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The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
Upon a viral outbreak, it is important to rapidly establish whether the outbreak is caused by a new or a previously known virus (Box 1), as this helps decide which approaches and actions are most appropriate to detect the causative agent, control its transmission and limit potential consequences of the epidemic. The assessment of virus novelty also has implications for virus naming and, on a different timescale, helps to define research priorities in virology and public health.
Box 1 Virus discovery and naming: from disease-based to phenotype-free
Understanding the cause of a specific disease that spreads among individuals of the same host species (infectivity) was the major driving force for the discovery of the first virus in plants, and subsequently many others in all forms of life, including humans. Historically, the range of diseases and hosts that specific viruses are associated with have been the two key characteristics used to define viruses, given that they are invisible to the naked eye 46 . Viral phenotypic features include those that, like a disease, are predominantly shaped by virus–host interactions including transmission rate or immune correlates of protection, and others that are largely virus-specific, such as the architecture of virus particles. These features are of critical importance to control, and respond to medically and economically important viruses — especially during outbreaks of severe disease — and dominate the general perception of viruses.
However, the host of a given virus may be uncertain, and virus pathogenicity remains unknown for a major (and fast-growing) proportion of viruses, including many coronaviruses discovered in metagenomics studies using next-generation sequencing technology of environmental samples 47,48 . These studies have identified huge numbers of viruses that circulate in nature and have never been characterized at the phenotypic level. Thus, the genome sequence is the only characteristic that is known for the vast majority of viruses, and needs to be used in defining specific viruses. In this framework, a virus is defined by a genome sequence that is capable of autonomous replication inside cells and dissemination between cells or organisms under appropriate conditions. It may or may not be harmful to its natural host. Experimental studies may be performed for a fraction of known viruses, while computational comparative genomics is used to classify (and deduce characteristics of) all viruses. Accordingly, virus naming is not necessarily connected to disease but rather informed by other characteristics.
In view of the above advancements and when confronted with the question of whether the virus name for the newly identified human virus should be linked to the (incompletely defined) disease that this virus causes, or rather be established independently from the virus phenotype, the CSG decided to follow a phylogeny-based line of reasoning to name this virus whose ontogeny can be traced in the figure in Box 1.
For many human virus infections such as influenza virus 1 or norovirus 2 infections, well-established and internationally approved methods, standards and procedures are in place to identify and name the causative agents of these infections and report this information promptly to public health authorities and the general public. In outbreaks involving newly emerged viruses, the situation may be different, and appropriate procedures to deal with these viruses need to be established or refined with high priority.
Here, we present an assessment of the genetic relatedness of the newly identified human coronavirus 3 , provisionally named 2019-nCoV, to known coronaviruses, and detail the basis for (re)naming this virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which will be used hereafter. Given the public interest in naming newly emerging viruses and the diseases caused by these viruses in humans, we will give a brief introduction to virus discovery and classification — specifically the virus species concept — and the roles of different bodies, such as the World Health Organization (WHO) and the International Committee on Taxonomy of Viruses (ICTV), in this process. We hope this will help readers to better understand the scientific approach we have taken to arrive at this name, and we will also discuss implications of this analysis and naming decision.
The Baltimore classification
The Baltimore classification, developed by David Baltimore in 1971, is a virus classification system that divides viruses into families, depending on their
- Type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds)
- Their method of replication
Viruses placed in a given category will all behave in much the same way, which can point out further the characters of the newly discovered viruses in a specific group.
Seven classes of viruses in the Baltimore Classification System
Seven Baltimore classes of the viruses are given below.
I: Double stranded (ds) DNA viruses( for example Adenoviruses, Herpesviruses, Poxviruses)
II: Single stranded (ss) DNA viruses (+ strand or “sense”) DNA(for example Parvoviruses)
III: Double stranded (ds) RNA viruses(for example Reoviruses)
IV: Single stranded RNA viruses with positive sense strand (+ssRNA) (for example Coronaviruses, Picornaviruses, Togaviruses)
V: Single stranded RNA viruses with negative sense strand (-ssRNA) RNA(for example Orthomyxoviruses, Rhabdoviruses)
VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle(for example Retroviruses)
VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle(for example Hepadnaviruses)
Group I: Double-stranded DNA viruses
These types of viruses enter the host cell nucleus before they are able to replicate. Furthermore, these viruses need host cell polymerases enzymes for replication of the viral genome and, so, are heavily dependent on the host cell cycle. For accurate infection and replication of virus the host cell should be in dividing stage as during replication the cell’s polymerases enzymes are active. The virus may also forcibly induce the cell to undergo cell division, which may lead to the transformation of the normal cell and to cancerous cell mass. Examples include Herpesviridae, Adenoviridae, and Papovaviridae.
Poxvirus family that infects vertebrates and causes the smallpox disease is the only one example in which a class I virus is not replicating within the nucleus
DNA viruses types
Group II: Single-stranded DNA viruses
Group II includes the, Circoviridae, Anelloviridae and Parvoviridae (that infect vertebrates animals), the Microviridae (infect prokaryotes) and the Nanoviridae and Geminiviridae (that infect plants). Majority of these have circular genomes.
