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Severe acute respiratory syndrome coronavirus 2

Severe acute respiratory syndrome coronavirus 2
Electron micrograph of SARS-CoV-2 virions
Electron micrograph of SARS-CoV-2 virions
Illustration of a SARS-CoV-2 virion
Illustration of a SARS-CoV-2 virion
Virus classification
(unranked): Virus
Realm: Riboviria
Phylum: incertae sedis
Order: Nidovirales
Family: Coronaviridae
Genus: Betacoronavirus
Subgenus: Sarbecovirus
Species:
Strain:
Severe acute respiratory syndrome coronavirus 2
Severe acute respiratory syndrome coronavirus 2 is located in China
Severe acute respiratory syndrome coronavirus 2
Wuhan, China, the center of the only recorded outbreak
Synonyms

2019-nCoV

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),[1][2] previously known by the provisional name 2019-nCoV,[3][4][5] is a positive-sense single-stranded RNA virus.[6][7] It is contagious in humans and is the cause of coronavirus disease 2019 (COVID-19).[8]

SARS-CoV-2 has strong genetic similarity to bat coronaviruses, from which it likely originated,[9][10][11] although an intermediate reservoir such as a pangolin is thought to be involved.[12][13] From a taxonomic perspective SARS-CoV-2 is classified as a strain of the species severe acute respiratory syndrome-related coronavirus.[1]

SARS-CoV-2 is the cause of the ongoing 2019–20 coronavirus outbreak, a Public Health Emergency of International Concern that originated in Wuhan, China.[14] Because of this connection, the virus is sometimes referred to informally as the "Wuhan coronavirus"[15][16], the "China virus"[17], among other names.

Name

During the ongoing 2019–20 coronavirus outbreak, the World Health Organization (WHO) originally recommended use of the temporary designation "2019-nCoV" (2019 novel coronavirus) to refer to the virus. However, this led to concerns that the absence of an official name might lead to the use of prejudicial informal names, and in common parlance the virus was often referred to as "the new coronavirus", "Wuhan coronavirus", or simply "coronavirus".[18][19] Per 2015 WHO guidelines on the naming of viruses and diseases,[19][20] the International Committee on Taxonomy of Viruses (ICTV) announced that it would introduce a suitable official name for the virus.[18]

On 11 February 2020, the ICTV introduced the name "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2) to refer to the virus strain previously known as 2019-nCoV.[1] Earlier the same day, the WHO officially renamed the disease caused by the virus strain from "2019-nCoV acute respiratory disease" to coronavirus disease 2019 (COVID-19).[2][21] To avoid confusion with the disease SARS, the WHO sometimes refers to the virus as "the COVID-19 virus" or "the virus responsible for COVID-19" in public health communications.[22]

Virology

Infection

Human-to-human transmission of the virus has been confirmed[8] and occurs primarily via respiratory droplets from coughs and sneezes within a range of about 6 feet (1.8 m).[23][24] Viral RNA has also been found in stool samples from infected patients.[25]

It is possible that the virus can be infectious even during the incubation period, but this has not been proven,[26] and the WHO stated on 1 February 2020 that "transmission from asymptomatic cases is likely not a major driver of transmission" at this time.[27]

Reservoir

Researchers are unsure of the original source of viral transmission to humans.[28][29][30] However, research into the origin of the 2003 SARS outbreak has resulted in the discovery of many SARS-like bat coronaviruses, most originating in the Rhinolophus genus of horseshoe bats. Two viral nucleic acid sequences from Rhinolophus sinicus published in 2015 and 2017 show a resemblance of 80% to SARS-CoV-2.[11][31][32] A third viral nucleic acid sequence from Rhinolophus affinis, "RaTG13" collected in Yunnan province, has a 96% resemblance to SARS-CoV-2.[9][33] For comparison, this amount of variation among viruses is similar to the amount of mutation observed over ten years in the H3N2 human influenza virus strain.[34]

Researchers from Guangzhou claimed to have discovered a "99% identical" viral nucleic acid sequence in a pangolin sample on February 7.[35][36] Pangolins are protected under Chinese law, but poaching and trading of pangolins for traditional medicine remains common. A metagenomic study published in 2019 previously revealed that SARS-CoV was the most widely distributed coronavirus among a sample of Malayan pangolins.[37] Microbiologists and geneticists in Texas have independently found evidence of recombination in coronaviruses suggesting pangolin origins of SARS-CoV-2; they acknowledged remaining unknown factors while urging continued examination of other mammals.[38] The paper releasing the sequence states that "the receptor-binding domain of the S protein of the newly discovered Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference."[39]

