays the foundation for how we will explore the 100+ million virus species we project to discover by 2030.