Eukaryote-infecting viruses replicate mostly within the nucleus by a rolling circle mechanism. By this all viruses in this group form a “double stranded DNA intermediate molecule” during their genome replication. This is normally created from the viral DNA with the help of the host’s own DNA polymerase.
In 1959, Sinshemer working with phage Phi X 174 showed that they possess single-stranded DNA genomes. Despite this discovery, until relatively recently it was believed that most DNA viruses contained double-stranded DNA.
But today it is well discovered that single-stranded DNA viruses can be highly abundant in the aquatic ecosystems, sediments, terrestrial environments, as well as metazoan-associated and marine microbial mats. Many of these “environmental” viruses belong to the family Microviridae.
Group III: Double-stranded RNA viruses
Double-stranded (ds) RNA viruses are a diverse group of viruses that infect a large range of hosts like animals, bacteria, plants and fungi. Members of this group include the rotaviruses, globally known as a common cause of gastroenteritis in kids, and bluetongue virus, an economically damaging pathogen of cattle and sheep.
This group includes number of families in which two major families, the Reoviridae and Birnaviridae are well known. Of these families, the Reoviridae is the largest and most diverse in terms of host range.
- These viruses are all nonenveloped and have icosahedral capsids and segmented genomes.
- Like the most RNA viruses, these viruses replicates in the “Core” capsid present in the cytoplasm of the host and do not use the replication polymerases of the host cell.
- In these, replication is monocistronic and includes individual segmented genome, which means that each of the genes codes for only one protein, unlike other viruses that exhibit more complex translation.
Group IV & V: Single-stranded RNA viruses
These single stranded RNA viruses belong to Class IV or V of the Baltimore classification. They could be grouped into positive sense or negative sense according to the sense or polarity of RNA molecule. The single stranded RNA is the common feature of these viruses. The replication of viruses happens in the cytoplasm or nucleus of the host cell. Class IV and V ssRNA viruses do not depend as heavily as DNA viruses on the cell cycle.
Group IV: Single-stranded, Positive-sense, RNA viruses
All RNA viruses defined as positive-sense can be directly accessed by the host ribosomes immediately to form proteins. Examples of this class include the families Astroviridae, Caliciviridae, Coronaviridae, Flaviviridae, Picornaviridae, Arteriviridae, and Togaviridae. These can be divided into two groups, both of which reproduce in the cytoplasm.
- Viruses with polycistronic mRNA: In this group, the genome RNA forms the mRNA which is translated into a polyprotein product that is converted to the mature proteins. This means that the gene can use a few methods in which to produce proteins from the same strand of RNA, all in the sake of reducing the size of its gene.
- Viruses with complex transcription, for which subgenomic mRNAs, ribosomal frameshifting, and proteolytic processing of polyproteins may be used. All of which are different mechanisms with which virus can produce proteins from the same strand of RNA.
Group V: Single-stranded RNA viruses – Negative-sense
All the genes defined as negative-sense cannot be directly accessed by host ribosomes to immediately form proteins. Instead, they must be transcribed by viral polymerases into a “readable” form, which is the positive-sense reciprocal. Examples in this class include the families Arenaviridae, Orthomyxoviridae, Paramyxoviridae, Filoviridae, and Rhabdoviridae (the latter of which includes the rabies virus). These can also be divided into two groups:
- Viruses containing nonsegmented genomes: In these, the first step in replication is transcription from the negative stranded genome by the viral RNA-dependent RNA polymerase to form monocistronic mRNAs that code for the various viral proteins. A positive-sense genome copy is then produced that serves as a template for the production of the negative strand genome. Replication occurs within the cytoplasm.
- Viruses with segmented genomes: Here, replication occurs in the nucleus and the viral RNA-dependent RNA polymerase forms monocistronic mRNAs from each segment of the genome. The largest difference between the two is the occurance of replication in different locations.
Group VI: Positive-sense single-stranded RNA viruses that replicate through a DNA intermediate
- A well-studied family of this class of viruses includes the retroviruses.
- One defining feature of this group is the use of reverse transcriptase to convert the +sense RNA into DNA.
- They do not use RNA as templates to make proteins, but use DNA to create the templates, which is spliced into the host genome using integrase. Replication then commences with the help of the host cell’s polymerases.
- Examples: Retroviruses
Group VII: Double-stranded DNA viruses that replicate through a single-stranded RNA intermediate
- This group of viruses has a double-stranded, gapped genome that is subsequently filled in to form a covalently closed circle (cccDNA) that serves as a template for production of viral mRNAs and a subgenomic RNA.
- The pregenome RNA serves as template for the viral reverse transcript to produce the DNA genome.
