SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2 | |||||||||||
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Colourised transmission electron micrograph of SARS-CoV-2 virions with visible coronae | |||||||||||
Model of the external structure of the SARS-CoV-2 virion[1]
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Virus classification | |||||||||||
(unranked): | Virus | ||||||||||
Realm: | Riboviria | ||||||||||
Kingdom: | Orthornavirae | ||||||||||
Phylum: | Pisuviricota | ||||||||||
Class: | Pisoniviricetes | ||||||||||
Order: | Nidovirales | ||||||||||
Family: | Coronaviridae | ||||||||||
Genus: | Betacoronavirus | ||||||||||
Subgenus: | Sarbecovirus | ||||||||||
Species: | Severe acute respiratory syndrome–related coronavirus | ||||||||||
Virus: | Severe acute respiratory syndrome coronavirus 2
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Notable variants | |||||||||||
Synonyms | |||||||||||
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Part of a series on the |
COVID-19 pandemic |
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COVID-19 portal |
Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2)
SARS‑CoV‑2 is a strain of the species
Terminology
During the initial outbreak in Wuhan, China, various names were used for the virus; some names used by different sources included "the coronavirus" or "Wuhan coronavirus".[27][28] In January 2020, the World Health Organization (WHO) recommended "2019 novel coronavirus" (2019-nCoV)[5][29] as the provisional name for the virus. This was in accordance with WHO's 2015 guidance[30] against using geographical locations, animal species, or groups of people in disease and virus names.[31][32]
On 11 February 2020, the International Committee on Taxonomy of Viruses adopted the official name "severe acute respiratory syndrome coronavirus 2" (SARS‑CoV‑2).[33] To avoid confusion with the disease SARS, the WHO sometimes refers to SARS‑CoV‑2 as "the COVID-19 virus" in public health communications[34][35] and the name HCoV-19 was included in some research articles.[8][9][10] Referring to COVID-19 as the "Wuhan virus" has been described as dangerous by WHO officials, and as xenophobic by many journalists and academics.[36][37][38]
Infection and transmission
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Human-to-human
The degree to which the virus is infectious during the incubation period is uncertain, but research has indicated that the pharynx reaches peak viral load approximately four days after infection[61][62] or in the first week of symptoms and declines thereafter.[63] The duration of SARS-CoV-2 RNA shedding is generally between 3 and 46 days after symptom onset.[64]
A study by a team of researchers from the University of North Carolina found that the nasal cavity is seemingly the dominant initial site of infection, with subsequent aspiration-mediated virus-seeding into the lungs in SARS‑CoV‑2 pathogenesis.[65] They found that there was an infection gradient from high in proximal towards low in distal pulmonary epithelial cultures, with a focal infection in ciliated cells and type 2 pneumocytes in the airway and alveolar regions respectively.[65]
Studies have identified a range of animals—such as cats, ferrets, hamsters, non-human primates, minks, tree shrews, raccoon dogs, fruit bats, and rabbits—that are susceptible and permissive to SARS-CoV-2 infection.[66][67][68] Some institutions have advised that those infected with SARS‑CoV‑2 restrict their contact with animals.[69][70]
Asymptomatic and presymptomatic transmission
On 1 February 2020, the World Health Organization (WHO) indicated that "transmission from asymptomatic cases is likely not a major driver of transmission".[71] One meta-analysis found that 17% of infections are asymptomatic, and asymptomatic individuals were 42% less likely to transmit the virus.[72]
However, an epidemiological model of the beginning of the
Reinfection
There is uncertainty about reinfection and long-term immunity.[76] It is not known how common reinfection is, but reports have indicated that it is occurring with variable severity.[76]
The first reported case of reinfection was a 33-year-old man from Hong Kong who first tested positive on 26 March 2020, was discharged on 15 April 2020 after two negative tests, and tested positive again on 15 August 2020 (142 days later), which was confirmed by whole-genome sequencing showing that the viral genomes between the episodes belong to different clades.[77] The findings had the implications that herd immunity may not eliminate the virus if reinfection is not an uncommon occurrence and that vaccines may not be able to provide lifelong protection against the virus.[77]
Another case study described a 25-year-old man from Nevada who tested positive for SARS‑CoV‑2 on 18 April 2020 and on 5 June 2020 (separated by two negative tests). Since genomic analyses showed significant genetic differences between the SARS‑CoV‑2 variant sampled on those two dates, the case study authors determined this was a reinfection.[78] The man's second infection was symptomatically more severe than the first infection, but the mechanisms that could account for this are not known.[78]
Reservoir and origin
No
The first known infections from SARS‑CoV‑2 were discovered in Wuhan, China.
