Viruses

November 15, 2021


Viruses are the most abundant biological entities on earth and they outnumber all the others put together. There are billions of Viruses. They infect all life forms, animals, plants, fungi, and even bacteria and Archaea. The viruses that infect plants are harmless to animals and most viruses that infect other animals are harmless to humans. They have a narrow host range. Many are species-specific. Some infect one species only. For example, the pox virus infects humans only while the rabies virus infects many species of mammals and is said to have a broad range. Although they have usually a limited host range they can and do spread across species barriers. For example AIDS pandemic, highly fatal Ebola hemorrhagic fever, severe acute respiratory syndrome (SARS), and COVID pandemic are recent examples of viral diseases that emerge from zoonotic infections.

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Viruses are infectious, obligate intracellular parasites. They are the most mysterious organism on earth. They do not have cellular organization and lack the enzymes needed for the synthesis of proteins and nucleic acid and are dependent for replication on the synthetic machinery of the host cell. They multiply by a complex process. They hijack the cellular machinery of the host cell and force it to make thousands of its copies rapidly.

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Structure of a Virus

structure of a virus

Viruses range in size from 20 – 300 nanometers. They have a central nucleic acid core ( either DNA or RNA ) surrounded by a protein coat called capsid (made up of Capsomeres). The capsid is antigenically unique for a particular virus. Some viruses have a lipoprotein envelope also called enveloped viruses. The capsid imparts a helical or icosahedral structure to a virus. The helical viruses appear rod-like, such as Ebola and Rabies virus. Adenovirus has a shape of an icosahedron. Influenza virus is an example of enveloped helical and Herpes Simplex is an enveloped polyhedral virus. Some viruses like bacteriophages have complicated structures so-called complex viruses. 

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Classification

In the past viruses were named according to the disease they cause or the site from where they were first isolated or discovered, for example:

  • Naming after the diseases they cause such as measles virus (means many tiny spots), smallpox virus, Chikungunya virus (derived from Makonde, means that which bends up -refers to the posture gained as a result of arthritis)
  • Site of the body from which they were first isolated e g. Rhinovirus.
  • Some are named after the city, town, or river e.g Ebola virus (river in Zaire), Norwalk virus and Coxsackie virus (US), and Hantaan virus (river in South Korea)
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  • On the name of the scientist who first discovered them e.g. Epstein- Barr virus.
  • According to host and signs of disease such as Cauliflower mosaic virus.
  • The way in which people imagined they were contracted e.g. dengue for evil spirit and influenza for bad air
  • Many names of virus taxonomic groups are based on Latin words, while some have Greek origins such as:
  • Flaviviridae- (Flavus: yellow) (cause yellow fever)
  • Family Togaviridae (Toga: clock) -enveloped virus
  • Family parvoviridae – ( Parvus: small) -small virion

There are billions of viruses in the environment. Only a few infect humans. Till 1950 little was known about them Since the first discovery of the Tobacco Mosaic Virus in 1898 greater than 9000 species now have been described in detail. In 1962 viruses were classified according to shared properties such as type of nucleic acid, phylum, class, order, family, genus, and species based on the Linnaean hierarchical system.

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 In 1966 ICTV (International Committee on Taxonomy of Virus was established. ICTV authorizes and organizes the classification and naming of viruses. The Linnaean hierarchical system initially was not accepted by the ICTV because the small genome size of viruses and their high rate of mutations made it difficult to determine their ancestry beyond ‘order’. ICTV grouped viruses into families based on the type of nucleic acid, means of replication, and morphology. ICTV introduced a 15-rank classification system ranging from realm to species for classifying viruses. Virus identification is recognized at the following levels, namely:

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  • Realm: Viria
  • Sub realm:  Vira
  • Kingdom: Virae
  • Sub Kingdom: Virites
  • Phylum: Viricota
  • Sub phylum: Viricotina
  • Class: Viricetes
  • Sub class: Viricetidae
  • Order: Virales
  • Suborder: Virineae
  • Family: Viridae
  • Subfamily: Virinae
  • Genus: Virus
  • Species
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How ICTV Works

For a newly discovered virus or a group of viruses to be classified researchers needs to submit a proposal detailing the rationale to ICTV. The proposal then goes through a multi-stage review process that involves ICTV study groups, sub-committees, and the executive committee. If the executive committee approves the proposal, it is established on the ICTV website, and members can ratify it through electronic votes. Newly approved classifications are announced at least once a year.

