This bizarre virus has genes never seen before
The newly discovered "Yaravirus" contains genes that have never been seen in any other viruses. (Image: © IHU Aix Marseille University and Microscopy Center/UFMG)
Our planet is teeming with mysterious microbes. Now, in the waters of an artificial lake, scientists may have discovered one of the most mysterious of all: a brand-new virus with genes that have never been seen before.
A couple of years ago, the group collected water samples from the creeks of Lake Pampulha, an artificial lagoon in the city of Belo Horizonte in Brazil, in search of giant viruses — or those with massive genomes — that infect single-celled organisms called amoebas. But when the team went back to the lab and added these samples to amoeba cells to try to catch giant viruses in their attempt to infect the cells, they found a much smaller intruder.
"It was really a big surprise since so far we only know giant viruses infecting amoebas, not small viruses," said senior author Jônatas Abrahão, an associate professor in the microbiology department of the Federal University of Minas Gerais in Brazil. This new virus was only around 80 nanometers in diameter, but all amoeba-infecting viruses that we know of to date are much larger, at more than 200 nanometers, Abrahão told Live Science
The researchers named the tiny virus the "Yaravirus" after "Yara," the mother of waters — an important character in the mythological stories of the Tupi-Guarani indigenous tribes, according to the study.
When the researchers analyzed the microbe's genome, they found that most of them had never been seen in any other viruses. They searched for the Yaravirus' gene signature in thousands of environmental genomic data and found no hint, "indicating how rare this virus is," Abrahão said.
Only six out of 74 genes showed some degree of similarity to other known genes, he added. Some of the known genes are also known to be present in giant viruses — but because Yaravirus is both small in size and genome, it's not a giant virus, Abrahão said. Yet, it infects amoebas like giant viruses do.
"This is one of the reasons why this new virus is so intriguing and we claim that it challenges the classification of DNA viruses," Abrahão said. What's more, DNA viruses are classified based on the protein that makes up their shell, or capsid. The Yaravirus' capsid doesn't resemble any previously known protein. It's also unclear when and where this virus originated and evolved.
"It would be necessary to isolate new viruses similar to Yaravirus to improve our analysis and try to define their origin," he said. Though they isolated the virus only recently, it is possible this virus has been circulating on Earth for ages, Abrahão said.
In any case, Yaravirus doesn't infect human cells.
"If we consider all known viruses by now, we can say that most of them do not represent any threat for our health," Abrahão said. But that doesn't mean we shouldn't care about them. "Viruses are extremely important in [the] environment," helping with nutrient recycling or controlling pests, Abrahão said.
The group hopes to further analyze the features of the virus in an effort to understand how it interacts with amoebas and other potential hosts, and to figure out the microbe's origin and how it evolved. And this study shows "we know only a very small fraction of this diversity" of viruses present on our planet, Abrahão said. "There is still a lot to explore."
This study has not yet been peer-reviewed and was posted online Jan. 28 to the BioRxiv database.
Our planet is teeming with mysterious microbes. Now, in the waters of an artificial lake, scientists may have discovered one of the most mysterious of all: a brand-new virus with genes that have never been seen before.
A couple of years ago, the group collected water samples from the creeks of Lake Pampulha, an artificial lagoon in the city of Belo Horizonte in Brazil, in search of giant viruses — or those with massive genomes — that infect single-celled organisms called amoebas. But when the team went back to the lab and added these samples to amoeba cells to try to catch giant viruses in their attempt to infect the cells, they found a much smaller intruder.
"It was really a big surprise since so far we only know giant viruses infecting amoebas, not small viruses," said senior author Jônatas Abrahão, an associate professor in the microbiology department of the Federal University of Minas Gerais in Brazil. This new virus was only around 80 nanometers in diameter, but all amoeba-infecting viruses that we know of to date are much larger, at more than 200 nanometers, Abrahão told Live Science
The researchers named the tiny virus the "Yaravirus" after "Yara," the mother of waters — an important character in the mythological stories of the Tupi-Guarani indigenous tribes, according to the study.
When the researchers analyzed the microbe's genome, they found that most of them had never been seen in any other viruses. They searched for the Yaravirus' gene signature in thousands of environmental genomic data and found no hint, "indicating how rare this virus is," Abrahão said.
Only six out of 74 genes showed some degree of similarity to other known genes, he added. Some of the known genes are also known to be present in giant viruses — but because Yaravirus is both small in size and genome, it's not a giant virus, Abrahão said. Yet, it infects amoebas like giant viruses do.
"This is one of the reasons why this new virus is so intriguing and we claim that it challenges the classification of DNA viruses," Abrahão said. What's more, DNA viruses are classified based on the protein that makes up their shell, or capsid. The Yaravirus' capsid doesn't resemble any previously known protein. It's also unclear when and where this virus originated and evolved.
"It would be necessary to isolate new viruses similar to Yaravirus to improve our analysis and try to define their origin," he said. Though they isolated the virus only recently, it is possible this virus has been circulating on Earth for ages, Abrahão said.
In any case, Yaravirus doesn't infect human cells.
"If we consider all known viruses by now, we can say that most of them do not represent any threat for our health," Abrahão said. But that doesn't mean we shouldn't care about them. "Viruses are extremely important in [the] environment," helping with nutrient recycling or controlling pests, Abrahão said.
The group hopes to further analyze the features of the virus in an effort to understand how it interacts with amoebas and other potential hosts, and to figure out the microbe's origin and how it evolved. And this study shows "we know only a very small fraction of this diversity" of viruses present on our planet, Abrahão said. "There is still a lot to explore."
This study has not yet been peer-reviewed and was posted online Jan. 28 to the BioRxiv database.
A mysterious 80 nm amoeba virus with a near-complete “ORFan genome” challenges the classification of DNA viruses
Paulo V. M. Boratto, Graziele P. Oliveira, Talita B. Machado, Ana Cláudia S. P. Andrade, Jean-Pierre Baudoin, Thomas Klose, Frederik Schulz, Saïd Azza, Philippe Decloquement, Eric Chabrière, Philippe Colson, Anthony Levasseur, Bernard La Scola, Jônatas S. Abrahão
Abstract
Here we report the discovery of Yaravirus, a new lineage of amoebal virus with a puzzling origin and phylogeny. Yaravirus presents 80 nm-sized particles and a 44,924 bp dsDNA genome encoding for 74 predicted proteins. More than 90% (68) of Yaravirus predicted genes have never been described before, representing ORFans. Only six genes had distant homologs in public databases: an exonuclease/recombinase, a packaging-ATPase, a bifunctional DNA primase/polymerase and three hypothetical proteins. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe.
The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a novel capsid protein with no significant homology with NCLDV major capsid proteins but with a predicted double-jelly roll domain. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.
Significance statement 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. Here we describe Yaravirus, an entity that could represent either the first isolated virus of Acanthamoeba spp. out of the group of NCLDVs or, in alternative evolutive scenario, it is a distant and extremely reduced virus of this group. 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, including one encoding a novel major capsid protein. Metagenomic approaches also testified for the rarity of Yaravirus in the environment.
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