# Alphavirus

Alphavirus is a genus of RNA viruses, the sole genus in the Togaviridae family. Alphaviruses belong to group IV of the Baltimore classification of viruses, with a positive-sense, single-stranded RNA genome. There are 32 alphavirus species, which infect various vertebrates such as humans, rodents, fish, birds, and larger mammals such as horses, as well as invertebrates. Alphaviruses that can infect both vertebrates and arthropods are referred dual-host alphaviruses, while insect-specific alphaviruses such as Eilat virus and Yada yada virus are restricted to their competent arthropod vector. Transmission between species and their vertebrate hosts (including human) occurs mainly via mosquitoes, making the alphaviruses a member of the collection of arboviruses – or arthropod-borne viruses. Alphavirus particles are enveloped, have a 70 nm diameter, tend to be spherical (although slightly pleomorphic), and have a 40 nm isometric nucleocapsid.

## Genome

The alphaviruses are small, spherical, enveloped viruses with a genome of a single strand of positive-sense RNA. The total genome length ranges between 11,000 and 12,000 nucleotides, and has a 5’ cap and a 3’ poly-A tail. The four non-structural protein genes are encoded in the 5′ two-thirds of the genome, while the three structural proteins are translated from a subgenomic mRNA colinear with the 3′ one-third of the genome.
There are two open reading frames (ORFs) in the genome, nonstructural and structural. The first is non-structural and encodes proteins (nsP1–nsP4) necessary for transcription and replication of viral RNA. The second encodes three structural proteins: the core nucleocapsid protein C, and the envelope proteins P62 and E1, which associate as a heterodimer. The viral membrane-anchored surface glycoproteins are responsible for receptor recognition and entry into target cells through membrane fusion.

### Structural proteins

The proteolytic maturation of P62 into E2 and E3 causes a change in the viral surface. Together the E1, E2, and sometimes E3, glycoprotein "spikes" form an E1/E2 dimer or an E1/E2/E3 trimer, where E2 extends from the centre to the vertices, E1 fills the space between the vertices, and E3, if present, is at the distal end of the spike. Upon exposure of the virus to the acidity of the endosome, E1 dissociates from E2 to form an E1 homotrimer, which is necessary for the fusion step to drive the cellular and viral membranes together. The alphaviral glycoprotein E1 is a class II viral fusion protein, which is structurally different from the class I fusion proteins found in influenza virus and HIV. The structure of the Semliki Forest virus revealed a structure that is similar to that of flaviviral glycoprotein E, with three structural domains in the same primary sequence arrangement. The E2 glycoprotein functions to interact with the nucleocapsid through its cytoplasmic domain, while its ectodomain is responsible for binding a cellular receptor. Most alphaviruses lose the peripheral protein E3, but in Semliki viruses it remains associated with the viral surface.

### Nonstructural proteins

Four nonstructural proteins (nsP1–4) which are produced as a single polyprotein constitute the virus' replication machinery. The processing of the polyprotein occurs in a highly regulated manner, with cleavage at the P2/3 junction influencing RNA template use during genome replication. This site is located at the base of a narrow cleft and is not readily accessible. Before cleavage, nsP3 creates a ring structure that encircles nsP2. These two proteins have an extensive interface.
Mutations in nsP2 that produce noncytopathic viruses or a temperature sensitive phenotypes cluster at the P2/P3 interface region. P3 mutations opposite the location of the nsP2 noncytopathic mutations prevent efficient cleavage of P2/3. This in turn affects RNA infectivity altering viral RNA production levels.

## Virology

The virus has a 60–70 nanometer diameter. It is enveloped, spherical and has a positive-strand RNA genome of ~12 kilobases. The genome encodes two polyproteins. The first polyprotein consists of four non-structural units: in order from the N terminal to the C terminal - nsP1, nsP2, nsP3, and nsP4. The second is a structural polyprotein composed of five expression units: from the N terminal to the C terminal - Capsid, E3, E2, 6K and E1. A sub genomic positive strand RNA - the 26S RNA - is replicated from a negative-stranded RNA intermediate. This serves as template for the synthesis of viral structural proteins. Most alphaviruses have conserved domains involved in regulation of viral RNA synthesis.
The nucleocapsid, 40 nanometers in diameter, contains 240 copies of the capsid protein and has a T = 4 icosahedral symmetry. The E1 and E2 viral glycoproteins are embedded in the lipid bilayer. Single E1 and E2 molecules associate to form heterodimers. The E1–E2 heterodimers form one-to-one contacts between the E2 protein and the nucleocapsid monomers. The E1 and E2 proteins mediate contact between the virus and the host cell.
Several receptors have been identified. These include prohibitin, phosphatidylserine, glycosaminoglycans and ATP synthase β subunit (ref needed).
Replication occurs within the cytoplasm, specifically in areas termed "spherules" separated by plasma membrane invaginations from the rest. Each complex occupies one such area of about 50-nm in inner diameter.
Virions mature by budding through the plasma membrane, where virus-encoded surface glycoproteins E2 and E1 are assimilated. These two glycoproteins are the targets of numerous serologic reactions and tests including neutralization and hemagglutination inhibition. The alphaviruses show various degrees of antigenic cross-reactivity in these reactions and this forms the basis for the seven antigenic complexes, 32 species and many subtypes and varieties. The E2 protein is the site of most neutralizing epitopes, while the E1 protein contains more conserved, cross-reactive epitopes.

