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Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the common cold, while more lethal varieties can cause SARS, MERS and COVID-19, which is causing the ongoing pandemic. In cows and pigs they cause diarrhea, while in mice they cause hepatitis and encephalomyelitis.
Severe-acute-respiratory-syndrome–related coronavirus is a species of virus consisting of many known strains. Two strains of the virus have caused outbreaks of severe respiratory diseases in humans: severe acute respiratory syndrome coronavirus 1, which caused the 2002–2004 outbreak of severe acute respiratory syndrome (SARS), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is causing the ongoing pandemic of COVID-19. There are hundreds of other strains of SARSr-CoV, which are only known to infect non-human mammal species: bats are a major reservoir of many strains of SARSr-CoV; several strains have been identified in Himalayan palm civets, which were likely ancestors of SARS-CoV-1.
Coronaviridae is a family of enveloped, positive-strand RNA viruses which infect amphibians, birds, and mammals. The group includes the subfamilies Letovirinae and Orthocoronavirinae; the members of the latter are known as coronaviruses.
The Coronavirus packaging signal is a conserved cis-regulatory element found in Betacoronavirus. It has an important role in regulating the packaging of the viral genome into the capsid. As part of the viral life cycle, within the infected cell, the viral genome becomes associated with viral proteins and assembles into new infective progeny viruses. This process is called packaging and is vital for viral replication.
ORF7a is a gene found in coronaviruses of the Betacoronavirus genus. It expresses the Betacoronavirus NS7A protein, a type I transmembrane protein with an immunoglobulin-like protein domain. It was first discovered in SARS-CoV, the virus that causes severe acute respiratory syndrome (SARS). The homolog in SARS-CoV-2, the virus that causes COVID-19, has about 85% sequence identity to the SARS-CoV protein.
Betacoronavirus is one of four genera of coronaviruses. Member viruses are enveloped, positive-strand RNA viruses that infect mammals, including humans. The natural reservoir for betacoronaviruses are bats and rodents. Rodents are the reservoir for the subgenus Embecovirus, while bats are the reservoir for the other subgenera.
Human coronavirus OC43 (HCoV-OC43) is a member of the species Betacoronavirus 1, which infects humans and cattle. The infecting coronavirus is an enveloped, positive-sense, single-stranded RNA virus that enters its host cell by binding to the N-acetyl-9-O-acetylneuraminic acid receptor. OC43 is one of seven coronaviruses known to infect humans. It is one of the viruses responsible for the common cold and may have been responsible for the 1889–1890 pandemic. It has, like other coronaviruses from genus Betacoronavirus, subgenus Embecovirus, an additional shorter spike protein called hemagglutinin-esterase (HE).
Human coronavirus 229E (HCoV-229E) is a species of coronavirus which infects humans and bats. It is an enveloped, positive-sense, single-stranded RNA virus which enters its host cell by binding to the APN receptor. Along with Human coronavirus OC43, it is one of the viruses responsible for the common cold. HCoV-229E is a member of the genus Alphacoronavirus and subgenus Duvinacovirus.
Tylonycteris bat coronavirus HKU4 is an enveloped, positive-sense single-stranded RNA virus mammalian Group 2 Betacoronavirus that has been found to be genetically related to the Middle East respiratory syndrome-related coronavirus (MERS-CoV) that is responsible for the 2012 Middle East respiratory syndrome coronavirus outbreak in Saudi Arabia, Jordan, United Arab Emirates, the United Kingdom, France, and Italy.
Bat SARS-like coronavirus WIV1, also sometimes called SARS-like coronavirus WIV1, is a strain of severe acute respiratory syndrome–related coronavirus (SARSr-CoV) isolated from Chinese rufous horseshoe bats in 2013. Like all coronaviruses, virions consist of single-stranded positive-sense RNA enclosed within an envelope.
SHC014-CoV is a SARS-like coronavirus (SL-COV) which infects horseshoe bats. It was discovered in Kunming in Yunnan Province, China. It was discovered along with SL-CoV Rs3367, which was the first bat SARS-like coronavirus shown to directly infect a human cell line. The line of Rs3367 that infected human cells was named Bat SARS-like coronavirus WIV1.