For a virus recently acquired through a cross-species transmission, rapid evolution is expected.[88] The mutation rate estimated from early cases of SARS-CoV-2 was of 6.54×10−4 per site per year.[86] Coronaviruses in general have high genetic plasticity,[89] but SARS-CoV-2's viral evolution is slowed by the RNA proofreading capability of its replication machinery.[90] For comparison, the viral mutation rate in vivo of SARS-CoV-2 has been found to be lower than that of influenza.[91]
Research into the natural reservoir of the virus that caused the
Bats are considered the most likely natural reservoir of SARS‑CoV‑2.[86][97] Differences between the bat coronavirus and SARS‑CoV‑2 suggest that humans may have been infected via an intermediate host;[84] although the source of introduction into humans remains unknown.[98][79]
Although the role of
Phylogenetics and taxonomy
Genomic organisation of isolate Wuhan-Hu-1, the earliest sequenced sample of SARS-CoV-2 | |
NCBI genome ID | 86693 |
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Genome size | 29,903 bases |
Year of completion | 2020 |
Genome browser (UCSC) |
SARS‑CoV‑2 belongs to the broad family of viruses known as
Like the SARS-related coronavirus implicated in the 2003 SARS outbreak, SARS‑CoV‑2 is a member of the subgenus
A distinguishing feature of SARS‑CoV‑2 is its incorporation of a polybasic site cleaved by furin,[102][112] which appears to be an important element enhancing its virulence.[113] It was suggested that the acquisition of the furin-cleavage site in the SARS-CoV-2 S protein was essential for zoonotic transfer to humans.[114] The furin protease recognizes the canonical peptide sequence RX[R/K] R↓X where the cleavage site is indicated by a down arrow and X is any amino acid.[115][116] In SARS-CoV-2 the recognition site is formed by the incorporated 12 codon nucleotide sequence CCT CGG CGG GCA which corresponds to the amino acid sequence P RR A.[117] This sequence is upstream of an arginine and serine which forms the S1/S2 cleavage site (P RR A R↓S) of the spike protein.[118] Although such sites are a common naturally-occurring feature of other viruses within the Subfamily Orthocoronavirinae,[117] it appears in few other viruses from the Beta-CoV genus,[119] and it is unique among members of its subgenus for such a site.[102] The furin cleavage site PRRAR↓ is highly similar to that of the feline coronavirus, an alphacoronavirus 1 strain.[120]
Viral genetic sequence data can provide critical information about whether viruses separated by time and space are likely to be epidemiologically linked.
On 11 February 2020, the
In July 2020, scientists reported that a more infectious SARS‑CoV‑2 variant with spike protein variant G614 has replaced D614 as the dominant form in the pandemic.[127][128]
Coronavirus genomes and subgenomes encode six open reading frames (ORFs).[129] In October 2020, researchers discovered a possible overlapping gene named ORF3d, in the SARS‑CoV‑2 genome. It is unknown if the protein produced by ORF3d has any function, but it provokes a strong immune response. ORF3d has been identified before, in a variant of coronavirus that infects pangolins.[130][131]
Phylogenetic tree
A phylogenetic tree based on whole-genome sequences of SARS-CoV-2 and related coronaviruses is:[132][133]
SARS‑CoV‑2 related coronavirus | |
SARS-CoV-1 , 79% to SARS-CoV-2
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Variants
This section needs to be updated.(April 2023) |
There are many thousands of variants of SARS-CoV-2, which can be grouped into the much larger
Several notable variants of SARS-CoV-2 emerged in late 2020. The
- P681H.
