Orthocoronavirinae

Orthocoronavirinae, commonly known as coronavirus, is a subfamily of positive single-stranded RNA viruses belonging to the family Coronaviridae. It is subdivided into the genera Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. These include phylogenetically similar genogroups of viruses. with an enveloped helical symmetry nucleocapsid whose virions can measure between approximately 50 and 200 nm in diameter. Their genetic material is the largest among RNA viruses, with genomes ranging from 26 to 32 kilonucleotides. They are called coronaviruses because of the crown of spikes seen around the surface of the virus. It was first described in 1965.

Coronaviruses can infect birds and mammals, producing a series of respiratory and digestive diseases, many of them fatal, resulting in serious damage to poultry and livestock; They can also infect humans, causing illnesses ranging from the common cold to more serious illnesses such as bronchitis, bronchiolitis, pneumonia, Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and COVID-19. among other. Most people become infected with these viruses at some point in their lives.

Forty-five species of coronavirus have been reported to date. Several species are of recent investigation because several particular strains have not been previously identified in humans. Little information exists on transmission, severity, and clinical impact. and there are no approved treatments to date, however several of the symptoms can be treated, the therapeutic options depend on the clinical status of each patient.

The genus Alphacoronavirus —previously known as Coronavirus group 1 (CoV-1)— includes subgroups 1a and 1b, whose most representative members are human coronavirus 229E (HCoV-229E) and HCoV- NL63, as well as the new species alphacoronavirus 1 —including porcine transmissible gastroenteritis virus (TGEV)—, respectively. The genus Betacoronavirus —formerly Betacoronavirus group 2 (Cov-2)— includes several subgroups. The most prominent (subgroups 2a and 2b) have murine coronavirus species—including mouse hepatitis virus (MHV)—and SARS-CoV, respectively, as type species. The genera Alphacoronavirus and Betacoronavirus come from the genetic pool that has bats as hosts. The genus Gammacoronavirus includes all avian coronaviruses identified up to 2009.

Natural history

The most recent common ancestor of the coronavirus has been found in the 9th century BC. C. Studies carried out during 1990 managed to date the most recent common ancestors of the genera:^{[citation required]}

• Betacoronavirus: 3300 a. C.
• Deltacoronavirus: 3000 a. C.
• Gammacoronavirus: 2800 a. C.
• Alphacoronavirus: 2400 a. C.

According to these studies, at that time the main source factor of the coronavirus was warm blood, particularly from bats and birds. The bovine coronavirus diverged from the equine coronavirus species at the end of the 18th century. The bovine coronavirus and the human coronavirus OC43 separated in 1899. Another estimate suggests that the human coronavirus OC43 diverged from the bovine coronavirus in 1890. The bovine coronavirus and the canine respiratory coronavirus diverged from a common ancestor in 1951. The most common ancestor The recent human coronavirus OC43 has been dated to the 1950s. The Middle East respiratory syndrome coronavirus, although related to several bat species, appears to have diverged from these several centuries ago. The bat coronavirus is most closely related to the SARS coronavirus, from which it split in 1986.

Structure

Animation of a representative virion of Orthocoronavirinae, the cross section indicates the components and proteins that can be part of its structure

The parts that make up the general structure of coronaviruses are, as in all animal viruses, the envelope and the nucleocapsid. In the case of coronaviruses, a membrane glycoprotein (M) of 20 to 35 kDa is found in the envelope, which forms a matrix in contact with the nucleocapsid. In addition, the S glycoprotein, from 180 to 220 kDa, is found in the envelope, which forms the spikes, spikes or peplomeres responsible for adhesion to the host cell. In the specific case of the SARS coronavirus, a defined receptor-binding domain on its spikes directs the virus to adhere to its cellular receptor, angiotensin-converting enzyme 2 (ACE-2). Some coronaviruses (specifically members of the Betacoronavirus subgroup A, also called the Embecovirus subgenus) also have an additional shorter protein on their surface called esterase-haemagglutinin.

