Severe acute respiratory syndrome coronavirus 2

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Severe acute respiratory syndrome coronavirus 2
Novel Coronavirus SARS-CoV-2.jpg
Transmission electron micrograph of SARS-CoV-2 virions with visible coronae
2019-nCoV-CDC-23312 without background.png
Illustration of a SARS-CoV-2 virion [1]
  Red protrusions: spike proteins (S) [1]
  Grey coating: the envelope, composed mainly of lipids, which can be destroyed with alcohol or soap [1]
  Yellow deposits: envelope proteins (E) [1]
  Orange deposits: membrane proteins (M) [1]
Virus classification Red Pencil Icon.png
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Pisuviricota
Class: Pisoniviricetes
Order: Nidovirales
Family: Coronaviridae
Genus: Betacoronavirus
Subgenus: Sarbecovirus
Species:
Strain:
Severe acute respiratory syndrome coronavirus 2
Synonyms
  • 2019-nCoV
HeLa cells engineered to express ACE2 become susceptible to SARS-CoV-2 infection. ACE2 SARS-COV-2 in HeLa CELLS.png
HeLa cells engineered to express ACE2 become susceptible to SARS-CoV-2 infection.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [2] [3] is the strain of coronavirus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the COVID-19 pandemic. Colloquially known as simply the coronavirus, it was previously referred to by its provisional name, 2019 novel coronavirus (2019-nCoV), [4] [5] [6] [7] and has also been called human coronavirus 2019 (HCoV-19 or hCoV-19). [8] [9] [10] [11] The World Health Organization declared the outbreak a Public Health Emergency of International Concern on 30 January 2020, and a pandemic on 11 March 2020. [12] [13]

Contents

SARS-CoV-2 is a Baltimore class IV [14] positive-sense single-stranded RNA virus [15] that is contagious in humans. [16] As described by the U.S. National Institutes of Health, it is the successor to SARS-CoV-1, [10] [17] the strain that caused the 2002–2004 SARS outbreak.

Taxonomically, SARS-CoV-2 is a strain of severe acute respiratory syndrome-related coronavirus (SARSr-CoV). [2] It is believed to have zoonotic origins and has close genetic similarity to bat coronaviruses, suggesting it emerged from a bat-borne virus. [18] [19] [20] [9] There is no evidence yet to link an intermediate host, such as a pangolin, to its introduction to humans. [21] [22] The virus shows little genetic diversity, indicating that the spillover event introducing SARS-CoV-2 to humans is likely to have occurred in late 2019. [23] In September 2020, based on data analysis, researchers reported the discovery of the genome of the virus's index case. [24] [25]

Epidemiological studies estimate each infection results in 5.7 new ones when no members of the community are immune and no preventive measures taken. [26] The virus primarily spreads between people through close contact and via respiratory droplets produced from coughs or sneezes. [27] [28] It mainly enters human cells by binding to the receptor angiotensin converting enzyme 2 (ACE2). [18] [29] [30] [31]

Terminology

The name "2019-nCoV" in use in a trilingual sign at a Lisbon health facility in February 2020. NOVO-NEW-Xin .2019-nCoV.jpg
The name "2019-nCoV" in use in a trilingual sign at a Lisbon health facility in February 2020.

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". [32] [33] In January 2020, the World Health Organisation recommended "2019 novel coronavirus" (2019-nCov) [34] [5] as the provisional name for the virus. This was in accordance with WHO's 2015 guidance [35] against using geographical locations, animal species, or groups of people in disease and virus names. [36] [37]

On 11 February 2020, the International Committee on Taxonomy of Viruses adopted the official name "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2). [21] To avoid confusion with the disease SARS, the WHO sometimes refers to SARS-CoV-2 as "the COVID-19 virus" in public health communications [38] [39] and the name HCoV-19 was included in some research articles. [8] [9] [10]

The general public often calls both the virus, and the disease it causes, "coronavirus". U.S. President Donald Trump referred to the virus as the "Chinese virus" in tweets, interviews, and White House press briefings, which drew some criticism that he was stigmatizing the disease with racial or nationalistic overtones. [40] [41] [42]

Virology

Infection and transmission

Human-to-human transmission of SARS-CoV-2 was confirmed on 20 January 2020, during the COVID-19 pandemic. [16] [43] [44] [45] Transmission was initially assumed to occur primarily via respiratory droplets from coughs and sneezes within a range of about 1.8 metres (6 ft). [28] [46] Laser light scattering experiments suggest speaking— as an additional mode of transmission. [47] [48] Other studies have suggested that the virus may be airborne as well, with aerosols potentially being able to transmit the virus. [49] [50] [51]

