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Alphacoronavirus

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Genus of viruses

This article is about the genus of coronavirus and is not to be confused with theAlpha variant of the SARS-CoV-2 virus that causes COVID-19.

Alphacoronavirus

Porcine epidemic diarrhea virus genome and virion structure
Virus classification
(unranked):	Virus
Realm:	Riboviria
Kingdom:	Orthornavirae
Phylum:	Pisuviricota
Class:	Pisoniviricetes
Order:	Nidovirales
Family:	Coronaviridae
Subfamily:	Orthocoronavirinae
Genus:	*Alphacoronavirus*
Subgenera and species
See text

Alphacoronaviruses (Alpha-CoV) are members of the first of the four genera (Alpha-,Beta-,Gamma-, andDelta-) ofcoronaviruses. They arepositive-sense, single-strandedRNA viruses that infectmammals, includinghumans. They have spherical virions with club-shapedsurface projections formed by trimers of thespike protein, and aviral envelope.

Alphacoronaviruses are in the subfamilyOrthocoronavirinae of the familyCoronaviridae. Both theAlpha- andBetacoronavirus lineages descend from thebat viral gene pool.^[1]^[2] Alphacoronaviruses were previously known as "phylogroup 1 coronaviruses".

The Alphacoronavirus genus is very diverse, particularly in bats. Most bat originating strains haven't been successfully isolated and cultured in laboratory. Alphacoronaviruses infecting other mammal species have been much better studied, seeList of Coronavirus live isolates.

Etymology

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The name alphacoronavirus is derived fromAncient Greek ἄλφα (álpha, "the firstletter of theGreek alphabet"), and κορώνη (korṓnē, "garland, wreath"), meaning crown, which describes the appearance of the surface projections seen under electron microscopy that resemble asolar corona.^[3]

Structure

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The virion is enveloped and spherical measuring 120–160 nm in diameter and a core shell of about 65 nm. Glycoproteins and trimers form large surface projections which create the appearance of solar corona. This genus, like other coronaviruses, has a spike protein with a type I fusion machine (S2) and a receptor-binding domain (S1). It assembles into a trimer. Unlike beta- and gammacoronaviruses, this protein is not cleaved into two halves.^[4]

Genome

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The genome ispositive-sense, single-stranded RNA with a length of 27 to 29kilobases and a 3'-polyA tail. Two large, overlappingORFs at the 5'-end of the genome encode the major non-structural proteins expressed as afusion protein byribosomal frameshift. These include regions withprotease,helicase and RNA polymerase motifs. There are seven other genes downstream which encode structural proteins. These are expressed from a 3'-coterminal nested set ofsubgenomic mRNAs.

Recombination

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Feline coronavirus (FCoV) andcanine coronavirus (CCoV) are known to exist in two serotypes. Serotype II targetsAminopeptidase N, while the receptor for Serotype I is unknown. The difference is due to a different spike protein.^[6] There is a common ancestor for FCoV and CCoV. This ancestor gradually evolved into FCoV I and CCoV I. An S protein from an unknown virus was recombined into the ancestor and gave rise to CCoV II. CCoV II once again recombined with FCoV to create FCoV II. CCoV II gradually evolved into TGEV. A spike deletion in TGEV creates PRCV. All these viruses are sorted into the subgenusTegacovirus.^[6]

Classification

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Phylogentic tree of the genusAlphacoronavirus with host animals indicated on the right hand side.

The genus contains the following subgenera and species:^[7]^[8]

Coronaviruses

Types Alphacoronavirus Betacoronavirus Gammacoronavirus Deltacoronavirus
Diseases Common cold SARS MERS COVID-19
Vaccines COVID-19 vaccine
Epidemics and pandemics SARS(2002–2004) MERS(2012-present) COVID-19(2019-present)
See also Coronaviridae Novel coronavirus History of coronavirus
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