Replication

Coronavirus replication begins upon entry into the cell, at which point it loses its envelope, and the RNA genome is released into the cytoplasm. The coronavirus genome has a methylated cap at the 5' end. (cap' end), and a polyadenylated tail (poly A) at the 3' end, giving it a great resemblance to eukaryotic messenger RNA. This allows the RNA to bind to the cytoplasmic ribosomes for translation. Coronaviruses also have a replicase protein encoded in their genetic code, which allows them to generate new copies of their RNA without the need to transcribe it into DNA, using the resources of the host cell. This replicase is the first protein to be synthesized since once the gene encoding the replicase is translated (protein synthesis), the process is halted by a stop codon. This is known as nested transcription. When the mRNA transcript only encodes one gene, it is known as monocistronic. The RNA genome is replicated in the negative strand and from this positive copies are formed, which is translated into a long polyprotein, which must be cleaved into the various functional proteins of the virus. To do this, coronaviruses have a protease called Mpro or 3CLpro that cuts the polyprotein to give rise to viral proteins (polyprotein maturation). This is a viral strategy for the genetic economy, as it allows it to encode a large number of proteins with a small number of transcripts while improving the failure rate during RNA polymerase execution. This protease is a target of drugs to prevent the replication of the virus.

Humans

Human coronaviruses were first described in the 1960s in the nasal cavities of patients with the common cold. These viruses were later named human coronavirus 229E and OC43. Two other members of this family have been identified, HCoV-NL63 in 2004 and HKU1 in 2005. They circulate globally in the human population and cause approximately one third of common cold cases. Like other types of viruses, they can cause more serious diseases of the respiratory system such as bronchitis or pneumonia, especially in people with risk factors, the elderly, children and immunocompromised patients. In addition to respiratory conditions, they can also cause intestinal and neurological diseases.

There are records of seven strains of coronaviruses related to human respiratory diseases (HCoV):

1. Human coronavirus 229E
2. Human Coronavirus OC43
3. SARS-CoV
4. Human Coronavirus NL63
5. Human Coronavirus HKU1
6. Coronavirus of Middle East respiratory syndrome (MERS-CoV).
7. SARS-CoV-2 (COVID-19).

After the profile of SARS outbreaks was published in 2003, interest in coronaviruses revived among virologists. For many years, scientists knew of only two human coronaviruses (HCoV-229E and OC43-HCoV). The discovery of SARS-CoV added a third human coronavirus. In late 2004, three independent research laboratories reported the discovery of a fourth human coronavirus, named NL63, NL, and New Haven coronavirus simultaneously by multiple research groups. The three laboratories are still arguing over which of them discovered the virus first and therefore has the right to name it. In early 2005, a research team from the University of Hong Kong reported finding a fifth human coronavirus in two patients with pneumonia. They named it human coronavirus HKU1. The 2019-20 pneumonia outbreak in Wuhan, China, led to the discovery of a novel coronavirus, listed as 2019-nCoV by the WHO.

Severe Acute Respiratory Syndrome

In 2003, following the outbreak of SARS (severe acute respiratory syndrome), which had started in 2002 in Asia, and then in other parts of the world, the World Health Organization (WHO) issued a press release indicating that a newly identified coronavirus by a series of laboratories was the causative agent of SARS. The virus was officially named as SARS coronavirus (SARS-CoV). More than 8,000 people were infected, around 10% of whom died.

Middle East Respiratory Syndrome

In September 2012, a new type of coronavirus was identified, initially named 2012 novel coronavirus, and now officially named Middle East respiratory syndrome coronavirus (MERS-CoV). The World Health Organization issued a global alert shortly after. The WHO update on September 28, 2012 stated that the virus did not appear to spread easily from person to person. However, on May 12, 2013, a case of human-to-human transmission in France was confirmed by the French Ministry of Social Affairs and Health. In addition, cases of human-to-human transmission have been reported by the Tunisian Ministry of Health. Two confirmed cases appear to have contracted the disease from his late father, who fell ill after a visit to Qatar and Saudi Arabia. Despite this, the virus appears to have problems with human-to-human spread, as most people who are infected do not transmit the virus.

As of October 30, 2013, there were 124 cases and 52 deaths in Saudi Arabia. After the Dutch Erasmus Medical Center sequenced the virus, they gave it a new name, human coronavirus-Erasmus Medical Center (HCoV-CEM). The final name for the virus is Middle East respiratory syndrome coronavirus (MERS-CoV). The only two cases of MERS-CoV infection in the United States were reported in May 2014, occurring in healthcare workers who worked in Saudi Arabia and later traveled to the United States. Both individuals were temporarily hospitalized and later released. In May 2015, an outbreak of MERS-CoV occurred in South Korea, when a man who had traveled to the Middle East visited 4 different hospitals in the Seoul area to treat his illness. This caused one of the largest outbreaks of MERS-CoV outside of the Middle East. As of December 2019, 2,468 cases of MERS-CoV infection had been confirmed by laboratory testing, of which 851 cases were fatal, a mortality rate of approximately 34.5%.