Indirect contact via contaminated surfaces is another possible cause of infection. [52] Preliminary research indicates that the virus may remain viable on plastic (polypropylene) and stainless steel (AISI 304) for up to three days, but does not survive on cardboard for more than one day or on copper for more than four hours; [10] the virus is inactivated by soap, which destabilises its lipid bilayer. [53] [54] Viral RNA has also been found in stool samples and semen from infected individuals. [55] [56]

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 [57] [58] or the first week of symptoms, and declines after. [59] On 1 February 2020, the World Health Organization (WHO) indicated that "transmission from asymptomatic cases is likely not a major driver of transmission". [60] However, an epidemiological model of the beginning of the outbreak in China suggested that "pre-symptomatic shedding may be typical among documented infections" and that subclinical infections may have been the source of a majority of infections. [61] That may explain how out of 217 onboard a cruise liner that docked at Montevideo, only 24 of 128 who tested positive for viral RNA showed symptoms. [62] Similarly, a study of ninety-four patients hospitalized in January and February 2020 estimated patients shed the greatest amount of virus two to three days before symptoms appear and that "a substantial proportion of transmission probably occurred before first symptoms in the index case". [63]

A study by a team of researchers from the University of North Carolina found that the nasal cavity is seemingly the dominant initial site for infection with subsequent aspiration-mediated virus seeding into the lungs in SARS-CoV-2 pathogenesis. [64] 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. [64]

There is some evidence of human-to-animal transmission of SARS-CoV-2, including examples in felids. [65] [66] Some institutions have advised those infected with SARS-CoV-2 to restrict contact with animals. [67] [68]

There are still a lot of questions about reinfection and long-term immunity. [69] It is not known how common reinfection is, but reports have indicated that it is occurring with variable severity. [69] 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. [70] 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. [70] 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. [71] The man's second infection was symptomatically more severe than the first infection, but the mechanisms that could account for this is not known. [71]

Reservoir and zoonotic origin

Transmission of SARS-CoV-1 and SARS-CoV-2 from mammals as biological carriers to humans SARS-CoV-1 and 2 - mammals as carriers.png
Transmission of SARS-CoV-1 and SARS-CoV-2 from mammals as biological carriers to humans

The first known infections from the SARS-CoV-2 strain were discovered in Wuhan, China. [18] The original source of viral transmission to humans remains unclear, as does whether the strain became pathogenic before or after the spillover event. [23] [72] [9] Because many of the first individuals found to be infected by the virus were workers at the Huanan Seafood Market, [73] [74] it has been suggested that the strain might have originated from the market. [9] [75] However, other research indicates that visitors may have introduced the virus to the market, which then facilitated rapid expansion of the infections. [23] [76] A phylogenetic network analysis of 160 early coronavirus genomes sampled from December 2019 to February 2020 revealed that the virus type most closely related to the bat coronavirus was most abundant in Guangdong, China, and designated type "A". The predominant type among samples from Wuhan, "B", is more distantly related to the bat coronavirus than the ancestral type "A". [77] [78]

Research into the natural reservoir of the virus strain that caused the 2002–2004 SARS outbreak has resulted in the discovery of many SARS-like bat coronaviruses, most originating in the Rhinolophus genus of horseshoe bats. Phylogenetic analysis indicates that samples taken from Rhinolophus sinicus show a resemblance of 80% to SARS-CoV-2. [20] [79] [80] Phylogenetic analysis also indicates that a virus from Rhinolophus affinis , collected in Yunnan province and designated RaTG13, has a 96% resemblance to SARS-CoV-2. [18] [81]

Samples taken from Rhinolophus sinicus, a species of horseshoe bats, show an 80% resemblance to SARS-CoV-2. Naturalis Biodiversity Center - RMNH.MAM.33160.b dor - Rhinolophus sinicus - skin.jpeg
Samples taken from Rhinolophus sinicus, a species of horseshoe bats, show an 80% resemblance to SARS-CoV-2.

Bats are considered the most likely natural reservoir of SARS-CoV-2, [82] [83] but differences between the bat coronavirus and SARS-CoV-2 suggest that humans were infected via an intermediate host. [75] Although studies have suggested some likely candidates, the number and identities of intermediate hosts remain uncertain. [84] Nearly half of the strain's genome has a phylogenetic lineage distinct from known relatives. [85]

The pangolin coronavirus has up to 92% resemblance to SARS-CoV-2. Zoo Leipzig - Tou Feng.jpg
The pangolin coronavirus has up to 92% resemblance to SARS-CoV-2.

