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APC researchers boost catalog of ssRNA viruses

The first biological entity to have its genome fully sequenced (in 1976) was that of an RNA virus. Unlike recent RNA viruses that have been in the news, this virus infects and kills a bacterium. In the intervening four decades, while many thousands of additional viruses and bacteria have had their genomes sequenced, bacterial RNA viruses have been largely overlooked.

Now Julie Callanan and Stephen Stockdale, a PhD student and postdoctoral scientist at APC Microbiome Ireland SFI Research Centre in University College Cork, have analysed data from environmental samples sourced from America, Austria, Japan and Singapore. They identified 15,611 new fragments of RNA viruses, including over 1000 full length genomes.

This massive expansion of genomic information allowed comparisons of these extraordinary viruses that was previously impossible. They showed there are two highly distinct lineages of ssRNA phages that share a highly conserved genome architecture. Unlike many other virus families, there is no evidence for homologous recombination or genome mosaicism.

The availability of so many additional ssRNA phage genomes has allowed them to propose a flexible taxonomic structure which includes two families, eight subfamilies, 247 genera and 331 species (to replace the current scheme that is comprised of only two genera).

“It is a rare and exciting event when our knowledge of an entire biological entity expands more than 60-fold in a single study” said Prof Colin Hill, leader of the research team. “Understanding the biology of these bacterial predators will inform our ability to detect and control viruses of bacteria, and perhaps eventually even those infecting humans”.

The new study is published in the prestigious journal Science Advances.

Full reference:

Expansion of known ssRNA phage genomes:  From tens to over a thousand

J.Callanan, S. R. Stockdale, A Shkoporov, L.A. Draper, R.P. Ross & C.Hill Sci. Adv. 2020; 6 : eaay5981 7 February 2020