Malathi 1 and P. Renuka Devi 2. Renuka Devi. Author information Article notes Copyright and License information Disclaimer. Malathi, Email: moc. Corresponding author. Received Mar 4; Accepted Mar This article has been cited by other articles in PMC. Abstract Single-stranded ss DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens.
Introduction Recent advances in metagenomic sequencing involving large population of viruses in environmental samples have revealed an astonishing volume of virome in every habitat in the biosphere. Open in a separate window. Classification of ssDNA viruses into families with progress of time. Table 1 Overall properties of ssDNA viruses. Capsid protein The virion particles of the most of the ssDNA viruses have icosahedral morphology, except Inoviridae and Spiraviridae with helical morphology: the pleomorphic 40 nm size enveloped virions are met with only in the case of Pleolipoviridae infecting archaea.
Ecology and distribution of ssDNA viruses ssDNA viral genome sequences have been detected in diverse environments, associated with diverse life forms which need to be analyzed to speculate the global impact such distribution will have.
Endogenisation and horizontal gene transfer of ssDNA viruses Deep sequencing of eukaryotic genome increasingly has thrown out abundant and more diverse viral sequences. Horizontal gene transfer Living organism acquire genes not only by vertical transmission but also from other distantly related species through horizontal gene transfer.
Evolutionary trends The eukaryotic ssDNA viruses infecting plants and pet animals emerge as threatening pathogens due to high rate of substitution in genome. Origin and evolution of ssDNA viruses In the context of ever-growing presence of diverse ssDNA viruses, it is interesting to speculate their origin and how different lineages might have separated from each other.
Transboundary movement With increasing trade and movement of agricultural commodities it is inevitable that ssDNA viruses move across continents. Concluding remarks The ssDNA viruses constitute the widespread, diverse and important group of viruses affecting all three domains of life. Footnotes Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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Annotation of these sequences will certainly contribute to studies on giruses. However, one obstacle to studying these viruses is that currently none of the eukaryotic viruses described in this review can be genetically modified by molecular techniques.
The development of successful and reproducible host transformation procedures should lead to the genetic analysis of these viruses, which would be a major achievement. It is obvious that the discovery and characterization of giruses are in their infancy and that many more interesting and unusual members await discovery.
For example, metagenomic studies on environmental microbial DNA sequences collected in the Sargasso Sea revealed many homologs of Mimivirus genes. Thus, many Mimivirus relatives certainly exist in nature, some of which probably infect novel protists. Classifying these newly discovered large viruses will be complicated because of horizontal gene swapping. The origin of giruses is controversial. One interesting suggestion is that amoebae, which harbor many diverse microorganisms, such as viruses, are melting pots for gene mixing, leading to new viruses, including large viruses with complex gene repertoires of various origins 6.
Really big dsDNA viruses giruses , with genomes up to 1. Giruses infect a variety of hosts, bacteria, protists, and animals. Thus, their sizes are not restricted to a specific host or phylogenetic clade.
Giruses are much more diverse than might be expected. For example, they have diverse capsid structures, lifestyles, and genome structures. Giruses that infect the same hosts and are members of the same family, e. Many giruses are evolutionarily old, possibly going back to the time prokaryotes and eukaryotes diverged. The majority of the predicted CDSs in giruses do not match anything in gene databases, indicating these viruses are a rich source of novel biochemical functions yet to be discovered.
We thank Michele Malchow for help with the figures. This puts an upper size limit on the genome, and in fact the DNA is usually packed as tightly as physically possible. This agrees with the circularly permuted and terminally redundant structure of the phage DNAs. National Center for Biotechnology Information , U.
Annu Rev Microbiol. Author manuscript; available in PMC Oct 1. James L. Van Etten , 1, 2 Leslie C. Lane , 1 and David D. Dunigan 1, 2. Van Etten. Leslie C. David D. Author information Copyright and License information Disclaimer. Corresponding author — J. Van Etten, ude. Copyright notice. The publisher's final edited version of this article is available at Annu Rev Microbiol. See other articles in PMC that cite the published article.
Abstract Viruses with genomes greater than kb and up to kb are being discovered with increasing frequency. Introduction Typically, one views viruses as small particles that readily pass through 0. Table 1 Giruses and their properties. Open in a separate window. Figure 1. Discovery of Large Viruses Most large viruses have been discovered and characterized in the last few years. Large DNA Virus Families Many of the viruses listed in Table 1 probably have a common evolutionary ancestor, perhaps arising before the divergence of the major eukaryotic kingdoms 26 , 51 , 64 , Brief Descriptions of Some Large Viruses Mimiviridae Mimivirus, Mamavirus, and Marseillevirus all infect amoebae; the first two are the largest viruses ever reported 9.