SARS-CoV-2

This section is a SARS-CoV-2 extract.[chuckles]edit]

Electronic micrography of virions transmission SARS-CoV-2isolated from a patient. Colored image, to highlight the viruses.

Type 2 coronavirus causing severe acute respiratory syndrome, abbreviated SARS-CoV-2 (English) severe respiratory syndrome coronavirus 2) or SRAS-CoV-2, is a type of coronavirus that causes coronavirus disease in 2019, whose global expansion caused the COVID-19 pandemic. It was initially called 2019-nCoV (in English, 2019-novel coronavirus, ‘new coronavirus of 2019’) and also, occasionally, HCoV-19 (in English, human coronavirus 2019). It was discovered and isolated for the first time in Wuhan, China. It has a zoonotic origin, that is, it was transmitted from an animal host to a human.

It's a nail inside the family of the Coronaviridae, genus Betacoronavirus, subgenus Sarbecovirus, species SARS virus (virus related to severe or severe acute respiratory syndrome).

The virus genome is formed by a single RNA chain, and is classified as a positive monocatenary RNA virus. Its genetic sequence has been isolated from a sample obtained from a patient affected by pneumonia in the Chinese city of Wuhan, although the lack of double-blind control experiment in the published sequencing technique can question the scientific validity of the technique. It was first detected on 12 November 2019. It can produce the contagion of one person to another by means of the saliva drops expelled through cough and sneezing or by breathing (see Flügge droplets). It can cause acute respiratory disease and severe pneumonia in humans.

Although previously there was no specific treatment officially approved, some existing antivirals had already been developed, as well as treatment with convalescent plasma and dexamethasone, which appear to be more effective in managing symptoms or seem to shorten the recovery period in special populations. In December 2020, a vaccination campaign began with the first pilot vaccines authorized in emergency, which lasted and maintained during 2021 and 2022.^{[chuckles]required]} It was Pfizer - BioNTech, with the Comirnaty vaccine, the pioneering laboratories to patent a vaccine and later, the Modern and AstraZeneca laboratories joined this race for the vaccine.

Veterinary Medicine

Coronaviruses have been recognized as the cause of pathological conditions in veterinary medicine since the early 1970s. With the exception of avian infectious bronchitis, the main related diseases have mainly an intestinal location.

Coronaviruses primarily infect the upper respiratory and gastrointestinal tracts of mammals and birds. Seven strains of the coronavirus are currently known to infect humans. Coronaviruses are believed to cause a significant percentage of all common colds in adults and children. Coronaviruses cause colds with significant symptoms; for example, fever, inflammation of the adenoids of the throat, in humans mainly in the winter and early spring seasons. Coronaviruses can cause pneumonia, either direct viral pneumonia or secondary bacterial pneumonia, and bronchitis, either direct viral bronchitis or secondary bacterial bronchitis. The best known human coronavirus was discovered in 2003, SARS-CoV, which causes severe acute respiratory syndrome (SARS), has a unique pathogenesis in that it causes both upper and lower respiratory tract infections. The economic importance and impact of coronaviruses as causative agents of the common cold are difficult to assess because, unlike rhinoviruses (another common cold virus), human coronaviruses are difficult to grow in the laboratory.

Coronaviruses also cause a number of diseases in farm animals and domesticated pets, some of which can be serious and are a threat to the agricultural industry. Infectious bronchitis virus (IBV) in chickens is a coronavirus that affects not only the respiratory tract, but also the urogenital tract. The virus can spread to the different organs of the hen's body. Those with economically significant consequences in farm animals include porcine coronavirus (transmissible gastroenteritis coronavirus, TGE) and bovine coronavirus, which causes diarrhea in young animals. Feline coronavirus: there are two forms, feline enteric coronavirus is a pathogen of minor clinical importance, but spontaneous mutation of this virus can cause feline infectious peritonitis (FIP), a disease associated with high mortality. Similarly, there are two types of coronaviruses that infect ferrets: ferret enteric coronavirus causes a gastrointestinal syndrome known as epizootic catarrhal enteritis (ECE), and a more lethal systemic version of the virus (like FIP in cats), known in ferrets as systemic ferret coronavirus (FSC). There are two types of canine coronavirus (CoVC), one that causes mild gastrointestinal illness and one that causes respiratory illness. Mouse hepatitis virus (MHV) is a coronavirus that causes an epidemic murine disease with high mortality, especially among colonies of laboratory mice. Sialodacryoadenitis virus (sialo saliva, dacryo tear) is a highly infectious coronavirus of laboratory rats, which can be transmitted between individuals by direct contact or indirectly by aerosolized secretions. Acute infections have high morbidity and tropism for the salivary, lacrimal, and Harderian glands.

