Welcome to CRESSdna.org
Maximum likelihood tree built using CRESS matrix. Light green for Geminiviridae, pink for Genomoviridae, blue for Smacoviridae, brown for Bacilladnaviridae, dark green for Circoviridae, yellow for Nanoviridae, gold for alphasatellites (Alphasatellitidae)
Part of the National Science Foundation's Assembling the Tree of Life.
Many animal-infecting CRESS-DNA viruses are classified into the Circoviridae family. There are two genera within the group, the older Circovirus and the more recently codified Cyclovirus, but both are well represented. At least one disease of economic importance is associated with circovirus infections: post-weaning maturation wasting syndrome in pigs (caused in part by porcine circovirus 2, which is now largely controlled through vaccination in commercial hog production). However, several worldwide veterinary diseases are due to circoviruses, including beak and feather disease and fatal acute diarrhea in dogs.
While some of the environmental isolates assigned to Circoviridae have genomes over 3,000 and 4,000 bases, it also contains some of the smallest genomes of CRESS-DNA viruses – some well-studied circoviruses have genomes ~1700nt long, and circularized putative genomes from metagenomics studies can be even smaller. Most analyzed sequences have two ORFs: the replication-associated protein (Rep, also referred to as the replication initiator protein) and capsid protein (Cp or Cap), with some isolates having had a third ORF experimentally verified, and some sequences having many hypothetical ORFs called that have not yet been studied in the lab.
Both cycloviruses and circoviruses have non-enveloped, icosahedral virions of 15-25nm encapsidating their circular, ssDNA genomes, but while members of Circovirus are found infecting or associated with mammals, birds and fish, cycloviruses have been found infecting or associated with mammals, birds and insects. Sequences assigned to Circovirus have ambisense genomes, with the Rep gene in sense, sequences in Cyclovirus typically are ambisense in the opposite orientation (Rep gene in anti-sense). A great primer on Circoviridae
For more information about Circovirus:
ICTV report on circovirus
ExPASy ViralZone summary of circovirus
Type species: Porcine circovirus 1 (NC_001792.2)
For more information about Cyclovirus:
ICTV report on cyclovirus
ExPASy ViralZone summary of cyclovirus
Type species: Human-associated cyclovirus 8 (KF031466)
The family Geminiviridae is the most speciose family in all of virology. It includes nine genera: Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastrevirus, Topocuvirus and Turncurtovirus. Members of these genera include devastating plant pathogens that have serious economic consequences. For example, African Cassava Mosaic Virus is one of the viruses causing Cassava Mosaic Disease (CMD). This is particularly an issue in sub-Saharan Africa where the disease severely limits the production of cassava, which is the primary starch source in the region. CMD results in an annual loss of 1.2 to 2.3 billion US dollars in sub-Saharan Africa.
Geminiviruses are non-enveloped ssDNA viruses that have monopartite or bipartite circular genomes that are 2.6 to 5.2 kb long. These viruses are transmitted by insect vectors including whiteflies, leafhoppers, aphids and treehoppers. The host ranges of geminiviruses are vast and include both monocot and dicot plants, both cultivated and uncultivated plants. Geminivirus virions are composed of two incomplete icosahedra in a structure that has been described as twinned or geminate. These virions are around 22 by 38 nm in size and contain only one structural protein (CP).
|Genus||ICTV report||ExPASy ViralZone summary||Type species|
Until recently, the family Genomoviridae included one genus with a single species, Sclerotinia gemycircularvirus 1 (SsHADV-1) in the genus Gemycircularvirus. Virions of SsHADV-1 are non-enveloped, isometrically shaped, 20-22 nm in diameter and contain one CP (capsid protein) gene. SsHADV-1 has a circular, ssDNA genome of length 2,166 nucleotides encoding two genes, CP and Rep. This virus infects a plant pathogenic fungus and is transmitted by a mycophagous insect, Lycoriella ingenua. In the year 2017, Rep-based phylogenetic analyses of 121 SsHADV-1 like viruses revealed eight additional genera including Gemykibivirus, Gemygorvirus, Gemykolovirus, Gemykrogvirus, Gemyvongvirus, Gemytondvirus, Gemykroznavirus and Gemyduguivirus.
For more information about Genomoviridae:
ExPASy ViralZone summary of genomoviruses
Type Species (1 of 8): Sclerotinia sclerotiorum hypovirulance associated DNA virus 1 (NC_013116)
The plant infecting CRESS-DNA viruses with more than two genomic segments belong in the family Nanoviridae,
which includes the genera Babuvirus and Nanovirus. One of the most economically important species in the family Nanoviridae is Banana bunchy top virus (BBTV), the type species of babuvirus. BBTV causes
banana bunchy top disease, which is common in banana growing areas such as Southeast Asia, the South Pacific, India and Africa. This virus is transmitted by the banana aphid and causes
plant crumpling, shrinking and chlorosis, which may develop into necrosis.
Viruses in the family Nanoviridae have multipartite genomes consisting of 6 to 8 ~1000 nucleotide segments of circular ssDNA. Five of these DNA components are shared between babuviruses and nanoviruses. (DNA-R, -N, -S, -C and –M). Nanoviruses infect dicots, have 8 genomic DNAs and may include three other DNA components with functions that have yet to be determined (DNA-U1, -U2 and –U4). Babuviruses infect monocots, have 6 genomic DNAs and may include another DNA component with an unknown function (DNA-U4). Each of these components encode a single ORF that is transcribed in one direction, though a second putative ORF has been identified on one segment of BBTV (DNA-R). The virions of these viruses are non-enveloped, sized 17-20nm in diameter and have one CP (coat protein). Additional DNA segments (alphasatellites) are also associated with many viruses in the family and can alter disease symptoms.
For more information about Nanovirus:
ICTV report on nanovirus.
ExPASy ViralZone summary of nanovirus
Type Species: Subterranean clover stunt virus (NC_003818.1)
For more information about Babuvirus:
ICTV report on babuvirus.
ExPASy ViralZone summary of babuvirus
Type Species: Banana bunchy top virus (NC_003479.1)
Smacoviridae is a monophyletic group of CRESS DNA viruses that was proposed in 2015. Many of the viruses now classified in this clade were initially named "stool-associated circular virus (SCV)." These viruses were reported in stool samples of cows, chimpanzees, pigs, turkeys and rats. Related viruses have been found in the feces of humans and other primates, including gorillas, lemurs and black howler monkeys. In 2016, viruses like smacoviruses (SmaCV2 and SmaCV3) were detected in stool samples of individuals suffering from diarrhea in Peru. The role of these viruses in the development of diarrhea in infected individuals is unknown but their presence in individuals suffering from diarrhea is intriguing. Additionally, recent fecal analyses have shown that African non-human primates are carriers of smacoviruses. Type species (1 of 17): Human smacovirus 1 isolate France/12/2008/3454 (NC_026252)
And has been trained on the following Genera:
ProtTest3 with CRESS DNA virus model
This version of ProtTest was modified from source code "prottest3-3.4.2-release.zip" to include an option for CRESS amino acid substitution matrix. The CRESS amino acid substitution matrix is an specific matrix derived from CRESS DNA viral protein sequences. The CRESS matrix .txt file can also be found inside "models" folder within this compressed file.The details concerning this matrix will be made available through future publication.
Please refer inquiries to Siobain Duffy
Email: duffy [at] sebs [dot] rutgers [dot] edu
Phone: 848 932 6299
Foran Hall Room 316
59 Dudley Road
New Brunswick, 08901
Results from Taxonomy prediction