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Viruses are divided into two main groups according to the genome, DNA, or RNA into subfamilies according to their structure.

DNA Viruses

DNA Viruses associated with human diseases are classified into six families :

  • Poxviridae : Pox: (pus-filled lesions) large-sized (250-300nm) brick-shaped or ovoid, single-stranded DNA Viruses. It has several genera. It includes Orthopoxvirus (smallpox virus and vaccinia virus), Molluscipoxvirus (Molluscum contagiosum)
  • Herpesviridae: large-sized, icosahedral,(120-200nm), enveloped viruses containing linear double-stranded DNA. These viruses multiply in the nucleus of host cells. Only one genus herpesviruses. They are designated herpes type 1-8, but common names are still used. Includes Herpes simplex viruses ( Type 1 and 2), Varicellovirus, Lymphocryptovirus (Epstein Barr virus), Cytomegalovirus, Roselovirus (HHV-6 and 7), Rhadinovirus ( Kaposi’s sarcoma-associated herpes virus) .
  • Adenoviridae: They were first isolated from adenoids. Medium-sized (70-90 nm) non-enveloped icosahedral viruses, It has 2 genera: Mastadenovirus and Aviadenoviruses.
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  • Papovaviridae: small-sized (40-55 nm) contains double-stranded DNA. They replicate in the host nucleus. This may cause the host cells to proliferate resulting in tumors. Papovavirdae is an acronym for papilloma (warts) and polyomas (tumors) and vacuolation (cytoplasmic vacuolation produced by some of these viruses) 2 genera: Papillomaviruses and Polyomaviruses
  • parvoviridae: very  small (18-26 nm) have 3 genera: Parvoviruses, Adenosatello viruses, and Densoviruses
  • Hepadnaviridae : (42 nm) (HEPA: liver;  DNA:  DNA core)  so named because they cause hepatitis and contain DNA core. These viruses differ from other DNA Viruses by synthesizing their DNA by copying RNA using reverse transcriptase. Include Human hepatitis B virus and related viruses of animals.
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RNA Viruses

The RNA viruses associated with human diseases are classified into 13 families.