Phylogenetics and taxonomy

Genomic information
SARS-CoV-2 genome.svg
Genomic organisation of SARS-CoV-2
NCBI genome IDMN908947
Genome size29,903 bases
Year of completion2020

SARS-CoV-2 belongs to the broad family of viruses known as coronaviruses. It is a positive-sense single-stranded RNA (+ssRNA) virus. Other coronaviruses are capable of causing illnesses ranging from the common cold to more severe diseases such as Middle East respiratory syndrome (MERS). It is the seventh known coronavirus to infect people, after 229E, NL63, OC43, HKU1, MERS-CoV, and the original SARS-CoV.[40]

Like the SARS-related coronavirus strain implicated in the 2003 SARS outbreak, SARS-CoV-2 is a member of the subgenus Sarbecovirus (Beta-CoV lineage B).[41][42][43] Its RNA sequence is approximately 30,000 bases in length.[7]

With a sufficient number of sequenced genomes, it is possible to reconstruct a phylogenetic tree of the mutation history of a family of viruses. By 12 January 2020, five genomes of SARS-CoV-2 had been isolated from Wuhan and reported by the Chinese Center for Disease Control and Prevention (CCDC) and other institutions;[7][44] the number of genomes increased to 81 by 11 February 2020.[45] A phylogenic analysis of the samples shows they are "highly related with at most seven mutations relative to a common ancestor", implying that the first human infection occurred in November or December 2019.[45]

On 11 February 2020, ICTV announced that according to existing rules that compute hierarchical relationships among coronaviruses on the basis of five conserved sequences of nucleic acids, the differences between what was then called 2019-nCoV and the virus strain from the 2003 SARS outbreak were insufficient to make it a separate viral species. Therefore, they identified 2019-nCoV as a strain of severe acute respiratory syndrome-related coronavirus.[1]

Structural biology

Protein modeling experiments on the spike (S) protein of the virus suggest that it has sufficient affinity to the angiotensin converting enzyme 2 (ACE2) receptors of human cells to use them as a mechanism of cell entry.[46] On 22 January 2020, a group in China working with the full virus genome and a group in the United States using reverse genetics methods independently and experimentally demonstrated that ACE2 could act as the receptor for SARS-CoV-2.[9][47][48][49][50][51] Studies have shown that SARS-CoV-2 has a higher affinity to human ACE2 than the original SARS virus strain.[52] An atomic-level image of the S protein has been created using cryogenic electron microscopy.[53][54]

Epidemiology

Based upon the low variability exhibited among known SARS-CoV-2 genomic sequences, the strain is thought to have been detected by health authorities within weeks of its emergence among the human population in late 2019.[55][28] The virus subsequently spread to all provinces of China and to more than fifty other countries in Asia, Europe, North America, South America, Africa, and Oceania.[56] Human-to-human transmission of the virus has been confirmed in all of these regions[8][57][58][59] except Africa and South America. On 30 January 2020, SARS-CoV-2 was designated a Public Health Emergency of International Concern by the WHO.[14][60]

As of 1 March 2020 (09:05 UTC), there were 86,986 confirmed cases of infection, of which 79,826 were within mainland China.[56] One mathematical model estimated the number of people infected in Wuhan alone at 75,815 as of 25 January 2020, at a time when confirmed infections were far lower.[61] While the proportion of infections that result in confirmed infection or progress to diagnosable disease remains unclear,[62][63] the total number of deaths attributed to the virus was 2,979 as of 1 March 2020 (09:05 UTC); 93% of all deaths have occurred in Hubei province,[56] where Wuhan is located.

The basic reproduction number (, pronounced R-nought or R-zero)[64] of the virus has been estimated to be between 1.4 and 3.9.[65][66][67][68] This means that, when otherwise unchecked, each infection from the virus would typically be expected to result in 1.4 to 3.9 new infections.

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Further reading

  • World Health Organization (2020). Laboratory testing of human suspected cases of novel coronavirus (nCoV) infection: interim guidance, 10 January 2020 (Report). World Health Organization. hdl:10665/330374. WHO/2019-nCoV/laboratory/2020.1.
  • World Health Organization (2020). WHO R&D Blueprint: informal consultation on prioritization of candidate therapeutic agents for use in novel coronavirus 2019 infection, Geneva, Switzerland, 24 January 2020 (Report). World Health Organization. hdl:10665/330680. WHO/HEO/R&D Blueprint (nCoV)/2020.1.
  • Habibzadeh P, Stoneman EK (February 2020). "The Novel Coronavirus: A Bird's Eye View". The International Journal of Occupational and Environmental Medicine. 11 (2): 65–71. doi:10.15171/ijoem.2020.1921. PMID 32020915.

External links

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