Virus World

New research has uncovered a social world of viruses full of cheating, cooperation and other intrigues, suggesting that viruses make sense only as members of a community.  Ever since viruses came to light in the late 1800s, scientists have set them apart from the rest of life. Viruses were far smaller than cells, and inside their protein shells they carried little more than genes. They could not grow, copy their own genes or do much of anything. Researchers assumed that each virus was a solitary particle drifting alone through the world, able to replicate only if it happened to bump into the right cell that could take it in. This simplicity was what attracted many scientists to viruses in the first place, said Marco Vignuzzi, a virologist at the Singapore Agency for Science, Research and Technology Infectious Diseases Labs. “We were trying to be reductionist.” That reductionism paid off. Studies on viruses were crucial to the birth of modern biology. Lacking the complexity of cells, they revealed fundamental rules about how genes work. But viral reductionism came at a cost, Vignuzzi said: By assuming viruses are simple, you blind yourself to the possibility that they might be complicated in ways you don’t know about yet....

Comparing a living cell to a virus is a bit like comparing the Sistine Chapel to a backyard dog house. Lacking the intricate machinery of living cells, viruses represent biology stripped down to an extreme level. They are the true minimalists of the biological world. Nevertheless, the field of virology is brimming with unanswered questions about these architecturally simple, yet mysterious entities. In new research, Arvind Varsani, a molecular virologist at Arizona State University, joins a prestigious international team to explore a particular class of viruses, ferreting out genetic fragments revealing the complexities of viral evolution.

The new study examines the evolutionary dynamics of circular Rep-encoding single-stranded (CRESS) DNA viruses. The findings show that this broad class of single-stranded DNA viruses, which infect all three cellular domains of life, have acquired their genetic components through complex evolutionary processes not traceable to a single ancestral event. Rather, viruses are obsessive borrowers, appropriating genetic material from many sources, including bacterial, archaeal and eukaryotic cells as well as circular parasitic replicons, known as plasmids, and other mobile genetic elements, such as transposons. When a group of mobile elements—like CRESS DNA viruses— arise from more than a single common evolutionary ancestor or ancestral group, they are known as polyphyletic. The phenomenon is common in the viral world.

Such explorations also hold the potential to shed new light on the origins of earth's earliest life, and resolve the question of how cell-based life came to co-exist with the planet's staggering array of viruses (dubbed the virome). "Over the last decade we have been discovering viruses in various ecosystems using metagenomic approaches and as a result populating the CRESS DNA virus databases," Varsani says. "This has paved the way for a global analysis for CRESS DNA viruses yielding insights into the origin of these and other related viruses." "It is remarkable to see all these evolutionary connections between viruses and non-viral selfish replicons, which once were considered to be unrelated," Krupovic says. The results reveal three distinct evolutionary events contributing to the genetic composition of CRESS-DNA viruses. An intriguing kinship appears to exist between CRESS-DNA viruses and rolling circle plasmids found in bacteria, archaea and some eukaryotes.  "As a result, the general mechanisms of virus evolution as well as the global organization of the vast viral world start to unravel."

Published July 31 2019 in Nature Communications:

https://doi.org/10.1038/s41467-019-11433-0