Tupanvirus is a
genus
Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
of
virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsky's 1 ...
es first described in 2018.
The genus is composed of two species of virus that are in the
giant virus
A giant virus, sometimes referred to as a girus, is a very large virus, some of which are larger than typical bacteria. All known giant viruses belong to the phylum '' Nucleocytoviricota''.
Description
While the exact criteria as defined in the ...
group. Researchers discovered the first isolate in 2012 from deep water sediment samples taken at 3000m depth off the coast of
Brazil
Brazil ( pt, Brasil; ), officially the Federative Republic of Brazil (Portuguese: ), is the largest country in both South America and Latin America. At and with over 217 million people, Brazil is the world's fifth-largest country by area ...
.
The second isolate was collected from a
soda lake
A soda lake or alkaline lake is a lake on the strongly alkaline side of neutrality, typically with a pH value between 9 and 12. They are characterized by high concentrations of carbonate salts, typically sodium carbonate (and related salt complex ...
in Southern Nhecolândia, Brazil in 2014.
They are named after Tupã (Tupan), a Guaraní thunder god, and the places they were found. These are the first viruses reported to possess genes for amino-acyl tRNA synthetases for all 20 standard
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...
s.
Classification
The genus Tupanvirus was first described in 2018 with the discovery of the two isolates of tupanviruses found in soda lake and deep oceanic sediments samples collected in Brazil.
The genus is currently unassigned but hypothesized to be a member of the family ''
Mimiviridae
''Mimiviridae'' is a family of viruses. Amoeba and other protists serve as natural hosts. The family is divided in up to 4 subfamilies., UCPMS ID: 1889607PDF/ref> Fig. 4 and §Discussion: "Considering that tupanviruses comprise a sister gr ...
'', along with the other amoeba-infecting viruses.
Members of the family ''Mimiviridae'' includes ''
Acanthamoeba polyphaga mimivirus'' (APMV) that is known for its large size of ~500 nm in diameter.
In contrast, the typical virus size range is approximately 20-200 nm. Mimiviruses also possess
fibril
Fibrils (from the Latin ''fibra'') are structural biological materials found in nearly all living organisms. Not to be confused with fibers or filaments, fibrils tend to have diameters ranging from 10-100 nanometers (whereas fibers are micro ...
structures on the capsid as well as genes encoding proteins for nucleotide synthesis and various metabolisms that are not found in other viruses.
Unlike the other mimiviruses in the ''Mimiviridae'', tupanvirus has a ~550 nm long cylindrical tail covered with fibrils that is attached to the base of the
capsid
A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or ma ...
.
This morphological feature makes tupanvirus the largest described virus (approximately ~ 1.2 μm in length with the tail) with the longest tail ever observed a in virus.
Tupanviruses are also capable of infecting a wider range of amoebae than other mimiviruses, and produce a
cytotoxic effect in host and non-host organisms that is not observed in APMV.
In addition, phylogenomic results revealed that the genus Tupanvirus is separate from the other viruses in the family ''Mimiviridae''.
Morphology
The morphology of Tupanvirus can be similarly compared to that of other ‘amoeba-infecting mimiviruses’.
This is because of similarities between the capsid of Tupanvirus and that of other amoebae-infecting mimiviruses.
The capsid of Tupanvirus measures approximately 450 nm.
One major difference is that the Tupanvirus virion presents a large cylindrical tail (~550 nm × 450 nm diameter) attached to the base of the capsid.
Both the capsid and cylindrical tail are covered in fibrils.
Tupanvirus can measure up to 1.2 um in length, and some particles can reach up to 2.3 μm because of the “high degree of plasticity in the size of the tail”.
Also to note is a lipid membrane is seen within the capsid. Additionally, their capsid is described as having a ‘stargate structure’.
This star-shaped vertex is present in other mimivurises, and acts as a seal for the apex of the capsid. It has also been stated that the tail of Tupanvirus is less electron dense than the capsid.
Genome
![Tupanvirus-Translational-Factors](https://upload.wikimedia.org/wikipedia/commons/0/09/Tupanvirus-Translational-Factors.png)
The genome contains roughly 1.5 million
base pairs of double-stranded
DNA, coding for 1276–1425 predicted proteins, making it the fourth largest among viral genomes.
While 30% of the genes are new and not found in other viruses, genomic analysis shows most of the known genes can be related to amoeba-infecting mimiviruses, with the rest corresponding to eukaryotes and bacteria. The shared genes of tupanvirus with different lineages of amoeba-infecting mimiviruses indicate it as a separate genus within family Mimiviridae.
For example, its A/T rich genome resembles that of other amoebal mimiviruses and suggests a preference for codons formed by A/T-rich sequences. As well, the frequent occurrence of the “AAAATTGA” promoter motif is also similar to that of other mimiviruses.
As a giant virus, tupanvirus presents the largest
translational apparatus within the known virosphere, carrying 20 aminoacyl tRNA synthetase (aaRS) and 70 transfer RNAs (tRNA), while the rest are involved in RNA maturation and splicing, as well as ribosomal protein modification.
Moreover, tupanviruses contain a number of DNA-independent RNA synthesizing polymerases and enzymes as well as transcription factors that are involved in viral transcription.