A related to the bat coronavirus Rinolophus HKU2 called swine acute diarrhea syndrome coronavirus (SADS-CoV) causes diarrhea in pigs.

Prior to the discovery of SARS-CoV, MHV had been studied both in vivo and in vitro, as well as at the molecular level. Some MHV strains caused progressive demyelinating encephalitis in mice that have been used as a mouse model for multiple sclerosis. Significant research efforts have been focused on elucidating the viral pathogenesis of these animal coronaviruses, especially by virologists interested in zoonotic diseases and veterinarians.

Cycle of coronavirus infection

List of domestic animal coronaviruses

• Infectious bronchitis virus (IBV) infectious causes avian bronchitis.
• Porcino coronavirus (transmissible gastroenteritis coronavirus of pigs, TGEV).
• Coronavirus bovine (BCV), responsible for the profuse serious enteritis in young calves.
• Coronavirus feline (FCoV) causes mild enteritis in cats, as well as severe feline infectious peritonitis (other variants of the same virus).
• The two types of canine coronavirus (CoVC) (one causing enteritis, the other one found in respiratory diseases).
• Coronavirus aviar causes enteritis in birds.
• Ferret entérica coronavirus causes epizootic catarral enteritis in ferrets.
• Coronavirus systemic ferret causes FIP-like systemic syndrome in ferrets.
• Canine coronavirus pantropics.
• Coronavirus canino

Another new veterinary disease, porcine epidemic diarrhea virus (PED or PEDV), has emerged around the world. Its economic importance is still unclear, but it shows high mortality in piglets.

Taxonomy

Coronavirus sculpture located at the UNAM Biomedical Research Institute, Mexico

The genera, subgenera and species included in Orthocoronavirinae are:

• Alphacoronavirus
  • Colacovirus
    • Coronavirus bat CDPHE15
  • Decacovirus
    • HKU10 Bat Coronavirus
    • Rhinolophus ferrumequinum alphacoronavirus HuB-2013
  • Duvinacovirus
    • Human coronavirus 229E
  • Fightcovirus
    • Lucheng Rn rat coronavirus
  • Minacovirus
    • Coronavirus ferron
    • Mink coronavirus 1
  • Minunacovirus
    • Miniopterus bat coronavirus 1
    • Miniopterus bat coronavirus HKU8
  • Myotacovirus
    • Myotis ricketti alphacoronavirus Sax-2011
  • Nyctacovirus
    • Nyctalus velutinus alphacoronavirus SC-2013
  • Pedacovirus
    • Virus of swine epidemic diarrhea
    • Scotvilus bat coronavirus 512
  • Rinacovirus
    • Coronavirus bat Rhinolophus HKU2
  • Setracovirus
    • Human Coronavirus NL63
    • Bat coronavirus strain related to NL63 BtKYNL63-9b
  • Tegacovirus
    • Alphacoronavirus 1 - Kind of.
• Betacoronavirus
  • Embevirus
    • Betacoronavirus 1
      • Human Coronavirus OC43 (member without rank or subspecies)
    • Coronavirus Rattus of China HKU24
    • Human Coronavirus HKU1
    • Coronavirus murine - Kind of.
  • Hibecovirus
    • Bat Hp-betacoronavirus Zhejiang2013
  • Merbecovirus
    • Erizo coronavirus 1
    • Coronavirus related to Middle East respiratory syndrome
    • Coronavirus bat Pipistrellus HKU5
    • Coronavirus bat Tyronycteris HKU4
  • Nobecovirus
    • Rousettus bat coronavirus GCCDC1
    • Coronavirus bat Rousettus HKU9
  • Sarbecovirus
    • Coronavirus related to severe acute respiratory syndrome
      • Coronavirus 2 of severe acute respiratory syndrome (empty or subspecies)
• Deltacoronavirus
  • Andecovirus
    • Coronavirus Wigeon HKU20
  • Buldecovirus
    • Bulbul coronavirus HKU11 - Kind of.
    • Coronavirus HKU15
    • Coronavirus Munia HKU13
    • HKU16 White Eye Coronavirus
  • Herdecovirus
    • HKU19 Night Tip Coronavirus
  • Moordecovirus
    • Coronavirus of the common water cock HKU21
• Gammacoronavirus
  • Cegacovirus
    • Beluga Whale Coronavirus SW1
  • Igacovirus
    • Coronavirus avian - Kind of.