A phylogenetics study published in 2020 indicates that pangolins are a reservoir host of SARS-CoV-2-like coronaviruses. [87] However, there is no direct evidence to link pangolins as an intermediate host of SARS-CoV-2 at this moment. [88] While there is scientific consensus that bats are the ultimate source of coronaviruses, the pangolin CoV is sister to both RaTG13 as well as SARS-CoV-2. Based on whole genome sequence similarity, a pangolin coronavirus candidate strain was found to be less similar than RaTG13, but more similar than other bat coronaviruses to SARS-CoV-2. Therefore, based on maximum parsimony and current sample data, a specific population of bats is more likely to have directly transmitted SARS-CoV-2 to humans than a pangolin, while an evolutionary ancestor to bats was the source of general coronaviruses. [86]

A metagenomics study published in 2019 had previously revealed that SARS-CoV, the strain of the virus that causes SARS, was the most widely distributed coronavirus among a sample of Sunda pangolins. [89] On 7 February 2020, South China Agricultural University in Guangzhou announced that researchers discovered a pangolin sample with a particular coronavirus – a single nucleic acid sequence of the virus was "99% similar" to that of a protein-coding RNA of SARS-CoV-2. [90] The authors state that "the receptor-binding domain of the S protein [that binds to the cell surface receptor during infection] of the newly discovered Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference." [91] Microbiologists and geneticists in Texas have independently found evidence of reassortment in coronaviruses suggesting the involvement of pangolins in the origin of SARS-CoV-2. [92] The majority of the viral RNA is related to a variation of bat coronaviruses. [93] The spike protein appears to be a notable exception, however, possibly acquired through a more recent recombination event with a pangolin coronavirus. [94] SARS-CoV-2’s entire receptor binding motif appears to have been introduced through recombination from coronaviruses of pangolins. [95] Such a recombination event may have been a critical step in the evolution of SARS-CoV-2’s capability to infect humans. [95] Recombination events have been key steps in the viral evolutionary process that lead to the emergence of new human diseases. [96] Structural analysis of the receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2) complex [97] revealed key mutations on the RBD, such as F486 and N501, which form contacts with ACE2. [98] These residues are found in the pangolin coronavirus. [98]

Pangolins are protected under Chinese law, but their poaching and trading for use in traditional Chinese medicine remains common in the black market. [99] [100] Deforestation, wildlife farming and trade in unsanitary conditions increases the risk of new zoonotic diseases. [101] [102] [103] [104]

All available evidence suggests that SARS-CoV-2 has a natural animal origin and is not genetically engineered. [105] Nevertheless, laboratory origin of SARS-CoV-2 can not be ruled out. [106] According to computational simulations on protein folding, the RBD of the spike protein of SARS-CoV-2 should have an unremarkable binding affinity. In actuality, however, it has very efficient binding to the human ACE2 receptor. To expose the RBD for fusion, furin proteases must first cleave the S protein. Furin proteases are abundant in the respiratory tract and lung epithelial cells. Additionally, the backbone of the virus does not resemble any previously described in scientific literature used for genetic modification. The possibility that the virus could have gained the necessary adaptations through cell culture in a laboratory setting is challenged by scientists who assert that "the generation of the predicted O-linked glycans... suggest[s] the involvement of an immune system." [107] [9]

Phylogenetics and taxonomy

Genomic information
SARS-CoV-2 genome.svg
Genomic organisation of isolate Wuhan-Hu-1, the earliest sequenced sample of SARS-CoV-2
NCBI genome ID 86693
Genome size 29,903 bases
Year of completion 2020
Genome browser (UCSC)

SARS-CoV-2 belongs to the broad family of viruses known as coronaviruses. [33] It is a positive-sense single-stranded RNA (+ssRNA) virus, with a single linear RNA segment. Other coronaviruses are capable of causing illnesses ranging from the common cold to more severe diseases such as Middle East respiratory syndrome (MERS, fatality rate ~34%). It is the seventh known coronavirus to infect people, after 229E, NL63, OC43, HKU1, MERS-CoV, and the original SARS-CoV. [108]

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). [109] [110] Its RNA sequence is approximately 30,000 bases in length. [15] SARS-CoV-2 is unique among known betacoronaviruses in its incorporation of a polybasic cleavage site, a characteristic known to increase pathogenicity and transmissibility in other viruses. [9] [111] [112]