- Example: Hepatitis B virus (which is in the Hepadnaviridae family)
The most commonly used system of virus classification was developed by Nobel Prize-winning biologist David Baltimore in the early 1970s. In addition to the differences in morphology and genetics mentioned above, the Baltimore classification scheme groups viruses according to how the mRNA is produced during the replicative cycle of the virus.
Group I viruses contain double-stranded DNA (dsDNA) as their genome. Their mRNA is produced by transcription in much the same way as with cellular DNA.
Group II viruses have single-stranded DNA (ssDNA) as their genome. They convert their single-stranded genomes into a dsDNA intermediate before transcription to mRNA can occur.
Group III viruses use dsRNA as their genome. The strands separate, and one of them is used as a template for the generation of mRNA using the RNA-dependent RNA polymerase encoded by the virus.
Group IV viruses have ssRNA as their genome with a positive polarity. Positive polarity means that the genomic RNA can serve directly as mRNA. Intermediates of dsRNA, called replicative intermediates, are made in the process of copying the genomic RNA. Multiple, full-length RNA strands of negative polarity (complimentary to the positive-stranded genomic RNA) are formed from these intermediates, which may then serve as templates for the production of RNA with positive polarity, including both full-length genomic RNA and shorter viral mRNAs.
Group V viruses contain ssRNA genomes with a negative polarity, meaning that their sequence is complementary to the mRNA. As with Group IV viruses, dsRNA intermediates are used to make copies of the genome and produce mRNA. In this case, the negative-stranded genome can be converted directly to mRNA. Additionally, full-length positive RNA strands are made to serve as templates for the production of the negative-stranded genome.
Group VI viruses have diploid (two copies) ssRNA genomes that must be converted, using the enzyme reverse transcriptase, to dsDNA the dsDNA is then transported to the nucleus of the host cell and inserted into the host genome. Then, mRNA can be produced by transcription of the viral DNA that was integrated into the host genome.
Group VII viruses have partial dsDNA genomes and make ssRNA intermediates that act as mRNA, but are also converted back into dsDNA genomes by reverse transcriptase, necessary for genome replication. The characteristics of each group in the Baltimore classification are summarized in Table 3 with examples of each group.
Nongenetic Categories for Medicine and Ecology
In medicine, microorganisms are identified by morphology, physiology, and other attributes in ecology by habitat, energy, and carbon source.
Outline the traits used to classify: bacteria, viruses and microrganisms in ecology
- A pathogen causes disease in its host. In medicine, there are several broad types of pathogens: viruses, bacteria, fungi, eukaryotic parasites, and prions.
- When identifying bacteria in the laboratory, the following characteristics are used: Gram staining, shape, presence of a capsule, bonding tendency, motility, respiration, growth medium, and whether it is intra- or extracellular.
- Viruses are mainly classified by phenotypic characteristics, such as morphology, nucleic acid type, mode of replication, host organisms, and the type of disease they cause.
- In ecology, microorganisms are classified by the type of habitat they require, or trophic level, energy source and carbon source.
- Biologists have found that microbial life has an amazing flexibility for surviving in extreme environments that would be completely inhospitable to complex organisms these are called extremophiles and many kinds exist.
- Different species of microorganisms use a mix of different sources of energy and carbon. These may be alternations between photo- and chemotrophy, between litho- and organotrophy, between auto- and heterotrophy or a combination of them.
- obligate: Able to exist or survive only in a particular environment or by assuming a particular role: an obligate parasite an obligate anaerobe.
- pathogen: Any organism or substance, especially a microorganism, capable of causing disease, such as bacteria, viruses, protozoa, or fungi. Microorganisms are not considered to be pathogenic until they have reached a population size that is large enough to cause disease.
- extremophile: An organism that lives under extreme conditions of temperature, salinity, and so on. They are commercially important as a source of enzymes that operate under similar conditions.
Classifying microorganisms in medicine
A pathogen (colloquially known as a germ) is an infectious agent that causes disease in its host. In medicine, there are several broad types of pathogens: viruses, bacteria, fungi, eukaryotic parasites, and prions.
Although most bacteria are harmless, even beneficial, quite a few are pathogenic. Each pathogenic species has a characteristic spectrum of interactions with its human hosts.
Conditionally, pathogenic bacteria are only pathogenic under certain conditions such as a wound that allows for entry into the blood, or a decrease in immune function. Bacterial infections can also be classified by location in the body, for example, the vagina, lungs, skin, spinal cord and brain, and urinary tract.
When identifying bacteria in the laboratory, the following chatacteristics are used: Gram staining, shape, presence of a capsule, bonding tendency (singly or in pairs), motility, respiration, growth medium, and whether it is intra- or extracellular.
Culture techniques are designed to grow and identify particular bacteria, while restricting the growth of the others in the sample. Often these techniques are designed for specific specimens: for example, a sputum sample will be treated to identify organisms that cause pneumonia. Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (aerobic or anaerobic), patterns of hemolysis, and staining.
Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate due to their pseudo-living nature. Essentially, they are non-living particles with some chemical characteristics similar to those of life thus, they do not fit neatly into an established biological classification system.