  • Picornaviridae : (Pico: small) are the smallest viruses. They are non-enveloped icosahedral viruses with single-stranded RNA. (20-30 nm ) 3 genera: Enterovirus, Rhinovirus,  Hepatovirus (HAV)
  • Orthomyxoviridae: Medium-sized, (80-120nm) elongated, enveloped viruses with single-stranded, segmented RNA. One genus – Influenzavirus is only one virus of medical importance belonging to this group.
  • Paramyxoviridae: These are pleomorphic, enveloped viruses measuring 150 nm in size. Containing non-segmented linear single-stranded RNA. 3 genera: Paramyxovirus, Morbillivirus,  Pneumovirus.
  • Togaviridae : (40-70 nm) are small enveloped viruses containing single-stranded positive sense RNA. Alphaviruses belong to group IV of the Baltimore classification of viruses. There are 3 genera: Alphaviruses, Rubiviruses, and Pestiviruses. There are 32 alphaviruses. It includes a large number of species that are mostly mosquito-borne and pathogenic in their vertebrate hosts. 
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  • Flaviviridae: Formerly grouped as group B Arboviruses  under Togaviridae
  • Bunyaviridae : (90-100 nm) These are enveloped, spherical viruses. It has 5 genera: Bunyavirus, Hantavirus, Nairovirus, Phlebovirus, and Uukuvirus.
  • Arenaviridae: These are pleomorphic, spherical viruses with variable sizes. (50-300 nm)  (Arena: sand) They contain electron-dense, chromosomes-like particles giving them a sandy appearance. One genus Arenaviruses. (rodent parasites but rarely can infect humans )
  • Rhabdoviridae : (Rhabdo: rod) are bullet-shaped viruses, (130- 300 nm ) in size, containing single-stranded RNA. It has 2 genera, Vesiculoviruses, and Lyssaviruses.
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  • Reoviridae : (60-80 nm) icosahedral, nonenveloped. They contain a double-layered capsid enclosing segmented double-stranded RNA. Their name was derived from the first letter of respiratory, enteric, and orphan. When first discovered, the viruses were not associated with any disease, hence were called orphans. 3 genera: Reoviruses, Orbiviruses, Rotaviruses.
  • Coronaviridae : (100 nm) One genus Coronaviruses. (enveloped, pleomorphic viruses).
  • Retroviridae : (100 nm) Retroviruses (re: reverse;  tr: transcriptase) are so named because they possess reverse transcriptase enzyme (RNA- dependent DNA polymerase) They are icosahedral, enveloped viruses. Many of these viruses are associated with tumors in infected hosts. 3 subfamilies: Oncovirinae,  spumavirinae, Lentivirinae. Lentiviruses include the subspecies HIV-1 and HIV-2, the causative agent of acquired immunodeficiency syndrome.
  • Calciviridae : (35-39 nm) These are small, spherical nonenveloped viruses. They show 32 cup-shaped depressions arranged in symmetry.
  • Filoviridae : (80 nm) size, are long filamentous, single-stranded RNA, enveloped viruses with variable sizes. Marburg and Ebola viruses are of medical importance.
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Baltimore Classification

This was initially suggested by David Baltimore and all families of viruses were divided into 7 groups. The division is based on the nature and polarity of their genomes. Baltimore’s classification is based on the fact that all viruses need to produce messenger RNA or positive sense RNA that produces proteins. The unique pathways from various viral genomes to mRNA define specific viral classes. The viral genome may or may not use reverse transcriptase (RT). Reverse transcriptase is an enzyme used to generate complementary DNA from an RNA template, a process termed reverse transcription. In retroviruses, this cDNA can then integrate into the host genome, from which new RNA copies can be made via host cell transcription. 

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  • Double-stranded DNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)
  • Single-stranded positive sense DNA viruses (e.g. Parvoviruses)
  • Double-stranded RNA viruses e.g. Reoviruses
  • Single-stranded positive sense RNA viruses e.g. Picornaviruses, Togaviruses, flaviviridae, Coronaviridae, Calciviridae)
  • Single-stranded negative sense RNA viruses e.g. Orthomyxoviruses, Rabdoviruses, filoviridae, paramyxoviridae, Arenaviridae)
  • Single-stranded positive sense RNA-RT viruses: RNA with DNA intermediate in life-cycle e.g. Retroviruses
  • Double-stranded DNA-RT viruses: DNA with RNA intermediate in lifecycle e.g. Hepadnaviruses.
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Microscopic Introduction to Virus Taxonomy

Microscopic classification of viruses came about from the routine usage of an electron microscope.  Viruses shared physical properties e.g. capsid symmetry, dimensions, and a lipid envelope. These criteria could help to distinguish between different families without using ICTV and Baltimore classifications. More recently a precise ordering of viruses within families based on DNA or RNA sequence is added.

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Satellites

Satellites are small single-stranded RNA (500-2000 nucleotides) molecules that lack genes required for their replication but do replicate in the presence of another virus (the helper virus). Most satellites are associated with plant viruses, but a well-known example of human satellite viruses is the hepatitis delta virus with its helper hepatitis B virus.

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Viroids

Potato spindle tuber viroid, which was discovered in 1971, is the prototype for the smallest known nucleic acid-based agent. Viroid is non-capsulated small circular, single-stranded RNA (246-399 nucleotides) molecules that replicate autonomously. They are widespread in plants. Some cause economically important diseases in plant crops. All known viroid are inhabitants of angiosperms.

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