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; [15] [113] the number of genomes increased to 42 by 30 January 2020. [114] A phylogenetic analysis of those samples showed they were "highly related with at most seven mutations relative to a common ancestor", implying that the first human infection occurred in November or December 2019. [114] As of 7 May 2020, 4,690 SARS-CoV-2 genomes sampled on six continents were publicly available. [115]

On 11 February 2020, the International Committee on Taxonomy of Viruses 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 them separate viral species. Therefore, they identified 2019-nCoV as a strain of Severe acute respiratory syndrome-related coronavirus . [2]

In July 2020, scientists report that a more infectious SARS-CoV-2 variant with spike protein variant G614 has replaced D614 as the dominant form in the pandemic. [116] [117]

In October 2020, researchers discovered a possible overlapping gene named ORF3d, in the Covid-19 virus 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. [118] [119]

Structural biology

Structure of a SARSr-CoV virion Coronavirus virion structure.svg
Structure of a SARSr-CoV virion

Each SARS-CoV-2 virion is 50–200 nanometres in diameter. [74] Like other coronaviruses, SARS-CoV-2 has four structural proteins, known as the S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins; the N protein holds the RNA genome, and the S, E, and M proteins together create the viral envelope. [120] The spike protein, which has been imaged at the atomic level using cryogenic electron microscopy, [121] [122] is the protein responsible for allowing the virus to attach to and fuse with the membrane of a host cell; [120] specifically, its S1 subunit catalyzes attachment, the S2 subunit fusion. [123]

SARS-CoV-2 spike homotrimer with one protein subunit highlighted. The ACE2 binding domain is magenta. 6VSB spike protein SARS-CoV-2 monomer in homotrimer.png
SARS-CoV-2 spike homotrimer with one protein subunit highlighted. The ACE2 binding domain is magenta.

Protein modeling experiments on the spike protein of the virus soon suggested that SARS-CoV-2 has sufficient affinity to the receptor angiotensin converting enzyme 2 (ACE2) on human cells to use them as a mechanism of cell entry. [124] By 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. [18] [125] [29] [126] Studies have shown that SARS-CoV-2 has a higher affinity to human ACE2 than the original SARS virus strain. [121] [127] SARS-CoV-2 may also use basigin to assist in cell entry. [128]

Initial spike protein priming by transmembrane protease, serine 2 (TMPRSS2) is essential for entry of SARS-CoV-2. [30] After a SARS-CoV-2 virion attaches to a target cell, the cell's protease TMPRSS2 cuts open the spike protein of the virus, exposing a fusion peptide in the S2 subunit, and the host receptor ACE2. [123] After fusion, an endosome forms around the virion, separating it from the rest of the host cell. The virion escapes when the pH of the endosome drops or when cathepsin, a host cysteine protease, cleaves it. [123] The virion then releases RNA into the cell and forces the cell to produce and disseminate copies of the virus, which infect more cells. [129]

SARS-CoV-2 produces at least three virulence factors that promote shedding of new virions from host cells and inhibit immune response. [120] Whether they include downregulation of ACE2, as seen in similar coronaviruses, remains under investigation (as of May 2020). [87]

SARS-CoV-2 49531042877.jpg
SARS-CoV-2 scanning electron microscope image.jpg
Digitally colourised scanning electron micrographs of SARS-CoV-2 virions (yellow) emerging from human cells cultured in a laboratory

Epidemiology

Transmission electron micrograph of SARS-CoV-2 virions (red) isolated from a patient during the COVID-19 pandemic Novel Coronavirus SARS-CoV-2 (49597020718).jpg
Transmission electron micrograph of SARS-CoV-2 virions (red) isolated from a patient during the COVID-19 pandemic

Based on 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. [23] [130] The earliest case of infection currently known is dated back to 17 November 2019 or possibly 1 December 2019. [131] The virus subsequently spread to all provinces of China and to more than 150 other countries in Asia, Europe, North America, South America, Africa, and Oceania. [132] Human-to-human transmission of the virus has been confirmed in all these regions. [133] On 30 January 2020, SARS-CoV-2 was designated a Public Health Emergency of International Concern by the WHO, [134] [12] and on 11 March 2020 the WHO declared it a pandemic. [13] [135]

The basic reproduction number () of the virus has been estimated to be around 5.7. [26] This means each infection from the virus is expected to result in 5.7 new infections when no members of the community are immune and no preventive measures are taken. The reproduction number may be higher in densely populated conditions such as those found on cruise ships. [136] Many forms of preventive efforts may be employed in specific circumstances to reduce the propagation of the virus. [137]