Viruses are mainly classified by phenotypic characteristics,such as:
- nucleic acid type
- mode of replication
- host organisms
- type of disease they cause
Currently there are two main schemes used for the classification of viruses: (1) the International Committee on Taxonomy of Viruses (ICTV) system and (2) the Baltimore classification system, which places viruses into one of seven groups. To date, six orders have been established by the ICTV:
These orders span viruses with varying host ranges, only some of which infect human hosts.
Baltimore classification is a system that places viruses into one of seven groups depending on a combination of:
- their nucleic acid (DNA or RNA)
- strandedness (single or double)
- method of replication
Other classifications are determined by the disease caused by the virus or its morphology, neither of which is satisfactory as different viruses can either cause the same disease or look very similar. In addition, viral structures are often difficult to determine under the microscope. Classifying viruses according to their genome means that those in a given category will all behave in a similar fashion, offering some indication of how to proceed with further research.
Other organisms invariably cause disease in humans, such as obligate intracellular parasites that are able to grow and reproduce only within the cells of other organisms.
CATEGORIES OF MICROORGANISMS IN ECOLOGY
In ecology, microorganisms are classified by the type of habitat they require, or trophic level, energy source and carbon source.
Biologists have found that microbial life has an amazing flexibility for surviving in extreme environments that would be completely inhospitable to complex organisms. Some even concluded that life may have begun on Earth in hydrothermal vents far under the ocean’s surface.
An extremophile is an organism that thrives in physically or geochemically extreme conditions, detrimental to most life on Earth. Most known extremophiles are microbes. The domain Archaea contains renowned examples, but extremophiles are present in numerous and diverse genetic lineages of both bacteria and archaeans. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles.
There are many different classes of extremophiles, each corresponding to the way its environmental niche differs from mesophilic conditions. Many extremophiles fall under multiple categories and are termed polyextremophiles. Some examples of types of extremophiles:
- Acidophile: an organism with optimal growth at levels of pH 3 or below
- Xerophile: an organism that can grow in extremely dry, desiccating conditions exemplified by the soil microbes of the Atacama Desert
- Halophile: an organism requiring at least 0.2M concentrations of salt (NaCl) for growth
- Thermophile: an organism that can thrive at temperatures between 45–122 °C
Trophic level, energy source and carbon source
The nutritional modes of an organism: A flowchart to determine if a species is autotroph, heterotroph, or a subtype.
- Phototrophs: carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. They are not obligatorily photosynthetic. Most of the well-recognized phototrophs are autotrophs, also known as photoautotrophs, and can fix carbon.
- Photoheterotrophs: produce ATP through photophosphorylation but use environmentally-obtained organic compounds to build structures and other bio- molecules.
- Photolithoautotroph: an autotrophic organism that uses light energy, and an inorganic electron donor (e.g., H2O, H2, H2S), and CO2 as its carbon source.
- Chemotrophs: obtain their energy by the oxidation of electron donors in their environments.
- Chemoorganotrophs: organisms which oxidize the chemical bonds in organic compounds as their energy source and attain the carbon molecules they need for cellular function. These oxidized organic compounds include sugars, fats and proteins.
- Chemoorganoheterotrophs (or organotrophs) exploit reduced-carbon compounds as energy sources, such as carbohydrates, fats, and proteins from plants and animals. Chemolithoheterotrophs (or lithotrophicheterotrophs) utilize inorganic substances to produce ATP, including hydrogen sulfide and elemental sulfur.
- Lithoautotroph: derives energy from reduced compounds of mineral origin. May also be referred to as chemolithoautotrophs, reflecting their autotrophic metabolic pathways. Lithoautotrophs are exclusively microbes and most are bacteria. For lithoautotrophic bacteria, only inorganic molecules can be used as energy sources.
- Mixotroph: Can use a mix of different sources of energy and carbon. These may be alternations between photo- and chemotrophy, between litho- and organotrophy, between auto- and heterotrophy or a combination of them. Can be either eukaryotic or prokaryotic.
Differing morphology in different Herpes viruses: Various viruses from the Herpesviridae family seen using an electron micrograph. Amongst these members is varicella-zoster (Chickenpox), and herpes simplex type 1 and 2 (HSV-1, HSV-2).
In order to replicate, viruses must first hijack the reproductive equipment of a host cell, redirecting it to ‘photocopy’ the genetic code of the virus and seal it inside a newly formed container, known as the capsid. Without a host cell, the virus simply can’t replicate.
Viruses fail the second question for the same reason. Unlike other living organisms that can self-divide, splitting a single cell into two, viruses must ‘assemble’ themselves by taking control of the host cell, which manufactures and assembles the viral components.
Finally, a virus isn’t considered living because it doesn’t need to consume energy to survive, nor is it able to regulate its own temperature. Unlike living organisms that meet their energy needs by metabolic processes that supply energy-rich units of adenosine triphosphate (ATP), the energy currency of life, viruses can survive on nothing. In theory, a virus can drift around indefinitely until it contacts the right kind of cell for it to bind to and infect, thus creating more copies itself.