Chlorella viruses The chlorella viruses genus Chlorovirus infect symbiotic chlorella, often called zoochlorellae, which are associated with the protozoan Paramecium bursaria , the coelenterate Hydra viridis , and the heliozoon Acanthocystis turfacea 58 , Emiliania huxleyi virus The coccolithophore Emiliania huxleyi is a globally important unicellular marine phytoplankton. Ectocarpus siliculosus virus Ectocarpus siliculosus virus 1 EsV-1 is the type species for the genus Phaeovirus and its infection strategy is regarded as typical for the genus 59 , Nimaviridae The first reported appearance of WSSV occurred in — in shrimp farms in southern provinces of mainland China and also in northern Taiwan.
Bacteriophage Large dsDNA bacteriophages are being discovered with increasing frequency Concluding Remarks Although giruses are probably ancient, they are relatively new to virologists.
Glossary WSSV White spot shrimp virus CDS protein-encoding gene Polydnaviruses Polydnaviruses that infect thousands of species of endoparasitic wasps have complex lifestyles and large, multipartite genomes. Two genera Bracovirus and Ichnovirus represent this family, and these viruses manipulate the defenses, development, and physiology of the parasitized lepidopteran larval hosts, where the virus facilitates a symbiotic or mutualistic condition of the wasp larvae with an otherwise resistant lepidopteran host.
The viruses are evolutionarily linked to the family Baculoviridae 3. The life cycle of polydnaviruses life cycle may be the most complex known in virology. In both wasp and lepidopteran cells, the virus has a closed circular DNA that replicates in the nucleus.
In the case of bracoviruses, replication and particle production occur only in the ovaries of the wasp and the virus is transmitted vertically, yet the virions contain no bracovirus structural proteins. Rather, the structural components are derived from a baculovirus. In addition, their protein-encoding genes have little relationship to free replicating viruses. Footnotes 1 For example, References 8 , 52 , 40 , and comments by seven others in Nat.
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The structure and evolution of the major capsid protein of a large, lipid-containing, DNA virus. Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus.
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Ultrastructural characterization of the giant volcano-like virus factory of Acanthamoeba polyphaga Mimivirus. This pattern has been reported for a range of emerging viral diseases Figure 3.
This framework has been used successfully to monitor the epidemiology of measles virus in the United Kingdom after a decrease in childhood vaccination rates in the late s and indicated the approach to the critical threshold that corresponded to loss of herd immunity Changes in pyramid level might be mediated by virus evolution or changes in virus ecology A major issue is whether the capacity of a virus to spread in human populations arises as a result of adaptation evolution of transmissibility that occurs during human infection or preadaptation genetic variation within nonhuman reservoirs that predisposes a virus not only to infect humans but also transmit between humans, noting that RNA viruses often show high levels of genetic variation such that they are sometimes described as quasi-species [ 29 ].
These alternatives have been characterized as tailor-made and off-the-shelf, respectively The first alternative implies a progression from no or low transmissibility between humans to moderate or high transmissibility. The second alternative implies moderate or high transmissibility at first infection of humans. We consider that our survey of documented changes of pyramid level is most consistent with the off-the-shelf model of virus emergence.
In particular, we can find no convincing examples of level 2 viruses becoming level 3 or 4 viruses, which suggests that, if this happens at all, it typically happens sufficiently rapidly i.
In contrast, we regularly observe viruses at levels 3 or 4 the first time they are detected in human populations.
Nonetheless, the possibility of virus evolution of transmissibility in a new host has been demonstrated experimentally for influenza A H5N1 virus in ferrets A theoretical study 31 suggested that the fact that this virus subtype has been circulating widely in poultry populations, with frequent human exposure and sporadic human infection for almost 20 years, provides little or no reassurance about its future evolutionary trajectory.
HIV lineages show clear evidence of adaptation to humans 16 , but as discussed earlier, it is not clear whether the SIV lineages that gave rise to HIV-1 or HIV-2 were capable of transmission between human hosts. We speculate that extended infection times make tailor-made emergence more likely for retroviruses.
Demonstrating that an infected human has the potential to transmit the infection to another human is not always straightforward. High virus titers in body secretions and excretions, blood, or skin are considered indicative. Case clusters are suggestive, but if persons occupy the same environment e. Case clusters must be epidemiologically plausible i. Genotyping techniques are useful tools for confirming a cluster but do not resolve the source of infection.
For several of the viruses we studied e. Such assessments can be even more difficult for vectorborne viruses. In many situations, the best evidence for the human-to-human transmission will come from analysis of virus genome sequences.
One approach to resolving the question of human-to-human transmission is analysis of nucleotide sequence data, sometimes referred to as forensic phylogenetics.
Estimates of the transmission chain from temporal sequence data can be improved by incorporating additional information on the date of onset of individual cases, duration of latent and infectious periods, and overall prevalence Figure 4. Phylogenetic trees for simulated emerging infectious disease outbreaks caused by RNA and DNA viruses in a mixed population of 1, human and 5, nonhuman hosts.