## Evolution

A study of this taxon suggests that this group of viruses had a marine origin—specifically the Southern Ocean—and that they have subsequently spread to both the Old and New World.
There are three subgroups in this genus: the Semliki Forest virus subgroup (Semliki Forest, O'nyong-nyong and Ross River viruses); the eastern equine encephalitis virus subgroup (eastern equine encephalitis and Venezuelan equine encephalitis viruses) and the Sindbis virus subgroup. Sindbis virus, geographically restricted to the Old World, is more closely related to the eastern equine encephalitis subgroup, which are New World viruses, than it is to the Semliki Forest virus subgroup which is also found in the Old World.

## Taxonomy

The following species are assigned to the genus, listed by scientific name and followed by their common names:
* Alphavirus aura, Aura virus
* Alphavirus barmah, Barmah Forest virus
* Alphavirus bebaru, Bebaru virus
* Alphavirus caaingua, Caaingua virus
* Alphavirus cabassou, Cabassou virus
* Alphavirus chikungunya, Chikungunya virus
* Alphavirus eastern, Eastern equine encephalitis virus
* Alphavirus eilat, Eilat virus
* Alphavirus everglades, Everglades virus
* Alphavirus fortmorgan, Fort Morgan virus
* Alphavirus getah, Getah virus
* Alphavirus highlandsj, Highlands J virus
* Alphavirus madariaga, Madariaga virus
* Alphavirus mayaro, Mayaro virus
* Alphavirus middelburg, Middelburg virus
* Alphavirus mossopedras, Mosso das Pedras virus
* Alphavirus mucambo, Mucambo virus
* Alphavirus ndumu, Ndumu virus
* Alphavirus negro, Rio Negro virus
* Alphavirus onyong, O'nyong'nyong virus
* Alphavirus pixuna, Pixuna virus
* Alphavirus rossriver, Ross River virus
* Alphavirus salmon, Salmon pancreas disease virus
* Alphavirus seal, Southern elephant seal virus
* Alphavirus semliki, Semliki Forest virus
* Alphavirus sindbis, Sindbis virus
* Alphavirus tonate, Tonate virus
* Alphavirus trocara, Trocara virus
* Alphavirus una, Una virus
* Alphavirus venezuelan, Venezuelan equine encephalitis virus
* Alphavirus western, Western equine encephalitis virus
* Alphavirus whataroa, Whataroa virus
The seven complexes are:
    Barmah Forest virus complex
       Barmah Forest virus
    Eastern equine encephalitis complex
       Eastern equine encephalitis virus (seven antigenic types)
    Middelburg virus complex
       Middelburg virus
    Ndumu virus complex
       Ndumu virus
    Semliki Forest virus complex
       Bebaru virus
       Chikungunya virus
       Getah virus
       Mayaro virus
          Subtype: Una virus
       O'nyong'nyong virus
          Subtype: Igbo-Ora virus
       Ross River virus
          Subtype: Sagiyama virus
       Semliki Forest virus
          Subtype: Me Tri virus
    Venezuelan equine encephalitis complex
       Cabassou virus
       Everglades virus
       Mosso das Pedras virus
       Mucambo virus
       Paramana virus
       Pixuna virus
       Rio Negro virus
       Trocara virus
          Subtype: Bijou Bridge virus
       Venezuelan equine encephalitis virus
    Western equine encephalitis complex
       Aura virus
       Babanki virus
       Kyzylagach virus
       Sindbis virus
       Ockelbo virus
       Whataroa virus
          Recombinants within this complex
          Buggy Creek virus
          Fort Morgan virus
          Highlands J virus
          Western equine encephalitis virus
    Unclassified
       Eilat virus
       Mwinilunga alphavirus
       Salmonid Alphavirus
       Southern elephant seal virus
       Tonate virus
       Caaingua virus