That’s three strikes against, but is there anything to suggest that viruses might be alive?
Are viruses alive? New evidence says yes
Influenza, SARS, Ebola, HIV, the common cold. All of us are quite familiar with these names. They are viruses—a little bit of genetic material (DNA or RNA) encapsulated in a protein coat. But what we don’t really understand, and what scientists have struggled with since the study of virology began, is whether viruses are actually living or not. A paper published today in Science Advances just might change that. By creating a reliable method of studying viruses’ long evolutionary history—hitherto nearly impossible—researchers have found new evidence that strongly suggests viruses are indeed living entities.
Scientists have long argued that viruses are nonliving, that they are bits of DNA and RNA shed from other cells. Indeed, based on everything else we know about what it takes to qualify as life, a virus doesn’t seem to fit the bill. There are many life processes, such as the ability to metabolize, that viruses do not do. Viruses seem to carry out only one life process, reproduction, but even then, individual viruses don’t carry translational machinery, namely, the proteins needed to read their DNA and RNA and build new viruses. They invade a cell and hijack its genetic tools to do it for them.
But within the last decade, developments in virology have started to reveal more and more that viruses might in fact be alive. One was the discovery of mimiviruses, giant viruses with large genomic libraries that are even bigger than some bacteria. To put this in perspective, some viruses, like the Ebola virus, have as few as seven genes. Some of these giants have genes for the proteins that are required for translation—those readers of DNA and RNA that in turn build new viruses. This throws the lack of translational machinery argument for classifying them as nonliving on its head.
A universal biology unifying viruses and cells.
Despite some of these new findings, however, one gigantic question mark in the whole discussion was what the evolutionary history of viruses looked like. So University of Illinois crop sciences and Carl R. Woese Institute for Genomic Biology professor Gustavo Caetano-Anolles, and graduate student Arshan Nasir, took on the ambitious task of trying to trace just such a history. Viruses clearly evolve—ask any medical professional—and they have tremendous diversity as well (There are less than 4,900 viruses described so far, but estimates have the total number of viral species at more than a million).
But, because the small DNA and RNA strands within a certain virus are replicated so many times within a single host, and even partially mixed with the host’s DNA during the process, mutations occur often and at a rapid pace, says Caetano-Anolles. This makes studying a virus’s genes to figure out its evolutionary history about as productive as explaining the tenets of quantum mechanics to the Cheshire Cat.
To solve this problem, Caetano-Anolles and Nasir looked instead at protein folds. These are simply, Caetano-Anolles explains, the puzzle-like shapes of proteins unique to viruses and cells that allow them to perform basic molecular functions. The specific shapes of these proteins are coded by genes, and do not change drastically over time, unlike DNA or RNA sequences, thus providing a good marker to look back in history.
An Analysis of Protein Folds Opens a Window on Early Evolutionary Events
And now for the numbers. Caetano-Anolles and Nasir analyzed the protein folds of 5,080 organisms—3,460 viruses and 1,620 cells from other organisms representing every branch of the tree of life. What they found was huge: 442 protein folds were shared between cells and viruses along with 66 folds that were unique to viruses. What this indicates then, is a branching of some kind.
It suggests that viruses were not simply shed genetic material of cells, but shared unique properties with cells (and thus were living) and eventually evolved as separate entities. “We are now able to build truly universal trees of life,” says Caetano-Anolles, “that describe the origin and diversification of organisms and viruses.”
These findings provide some of the strongest evidence yet that viruses are indeed living. “The mere fact of the existence of a universal biology unifying viruses and cells now justifies the construction of a Tree of Life that embraces viruses side by side with cells.” says Caetano-Anolles. The interesting thing about these results is that they indicate that viruses must have diversified from ancient cells by a process called reductive evolution, where organisms simplify instead of becoming more complex. Viruses were likely “more cellular in nature and existed in the form of primitive cells,” explains Nasir. The ancient cells that these primordial viruses resided in were those of the last universal common ancestor that preceded diversified life about 2.45 billion years ago.
At some point, the genomes of these ancient viral cells were reduced or eliminated, to the point where they lost their cellular nature and became modern viruses. Nasir says that “viruses restore their ‘cellular’ existence today when they enter and take control of any cell.” When an infected cell spits out new viruses, it is likely very much like those ancient cells making primitive viruses. “Thus,” Nasir concludes, “in the beginning, virus plus cell existed as a unit. Today, they are split but can restore their association upon viral infection of a cell.”
This study comes on the heels of recent discoveries. Greater understanding of reductive evolution has revealed numerous examples of parasitic organisms like bacteria and fungi that rely on hosts to complete their life cycles. Nasir hopes that their findings added to existing evidence will require scientists to include viruses in the picture of cellular evolution. “Excluding them will always yield an incomplete picture,” he says. That may be overly hopeful, but the researchers are undeterred. Says Caetano-Anolles, “I do hope this will facilitate a sea change in our perceptions of the virosphere.”