Trees were constructed by using a We provide some example phylogenetic trees generated from simulated epidemics Figure 4. In an epidemic in an animal reservoir with occasional transmission to humans Figure 4 , panel A , for each human sequence, the most closely related next sequence is of animal origin. Clusters of closely related human sequences are shown, and the distribution of the expected cluster sizes is a function of R 0 Figure 4 , panels B, C In an outbreak, it might be difficult to find and sample the putative source animal cases.
However, estimating the time to most recent common ancestor TMRCA of the human cases will indicate how long the infection has been spreading.
For sporadic zoonoses Figure 4 , panel A , most transmission has occurred unobserved in the animal reservoir, and the TMRCA of pairs of human cases will be long because these sequences are not closely related. For outbreaks involving human-to-human transmission Figure 4 , panels B, C , the TMRCA of the cluster of human cases will be closer to the date of the first human infection whether sampled or not and provides the estimated date of the zoonotic event.
Use of sequence data to distinguish between multiple instances of human infection from a common animal source and human-to-human transmission in the early stages of an outbreak is extremely challenging because of short timescales, and involvement of few mutations. However, genetic differences and phylogenetic evidence show that at least 2 of the first 3 reported cases of influenza A H7N9 virus infection in humans were believed to originate from distinct domestic avian sources Similarly, detection of genetically distant lineages of MERS-CoV, which persisted for only a few months each, suggest multiple introductions from an animal reservoir and only limited human-to-human transmission to date In contrast, the influenza A H1N1 pandemic in and the EVD epidemic in West Africa in were believed to be the results of single zoonotic events, followed by sustained human-to-human transmission 33 , as shown by a single rapidly expanding lineage.
Our survey of the capacity of RNA and DNA virus infections to be transmitted, directly or indirectly, between humans leads to several conclusions and practical suggestions for improving surveillance of emerging infectious diseases and targeting efforts to identify future public health threats. In support of these conclusions, the World Health Organization recently published list of priority emerging infectious diseases and corresponding viruses 38 included 6 of the viruses in Table 2.
A major observation is that the taxonomic diversity of viruses that are possible threats to public health is wide, but bounded. Most human infective viruses are closely related to viruses of other mammals and some to viruses of birds. There are no indications that humans acquire new viruses from any other source. However, diversification within human populations occurs and is a prominent feature of some DNA virus taxa e. In general, however, our knowledge of origins of human viruses is still incomplete.
Although the origins of HIV-1 have been extensively investigated 16 , for most other viruses, even level 4 viruses, little or no research has occurred. An origins initiative 9 would help establish the routes into human populations that have been used by other viruses. Transmissibility within human populations is a key determinant of epidemic potential. Many viruses that can infect humans are not capable of being transmitted by humans; most human transmissible viruses that emerge already have that capability at first human infection or acquire it relatively rapidly.
If transmission from humans would require a change in a phylogenetically conserved trait, such as tissue tropism or transmission route 4 , then such viral paradigm shifts will probably be extremely rare However, because changes in virus traits or host population characteristics can influence R 0 , level 3 viruses Table 2 are of special interest from a public health perspective, and of special concern when, like MERS-CoV, they also cause severe illness.
Demonstrating human transmissibility is often difficult, but essential. The best evidence is likely to come from virus genome sequencing studies. These studies should be a public health priority We currently have few clues to help us predict which mammalian or avian viruses might pose a threat to humans and, especially, which might be transmissible between humans.
One argument in favor of experimental studies of these traits, including controversial gain of function experiments 30 , is that they could help guide molecular surveillance for high-risk virus lineages in nonhuman reservoirs. The first line of defense against emerging viruses is effective surveillance A better understanding of which kinds of viruses in which circumstances pose the greatest risk to human health would enable evidence-based targeting of surveillance efforts, which would reduce costs and increase probable effectiveness of this endeavor.
His primary research interests are pathogen emergence and antimicrobial drug resistance. Table of Contents — Volume 22, Number 12—December Please use the form below to submit correspondence to the authors or contact them at the following address:.
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The score is derived from an automated algorithm, and represents a weighted count of the amount of attention Altmetric picked up for a research output. Section Navigation. Facebook Twitter LinkedIn Syndicate. Figure 1 Figure 2 Figure 3 Figure 4. Table 1 Table 2. Article Metrics. Abstract Many new and emerging RNA and DNA viruses are zoonotic or have zoonotic origins in an animal reservoir that is usually mammalian and sometimes avian.
Figure 1 Figure 1. Data and Analysis. Identifying and Characterizing Level 3 and 4 Viruses We updated our previous systematic literature review 10 of the capacity of virus species to transmit between humans i. Level 1 to Levels 3 and 4 Virus species of mammalian and, more rarely, avian origin are sometimes observed to be transmissible between humans when first found in humans, which constitutes a jump from level 1 straight to level 3 or 4 Figure 1 , and events of this kind have been reported regularly.
Level 2 to Levels 3 and 4 The possibility that level 2 viruses might acquire the capacity to be transmitted between humans i.
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