Furthermore, many genes that encode for processes found in cellular organisms are also found in the Tupanvirus genome, which contains a richer gene set than some bacteria and archaea, and even some eukaryotes.
As a result, the analysis of tupanviruses constitutes a new step towards understanding the evolution of giant viruses, because such diverse and complete gene sets not only surpass that of other viral genomes, but also rival that of bacteria and even eukaryotes. In fact, tupanvirus is the only known virus to host all 20 aaRS, exceeding other giant viruses like
Klosneuvirus
''Klosneuvirus'' (KNV, also KloV) is a new type of giant virus found by the analysis of low-complexity metagenomes from a wastewater treatment plant in Klosterneuburg, Austria. It has a 1.57-Mb genome coding unusually high number of genes typic ...
; yet, there is no agreement on whether these genes are host-derived or passed down from an ancestral mimivirus.
One such extraordinary example are two copies of an 18 S rRNA intronic region that are highly expressed during viral replication. Although these intronic regions also exist in other mimiviruses, the tupanvirus 18S rRNA is phylogenetically different with their function still unknown.
Host
![Amoebal-Clustering-Tupanvirus](https://upload.wikimedia.org/wikipedia/commons/c/cc/Amoebal-Clustering-Tupanvirus.jpeg)
Tupanviruses have the ability to infect a wider range of hosts than other giant viruses, including many
amoeba
An amoeba (; less commonly spelled ameba or amœba; plural ''am(o)ebas'' or ''am(o)ebae'' ), often called an amoeboid, is a type of cell or unicellular organism with the ability to alter its shape, primarily by extending and retracting pseudop ...
e of the genus
Acanthameoba (as well as members of the species Vermamoeba vermiformis,
Dictyostelium discoideum
''Dictyostelium discoideum'' is a species of soil-dwelling amoeba belonging to the phylum Amoebozoa, infraphylum Mycetozoa. Commonly referred to as slime mold, ''D. discoideum'' is a eukaryote that transitions from a collection of unicellular ...
and Willartia magna),
and may also infect other
protist
A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the exc ...
s. There are no documented threats to humans.
The tupanvirus’
generalist
A generalist is a person with a wide array of knowledge on a variety of subjects, useful or not. It may also refer to:
Occupations
* a physician who provides general health care, as opposed to a medical specialist; see also:
** General pract ...
approach may be attributed to the low species richness and abundance of the virus’ habitat.
Tupanvirus-infected amoebas also present a new virus-host interaction not previously observed among other amoebae. Infected cells were found to aggregate with non-infected cells, a mechanism suggested to be mediated by
mannose binding protein gene expression (MBP).
The clusters of affected cells were shown to increase viral dissemination within the host, thus increasing virulence of the virus.
The generalist approach, in conjunction with aggregation behaviour, decreases the dilution effect and increases host-encounter rates.
Life cycle and host interaction
Attachment
Viral particles attach directly to the host cell surface.
The attachment process occurs very rapidly. Virions can be visibly attached at 0 hours past infection. The specific mechanism is still unknown.
Entry
Virions enter via
phagocytosis
Phagocytosis () is the process by which a cell uses its plasma membrane to engulf a large particle (≥ 0.5 μm), giving rise to an internal compartment called the phagosome. It is one type of endocytosis. A cell that performs phagocytosis is ...
.
Generally only one particle will be present in each
phagosome
In cell biology, a phagosome is a vesicle formed around a particle engulfed by a phagocyte via phagocytosis. Professional phagocytes include macrophages, neutrophils, and dendritic cells (DCs).
A phagosome is formed by the fusion of the cell ...
, although several particles may enter the intracellular matrix in different phagosomes at the same time.
This Tupanvirus uses
membrane fusion
A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Membranes can be generally classified into synthetic membranes and biological membranes. B ...
in order to release its genome. The viral capsid contains a lipid membrane that facilitates fusion with the phagosome membrane to release the viral genome. The virus also releases the contents kept in the tail after an invagination of the phagosome between the two tail components results in fusion.
Replication
The viral genome is released from the phagosome into the amoeba’s
cytoplasm
In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. ...
.
This virus facilitates aggregation of amoeba hosts in order to replicate rapidly and have a supply of hosts for progeny particles.
Bunch formation happens rapidly after infection and will continue as long as host cells are living. Bunches can re-form after mechanical separation as long as host cells are living.
Replication factories are formed as early as 8 h.p.i. up to 12 h.p.i.
Assembly
Initially, when replication factories are still immature, new virions are assembled as soon as possible.
Therefore, many particles at various stages of assembly may be present inside a single factory. Once the factory has matured capsid assembly is finished and the genome is incorporated. The tails are attached to the capsid following genome incorporation.
Assembly of particles happens on a loose timeline, resulting in particles at varying stages of assembly at the time of release.
Release
Viral particles are released, facilitated by cell
lysis.
When infecting the amoeba in the species ''Vermamoeba vermiformis'' many assembled particles are not functional at the time of release. As many as half of released particles are not infectious; this phenomenon is also present when infecting host amoeba ''Acanthamoeba castellanii''.
Although more research is required it is hypothesized that the production of non-infectious particles may be a normal part of the replication cycle.
References
{{Taxonbar, from=Q50323864
Virus genera
Bamfordvirae