Properties of Viruses (with diagram)
Some of the most important properties of viruses are as follows:
1. Viral Size:
The viruses are smallest disease causing agent in living organisms.
The plant viruses range in size from 17nm to 2000nm, while animal viruses range in size from 20- 350 nm.
2. Viral Shape:
The shape of virions greatly varies. For example, rod-shaped or filamentous (TMV), brick-shaped (e.g. Poxvirus), bullet- shaped (e.g. rhabdoviruses or rabies virus), spherical (HIV, influenza, Herpes viruses etc.), tadpole-shaped (e.g. bacteriophages).
Smallest and Largest Viruses:
Smallest Plant Virus: Satellite Tobacco Necrosis virus, 17 nm
Largest Plant Virus: Citrus Triesteza virus, 2000 x 12nm
Smallest Animal Virus: Foot and mouth disease virus, 20 nm
Largest Animal Virus: Small Poxvirus (Variola), 350 x 250 x l00 nm
3. Viral Symmetry:
Viruses have three types of symmetry- helical, polyhedral (cubical) and binal symmetry. The helical symmetry found in rod-shaped virions where the capsomeres (protein subunits) arranged in a helical manner around a central axis, e.g., in TMV. The polyhedral symmetry found in roughly spherical (isometric) virions where the capsomeres are arranged in the form of an icosahedron, a structure with 20 equilateral triangular facets or sides, 12 vertices or corners and has 30 edges, e.g., Polio viruses, adenoviruses, chicken pox, herpes simplex etc. The complex symmetry found in binal virions where head capsid is polyhedral and connected to the helical tail, e.g., bacteriophages.
4. Viral Genome:
All virions are nucleocapsids. Each virion consists of a core of nucleic acid (viral chromosome or genome) and a proteinous sheath called capsid. The viral genome is the molecular blueprints for the building of intact virion. It maybe DNA or RNA which maybe double stranded (ds) or single stranded (ss), and linear or circular.
Viruses with RNA genomes are called ribo-viruses and those with DNA genomes are called deoxyviruses. Plant viruses generally possess RNA genomes, with a few exceptions, such as Cauliflower Mosaic Virus (CMV), which contain DNA. Animal viruses and bacteriophages, on the other hand, generally possess DNA. Only very rarely animal virus possesses RNA.
On the basis of number of strand in the genome (nucleic acid), viruses may be four types:
(a) ss DNA viruses (e.g., colipliages)
(b) ds DNA viruses (e.g., Herpes Virus, Smallpox virus, Vaccina,T-even bacteriophages)
(c) ss RNA viruses (e.g., TMV, Polio virus)
(d) ds RNA viruses (e.g., Reo virus)
Viruses with ss DNA as genome is rare, e.g., parvovirus, bacteriophages like Ø x 174, ml3, fd etc. In ss RNA viruses, the genome ss RNA may be plus-strand RNA (when function as m RNA) or minus-strand RNA (when function to serve as mRNA). In some cases virions possess a segmented genome, e.g., in orthomyxoviruses /minus-strand RNA molecules found.
5. Viral Capsid:
The protective proteinous sheath that surrounds the viral genome is called a capsid. The capsid consists of identical repeating subunits called capsomeres. Each capsomere consists of one or more polypeptide chain called protomere. The number of capsomeres is characteristics for a particular type of viruses. For example, the capsid of Herpes simplex has 162 capsomeres, the adenoviruses have 252 capsomeres. Near the meeting point of capsomeres clefts or canyons present that may accommodate receptors when virus attach to a host cell.
The viral capsid gives shape to the virion. It maybe helical, isometric (nearly spherical), cubical (icosahedron) or binal (tadpole-shaped).
6. Viral Envelop:
Virus particles maybe enveloped or non-enveloped (naked). In enveloped viruses (e.g., most animal viruses like measles, mumps, rabies, influenza and herpes viruses), the nucleocapsid is externally covered by a lipoprotein membrane called envelope. The lipid part is derived from host cell while the protein part is coded by viral genes.
The viral envelope may contain glycoprotein as surface projections which are called as spikes or peplomers. A virion may have more than one type of spike. For example, the influenza virus carries triangular spike (hem-agglutinin) and the mushroom shaped spike (neuraminidase). The viruses that lack envelops are called naked viruses, e.g., plant viruses and bacteriophages.
7. Viral Enzymes:
Earlier, it was believed that viruses lack enzymes. But now, many viruses are known to contain enzymes. The spikes of enveloped viruses like influenza, measles and mumps contain the enzyme neuraminidase which helps in penetrating the host cell. In some cases the spikes also contain haemoglutinin that allow clumping of RBCs and help in adsorption to specific host cell, e.g., polioviruses, adenoviruses, influenza, measles and mumps etc. The tips of bacteriophage tails contain enzyme lysozyme which facilitates the penetration into host cell.