The history of coronaviruses is an account of the discovery of the diseases caused by coronaviruses and the diseases they cause. It starts with the first report of a new type of upper-respiratory tract disease among chickens in North Dakota, U.S., in 1931. The causative agent was identified as a virus in 1933. By 1936, the disease and the virus were recognised as unique from other viral disease. They became known as infectious bronchitis virus (IBV), but later officially renamed as Avian coronavirus.
Civet SARS-CoV is a coronavirus associated with severe acute respiratory syndrome coronavirus (SARS-CoV), which infected humans and caused SARS events from 2002 to 2003. It infected the masked palm civet. The severe acute respiratory syndrome coronavirus (SARS-CoV) is highly similar, with a genome sequence similarity of about 99.8%. Because several patients infected at the early stage of the epidemic had contact with fruit-eating Japanese raccoon dog in the market, tanuki may be a direct source of human SARS coronavirus. At the end of 2003, four more people in Guangzhou, China, were infected with the disease. Sequence analysis found that the similarity with the tanuki virus reached 99.9%, and the SARS coronavirus was also caused by cases of tanuki transmission.
The envelope (E) protein is the smallest and least well-characterized of the four major structural proteins found in coronavirus virions. It is an integral membrane protein less than 110 amino acid residues long; in SARS-CoV-2, the causative agent of Covid-19, the E protein is 75 residues long. Although it is not necessarily essential for viral replication, absence of the E protein may produce abnormally assembled viral capsids or reduced replication. E is a multifunctional protein and, in addition to its role as a structural protein in the viral capsid, it is thought to be involved in viral assembly, likely functions as a viroporin, and is involved in viral pathogenesis.
The membrane (M) protein is an integral membrane protein that is the most abundant of the four major structural proteins found in coronaviruses. The M protein organizes the assembly of coronavirus virions through protein-protein interactions with other M protein molecules as well as with the other three structural proteins, the envelope (E), spike (S), and nucleocapsid (N) proteins.
ORF3a is a gene found in coronaviruses of the subgenus Sarbecovirus, including SARS-CoV and SARS-CoV-2. It encodes an accessory protein about 275 amino acid residues long, which is thought to function as a viroporin. It is the largest accessory protein and was the first of the SARS-CoV accessory proteins to be described.
ORF8 is a gene that encodes a viral accessory protein, Betacoronavirus NS8 protein, in coronaviruses of the subgenus Sarbecovirus. It is one of the least well conserved and most variable parts of the genome. In some viruses, a deletion splits the region into two smaller open reading frames, called ORF8a and ORF8b - a feature present in many SARS-CoV viral isolates from later in the SARS epidemic, as well as in some bat coronaviruses. For this reason the full-length gene and its protein are sometimes called ORF8ab. The full-length gene, exemplified in SARS-CoV-2, encodes a protein with an immunoglobulin domain of unknown function, possibly involving interactions with the host immune system. It is similar in structure to the ORF7a protein, suggesting it may have originated through gene duplication.
ORF6 is a gene that encodes a viral accessory protein in coronaviruses of the subgenus Sarbecovirus, including SARS-CoV and SARS-CoV-2. It is not present in MERS-CoV. It is thought to reduce the immune system response to viral infection through interferon antagonism.
16BO133 is a SARS-like coronavirus (SL-COV) which was found in the greater horseshoe bat in South Korea. It was published in 2019 and its genome was completely sequenced. The sequenced Korean SARSr-CoV strain belongs to the severe acute respiratory syndrome coronavirus 1, and its genome sequence similarity is 82.8%.
LYRa11 is a SARS-like coronavirus (SL-COV) which was identified in 2011 in samples of intermediate horseshoe bats in Baoshan, Yunnan, China. The genome of this virus strain is 29805nt long, and the similarity to the whole genome sequence of SARS-CoV that caused the SARS outbreak is 91%. It was published in 2014. Like SARS-CoV and SARS-CoV-2, LYRa11 virus uses ACE2 as a receptor for infecting cells.
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