- An E484K mutation in some lineage B.1.1.7 virions has been noted and is also tracked by various public health agencies.
- An
- K417N, E484K and N501Y.
- Gamma: Lineage P.1 emerged in Brazil in November 2020, also with evidence of increased transmissibility and virulence, alongside changes to antigenicity. Similar concerns about vaccine efficacy have been raised. Notable mutations also include K417N, E484K and N501Y.
- Delta: Lineage B.1.617.2 emerged in India in October 2020. There is also evidence of increased transmissibility and changes to antigenicity.
- Omicron: Lineage B.1.1.529 emerged in Botswana in November 2021.
Other notable variants include 6 other WHO-designated variants under investigation and Cluster 5, which emerged among mink in Denmark and resulted in a mink euthanasia campaign rendering it virtually extinct.[145]
Virology
Virus structure
Each SARS-CoV-2
Genome
As of early 2022, about 7 million SARS-CoV-2 genomes had been sequenced and deposited into public databases and another 800,000 or so were added each month.[151] By September 2023, the GISAID EpiCoV database contained more than 16 million genome sequences.[152]
SARS-CoV-2 has a linear,
Replication cycle
Virus infections start when viral particles bind to host surface cellular receptors.
Initial spike protein priming by
SARS‑CoV‑2 produces at least three
Treatment and drug development
Very few drugs are known to effectively inhibit SARS‑CoV‑2.
Epidemiology
Retrospective tests collected within the Chinese surveillance system revealed no clear indication of substantial unrecognized circulation of SARS‑CoV‑2 in Wuhan during the latter part of 2019.[86]
A meta-analysis from November 2020 estimated the basic reproduction number () of the virus to be between 2.39 and 3.44.
Variant | R0 | Source |
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Reference/ancestral strain | ~2.8 | [177] |
Alpha (B.1.1.7) | (40-90% higher than previous variants) | [178] |
Delta (B.1.617.2) | ~5 (3-8) | [179] |
There have been about 96,000 confirmed cases of infection in mainland China.[180] While the proportion of infections that result in confirmed cases or progress to diagnosable disease remains unclear,[181] one mathematical model estimated that 75,815 people were infected on 25 January 2020 in Wuhan alone, at a time when the number of confirmed cases worldwide was only 2,015.[182] Before 24 February 2020, over 95% of all deaths from COVID-19 worldwide had occurred in Hubei province, where Wuhan is located.[183][184] As of 10 March 2023, the percentage had decreased to 0.047%.[180]
As of 10 March 2023, there were 676,609,955 total confirmed cases of SARS‑CoV‑2 infection.[180] The total number of deaths attributed to the virus was 6,881,955.[180]
See also
- 3C-like protease (NS5)
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Further reading
- Bar-On YM, Flamholz A, Phillips R, Milo R (April 2020). "SARS-CoV-2 (COVID-19) by the numbers". eLife. 9. PMID 32228860.
- Brüssow H (May 2020). "The Novel Coronavirus - A Snapshot of Current Knowledge". Microbial Biotechnology. 13 (3): 607–612. PMID 32144890.
- Cascella M, Rajnik M, Aleem A, Dulebohn S, Di Napoli R (January 2020). "Features, Evaluation and Treatment Coronavirus (COVID-19)". StatPearls. from the original on 6 April 2020. Retrieved 4 April 2020.
- Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases (Report). hdl:10665/331329.
- Zoumpourlis V, Goulielmaki M, Rizos E, Baliou S, Spandidos DA (October 2020). "[Comment] The COVID‑19 pandemic as a scientific and social challenge in the 21st century". Molecular Medicine Reports (Review). 22 (4): 3035–3048. PMID 32945405.
External links
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