It was discovered in Lake Pampulha, an artificial lake in Belo Horizonte, a city in Brazil, and infects amoeba.
As the world focuses on the coronavirus outbreak centered in China, viruses may be on everyone’s mind, even if some people don’t know what a virus is. For example, many scientists don’t classify viruses as a form of life, despite its ability to infect, duplicate and evolve. Because it cannot reproduce by itself but requires the machinery of the cells it infects to reproduce, most scientists don’t classify it as a form of life.
A virus is essentially a small piece of DNA or RNA inside a protein particle or capsid. The DNA or RNA code for the proteins by which the virus acts. Almost every part of the ecosystem on Earth is susceptible to viruses—animals, plants, bacteria, fungi, amoeba, pretty much everything.
This makes the recent discovery of the Yaravirus so unusual. It was discovered in Lake Pampulha, an artificial lake in Belo Horizonte, a city in Brazil, and infects amoeba.
In the pre-print article published in bioRxiv, the authors say the virus, Yaravirus brasiliensis, constitutes “a new lineage of amoebal virus with a puzzling origin and phylogeny.”
That’s interesting enough, particularly to virologists, but Yaravirus is weird even by the standard of viruses. The two researchers, Bernard La Scola from Aix-Marseille University in France, and Jônatas S. Abrahão from Brazil’s Federal University of Minas Gerais specialize in hunting down new viruses from water sources. Two years ago, for example, they discovered Tupanvirus, a giant virus found in extreme aquatic habitats.
Yaravirus is not a giant virus, however, many viruses have similarities to each other. For example, the coronavirus that is currently causing outbreaks in China and elsewhere, fits clearly into the family of other coronaviruses, which cause colds, and has genetic similarities to SARS and MERS.
Yaravirus really doesn’t.
“Most of the known viruses of amoeba have been seen to share many features that eventually prompted authors to classify them into common evolutionary groups,” the researchers wrote. “Contrary to what is observed in other isolated viruses of amoeba, Yaravirus is not represented by a large/giant particle and a complex genome, but at the same time carries an important number of previously undescribed genes.”
In fact, in analyzing the genome of the Yaravirus, that found more than 90% of its genes had never been described before. This classifies them as orphan genes, also known as ORFans.
Out of the genes, only six in Yaravirus resembled known viral genes in public scientific databases. And they researched more than 8,500 publicly available metagenomes trying to find out what the virus might be closely related to.
“Using standard protocols, our very first genetic analysis was unable to find any recognizable sequences of capsid or other classical viral genes in Yaravirus,” they wrote. “Following the current metagenomic protocols for viral detection, Yaravirus would not even be recognized as a viral agent.”
Nor is this completely unusual. In October 2019, researchers from the Tokyo University of Agriculture and Technology (TUAT) identified a new type of virus found in pig feces. As mentioned earlier, although there is some argument on whether viruses are living or dead or life forms, scientists typically agree on what makes up a virus: a particle with genetic material inside a protective protein container that can infect other cells and then replicate itself.
Which is where the virus they found, which belongs to the family of Picornaviridae, is odd. It doesn’t have structural proteins.
“The recombinant virus we found in this study has no structural proteins,” Tetsua Mizutani, from TUAT, said. “This means the recombinant virus cannot make a viral particle.”
As such, they described it as being a “novel defective” variant with unidentified flanking genes in place of the viral structural proteins these types of viruses, known as enterovirus G (EV-G), typically have.
They dubbed this new virus EV-G type 2, and its lack of structural proteins means it can’t invade a host cell by itself. Which means it can’t reproduce itself. Which brings up the question: then how does it exist?
They theorize that EV-G type 2 might use another virus, called a “helper virus,” to borrow viral structural proteins to infect other cells.
The supporting evidence for this was found in the pig feces they analyzed, where they found about the same amounts of type 1 and type 2 recombinant EV-G genomes.
“Because the type 1 recombinant EV-G was detected in the same feces sample as the new type 2 recombinant EV-G, this type 1 recombinant EV-G, which belongs to [a] different subtype, might have served as the helper virus,” the researchers wrote.
But how this works, and if that’s really what is happening, is still unknown.
“We may be facing an entirely new system of viral evolution,” Mizutani said. “We are wondering how this new virus came to be, how it infects cells or how it develops a viral particle. Our future work will be on solving this mystery of viral evolution.”
These two examples are just some of the puzzles around viruses. There’s quite a bit of speculation on where (and when) viruses come from. The two main hypotheses are the progressive or escape hypothesis and the regressive or reduction hypothesis.
The progressive hypothesis is that viruses originated via a progressive process. Pieces of genetic material that were mobile, that could move around the genome, escaped one cell and entered another.
The regressive hypothesis is that viruses may have originated from something more complex, potentially free-living organisms that lost genetic material over time as they become more parasitic in nature.
But most virologists concede there’s nowhere near enough data for a clear explanation about viral origins. Other theories suggest that viruses may have existed before more complex, cellular life and it is their ability, directly and indirectly, to transfer genetic material, that led to the evolution of cellular life.
