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Wednesday, 12 February 2020

Discovery of a mysterious virus in Brazil whose genome is almost completely unknown


Paulo VM Boratto et al. 2020

With almost 5000 species currently described, viruses are ubiquitous on Earth. From the bottom of the oceans to the human blood via the atmosphere, these acaryotic infectious agents can adopt extremely simple as well as extremely complex structures; as such, virologists have been studying them for many years, focusing more and more on viral genomes. And recently, a team of researchers discovered a virus whose genome is unlike any other known viral genome.

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The Yaravirus , named after Yara - or Iara, a figure of water queen in Brazilian mythology -, was recovered from Lake Pampulha, an artificial lake in the Brazilian city of Belo Horizonte. The Yaravirus ( Yaravirus brasiliensis ) constitutes a new line of amoebic viruses with a confusing origin and phylogeny, according to the research team.

Virologists Bernard La Scola from the University of Aix-Marseille in France and Jônatas S. Abrahão from the Federal University of Brazil Minas Gerais, however, are not beginners. Two years ago, the duo helped discover another aquatic viral novelty: the Tupanvirus, a potentially giant virus found in extreme aquatic habitats.



Giant viruses: that can perform complex biological tasks

Giant viruses, unlike the regular variety, are so called because of their huge capsids (protein shells that encapsulate virions). These much larger viral forms were only discovered this century, but they are not only remarkable for their size. They also have more complex genomes, giving them the ability to synthesize proteins, and therefore to perform complex tasks such as DNA repair, as well as DNA replication, transcription and translation.

Before their discovery, it was thought that viruses could not do such things, being considered as relatively inert and non-living entities, only capable of infecting their hosts. We now know that viruses are much more complex than previously believed, and in recent years scientists have discovered other types of viral forms that also challenge our thinking about how viruses can spread. and operate. The new discovery, the Yaravirus, does not appear to be a giant virus, made up of small 80 nm particles.

Transmission electron microscopy images of the Yaravirus (A) and its infection cycle (B, C, D, E). Credits: Paulo VM Boratto et al. 2020

Yaravirus: an almost completely new genome virus

But what is remarkable is how unique its genome is. “Most of the known amoeba viruses have been seen to share many features that ultimately prompted the authors to classify them into common evolving groups. Contrary to what is observed in other viruses isolated from the amoeba, the Yaravirus is not represented by a giant size and a complex genome, but at the same time carries a significant number of genes not previously described", write the authors.

Circular representation of the Yaravirus genome. Only six genes (red arrows) in total are identical to known viral genes. Credits: Paulo VM Boratto et al. 2020

In their investigations, the researchers discovered that more than 90% of the genes of Yaravirus had never been described before, constituting what are called orphan genes (ORFans). Only six genes found by far resembled known viral genes documented in public scientific databases, and a search among more than 8,500 metagenomes available to the public gave no clue as to what the Yaravirus could be closely linked to.

Giant viruses with more reduced viral forms?

“Using standard protocols, our very first genetic analysis could not find any recognizable capsid or other conventional viral genes sequences in the Yaravirus. According to current metagenomic protocols for viral detection, the Yaravirus would not even be recognized as a viral agent”.



As for what Yaravirus really is , the researchers can only speculate for the moment, but suggest that it could be the first isolated case of an unknown group of amoebic viruses, or potentially of a distant type giant virus that could have evolved into a reduced form.


Bibliography:

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

doi: https://doi.org/10.1101/2020.01.28.923185

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