In retroviruses like HIV, Rous Sarcoma Virus, an RNA-dependant DNA polymerase called reverse transcriptase found associated with the genome. This enzyme synthesizes DNA from viral RNA and the process is called reverse transcription or teminism (H.M.Temin &D. Baltimore. 1970).
8. Viral Host Range:
The group of suitable cell types that a specific virus can infect collectively called as its host range. In most viruses host ranges are narrow. For example coliphages can infect only E. coli. A few viruses can infect both insects and plants, e.g., potato yellow dwarf virus. But some other viruses have wide host ranges, e.g., vesicular stomatitis viruses infect insects and many different mammalian cells.
9. Viral Transmission:
The transmission of viruses from diseased to healthy host occurs through various agencies or vectors. Plant viruses are Known to be transmitted through soil (e.g. wheat mosaic viruses), seed (e.g., mosaics of beans, cowpea, lettuce etc.), pollen (e.g., mosaics of beans), weeds (e.g., Cuscuta, a total parasite), nematodes (e.g., tobacco rattle, Colocasia mosaic, early browning of pea), fungi (e.g., tobacco necrosis, lettuce big veins etc.), by grafting a. healthy scion to an infected stock or vice versa. Potato, oat and wheat mosaic viruses are usually transmitted by hands, tools and other agricultural implements.
Transmission of some animal viral diseases:
1. Chicken pox is transmitted through close contact, vomits etc.
2. Smallpox spreads through close contact, sputum, vomits, scales, and, as reported by Biswas and Biswas (1976), sometimes through the placenta of the mother also.
3. Pollo is transmitted through sputum and faces. Cockroaches also act as vector of polio virus.
4. Influenza and cold spread through close contact and nasal discharge.
5. Yellow fever is transmitted through cockroaches.
6. Foot and mouth disease is mostly transmitted through the milk of infected cattle. Birds may also act its vector.
7. Certain viral diseases, such as Rift valley fever, are hereditary.
8. Equine encephalitis, yellow fever and dengue are mostly transmitted through mosquito.
10. Viral Reproduction (Replication or life cycle)
Viruses neither reproduce by themselves nor undergo division. Rather, they reproduce by replication only within host cells. In viral replication all viral components synthesize separately and assembled into progeny viruses. In all viruses, the replication cycles involve the entry of a virus into a susceptible host cell, intracellular reproduction to produce daughter or progeny virions and escape of these into the environment for a fresh infection.
A generalized viral replication cycle involves following steps:
(a) Entry of viruses into host cells, either through breaches in cell wall (in plant viruses) or by adsorption (animal and bacterial viruses).
(b) Eclipse or biosynthesis phase which includes replication of viral genome and synthesis of viral proteins.
(d) Release of progeny virions
The time interval between viral infection (i.e. entry of viral genome into the cell) and the appearance of the first intracellular virus particle is called as the eclipse period. The time taken between viral infection and the first release of progeny viruses is called latent period. For bacteriophages, it is 15-30 minutes and for animal viruses it is 15-30 hours.
The host cells are called permissive when they allow replication cycle to produce virions. In some cells, called non-permissive cells, the viral infection does not produce any progeny virions or if produced are not infectious. This is called abortive infection. Some viruses are genetically defective and, therefore, incapable of producing infectious daughter virions without the assistance of helper virus. These are called defective, incomplete or satellite viruses.
11. Nomenclature of Viruses:
Cryptogram is a code adopted for describing a virus consisting four pairs of symbols. It was proposed by Gibbs and Harrison (1968).
1st pair – Type of nucleic acid / number of strands in nucleic acid.
2 nd pair – Represent molecular weight of nucleic acid in millions / percentage of nucleic acid.
3rd pair – Shape of virion / shape of nucleocapsid.
(S – represent spherical, E – Elongated with parallel sides, ends not rounded U – for elongated with parallel sides, end rounded and X- for complex or none of the above).
4th pair-Type of host infected / nature of vector.
(Symbols : A – actinomycetes B – bacterium F – fungus I – invertebrates S – seed plants V- vertebrate and so on).
For example – Cryptogram of TMV: R/l: 2/5: E/E: S/A. Influenza virus: R/l: 2-3/10: S/E-.V/A Polio virus: R/l: 2.5/30: S/S: V/O. T4 bacteriophage: D/2:130/40: X/X: B/O
TMV- A Plant virus:
TMV (Tobacco Mosaic Virus) is the most thoroughly studied and historically important plant virus. TMV causes mosaic disease of tobacco. It can also infect the plants of family-Solanaceae. TMV is hollow, rod-shaped virus with helical symmetry. It is about 300nm (3000 A) long and I8nm (180A) is diameter (Fig. 10.4). TMV is a ribovirus composed of ss RNA and capsid. The capsid consists of 2130 capsomeres arranged helically around a central hollow core of 4nm (40 A) in diameter. A complete virion contains about 130 turns.
Each helical turn contains about 16 1/3 capsomeres, and three turn contains about 49 capsomeres. Each capsomere consists of one polypeptide chain with 168 amino acids. A furrow present on the inner side of each capsomere. Because of this, a helical groove is present in the whole length of capsid which accommodate ss RNA genome (7300 ribotides & 330 nm in length).
GK Questions and Answers on Types of Viruses (Biology)
Viruses can infect animals, plants, fungi, and bacteria. The virus sometimes can cause a disease that may be fatal. Some virus may also have one effect on one type of organism, but a different effect on another. Viruses cannot replicate without a host so they are classified as parasitic.
1. Which of the following diseases are caused due to a virus?
D. All the above
Explanation: Viral diseases are diseases that are caused due to virus namely AIDS, Ebola, Influenza, SARS (Severe Acute Respiratory Syndrome), Chikungunya, Small Pox, etc.
2. Name the virus that is transmitted through the biting of infected animals, birds, and insects to a human?
A. Rabies Virus
B. Ebola Virus
D. All the above
Explanation: Transmission of the virus through the biting of infected animals, birds, and insects to humans is known as Zoonoses. Examples: Rabies virus. Alphavirus, Flavivirus, Ebola virus, etc.
3. Based on host range, viruses are classified into:
B. Insect virus
C. Stem Virus
D. Both A and B
Explanation: There are four different types of viruses based on the type of host namely Animal viruses, Plant viruses, Bacteriophage and Insect virus.
4. In the host cell, replication of RNA virus took place in.
Explanation: An example of the replication of the virus within the cytoplasm in the host cell is all RNA virus except the influenza virus.
5. Which of the following statement is correct about viruses?
A. Viruses do not contain a ribosome.
B. Viruses can make protein.
C. Viruses can be categorised by their shapes.
D. Both A and C are correct
Explanation: Viruses do not contain ribosomes, so they cannot make proteins. That is why they are dependent on their host. Viruses have different shapes, sizes and can be categorised by their shapes.
6. Name the virus that covers himself with a modified section of the cell membrane and create a protective lipid envelope?
A. Influenza virus
C. Neither A nor B
D. Both A and B
Explanation: Some viruses cover themselves with a modified section of the cell membrane by creating a protective lipid envelope example the influenza virus and HIV.
7. A virus can spread through:
A. Contaminated food or water
D. All the above
Explanation: Viruses can spread through touch, exchanges of saliva, coughing or sneezing, contaminated food or water and also through insects that carry them from one person to another.
8. After which period virus replicates in the body and starts to affect the host?
A. Incubation period
D. None of the above
Explanation: Virus replicates in the body and starts to affect the host after a period known as the incubation period and symptoms may start to show.
9. Double-stranded DNA is found in which viruses?
C. Influenza viruses
D. None of the above
Explanation: Double-stranded DNA is found in poxviruses, the bacteriophages T2, T4, T6, T3, T7, Lamda, herpes viruses, adenoviruses, etc.
10. A virus is made up of a DNA or RNA genome inside a protein shell known as:
Explanation: A virus that is made up of a DNA or RNA genome inside a protein shell is known as a capsid. Some viruses have an external membrane envelope.
These are a few questions related to viruses, types, structure, classification, etc.
The nucleic acid
As is true in all forms of life, the nucleic acid of each virus encodes the genetic information for the synthesis of all proteins. In almost all free-living organisms, the genetic information is in the form of double-stranded DNA arranged as a spiral lattice joined at the bases along the length of the molecule (a double helix). In viruses, however, genetic information can come in a variety of forms, including single-stranded or double-stranded DNA or RNA.
The nucleic acids of virions are arranged into genomes. All double-stranded DNA viruses consist of a single large molecule, whereas most double-stranded RNA viruses have segmented genomes, with each segment usually representing a single gene that encodes the information for synthesizing a single protein. Viruses with single-stranded genomic DNA are usually small, with limited genetic information. Some single-stranded DNA viruses are composed of two populations of virions, each consisting of complementary single-stranded DNA of polarity opposite to that of the other.
The virions of most plant viruses and many animal and bacterial viruses are composed of single-stranded RNA. In most of these viruses, the genomic RNA is termed a positive strand because the genomic RNA acts as mRNA for direct synthesis (translation) of viral protein. Several large families of animal viruses, and one that includes both plant and animal viruses (the Rhabdoviridae), however, contain genomic single-stranded RNA, termed a negative strand, which is complementary to mRNA. All of these negative-strand RNA viruses have an enzyme, called an RNA-dependent RNA polymerase ( transcriptase), which must first catalyze the synthesis of complementary mRNA from the virion genomic RNA before viral protein synthesis can occur. These variations in the nucleic acids of viruses form one central criterion for classification of all viruses.
A distinctive large family of single-stranded RNA viruses is called Retroviridae the RNA of these viruses is positive, but the viruses are equipped with an enzyme, called a reverse transcriptase, that copies the single-stranded RNA to form double-stranded DNA.