There have been about 82,000 confirmed cases of infection in mainland China. [132] While the proportion of infections that result in confirmed cases or progress to diagnosable disease remains unclear, [138] 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. [139] Before 24 February 2020, over 95% of all deaths from COVID-19 worldwide had occurred in Hubei province, where Wuhan is located. [140] [141] As of 29 November 2020, the percentage had decreased to

As of 29 November 2020, there have been 62,094,127 total confirmed cases of SARS-CoV-2 infection in the ongoing pandemic. [132] The total number of deaths attributed to the virus is 1,449,709. [132] Many recoveries from confirmed infections go unreported, but at least 39,750,055 people have recovered from confirmed infections. [132]

See also

Related Research Articles

Severe acute respiratory syndrome Disease caused by severe acute respiratory syndrome coronavirus

Severe acute respiratory syndrome (SARS) is a viral respiratory disease of zoonotic origin caused by severe acute respiratory syndrome coronavirus, the first identified strain of the SARS coronavirus species Severe acute respiratory syndrome–related coronavirus (SARSr-CoV). The syndrome caused the 2002–2004 SARS outbreak. In late 2017, Chinese scientists traced the virus through the intermediary of Asian palm civets to cave-dwelling horseshoe bats in Yunnan.

Coronavirus Subfamily of viruses in the family Coronaviridae

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. In cows and pigs they cause diarrhea, while in mice they cause hepatitis and encephalomyelitis. There are as yet no vaccines or antiviral drugs to prevent or treat human coronavirus infections.

<i>Severe acute respiratory syndrome–related coronavirus</i> Species of coronavirus causing SARS and COVID-19

Severe acute respiratory syndrome–related coronavirus is a species of coronavirus that infects humans, bats and certain other mammals. It is an enveloped positive-sense single-stranded RNA virus that enters its host cell by binding to the angiotensin-converting enzyme 2 (ACE2) receptor. It is a member of the genus Betacoronavirus and subgenus Sarbecovirus.

<i>Coronaviridae</i> Family of viruses in the order Nidovirales

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.

Sunda pangolin Species of pangolin found in southeast Asia

The Sunda pangolin, also known as the Malayan or Javan pangolin, is a species of pangolin.

Angiotensin-converting enzyme 2 Exopeptidase enzyme that acts on angiotensin I and II

Angiotensin-converting enzyme 2 (ACE2) is an enzyme attached to the cell membranes of cells located in the lungs, arteries, heart, kidney, and intestines. ACE2 lowers blood pressure by catalyzing the hydrolysis of angiotensin II into angiotensin (1–7). ACE2 counters the activity of the related angiotensin-converting enzyme (ACE) by reducing the amount of angiotensin-II and increasing Ang(1-7), making it a promising drug target for treating cardiovascular diseases.

Severe acute respiratory syndrome coronavirus Virus strain causing severe acute respiratory syndrome

Severe acute respiratory syndrome coronavirus is a strain of virus that causes severe acute respiratory syndrome (SARS). It is an enveloped, positive-sense, single-stranded RNA virus which infects the epithelial cells within the lungs. The virus enters the host cell by binding to angiotensin-converting enzyme 2. It infects humans, bats, and palm civets.

<i>Human coronavirus NL63</i> Species of virus

Human coronavirus NL63 (HCoV-NL63) is a species of coronavirus, specifically a Setracovirus from among the Alphacoronavirus genus. It was identified in late 2004 in a seven-month-old child with bronchiolitis in the Netherlands. The virus is an enveloped, positive-sense, single-stranded RNA virus which enters its host cell by binding to ACE2. Infection with the virus has been confirmed worldwide, and has an association with many common symptoms and diseases. Associated diseases include mild to moderate upper respiratory tract infections, severe lower respiratory tract infection, croup and bronchiolitis.

Antibody-dependent enhancement A way in which antibodies can (rarely) make an infection worse instead of better

Antibody-dependent enhancement (ADE), sometimes less precisely called immune enhancement or disease enhancement, is a phenomenon in which binding of a virus to suboptimal antibodies enhances its entry into host cells, followed by its replication. Antiviral antibodies promote viral infection of target immune cells by exploiting the phagocytic FcγR or complement pathway. After interaction with the virus the antibody binds Fc receptors (FcR) expressed on certain immune cells or some of the complement proteins. FcγR binds antibody via its fragment crystallizable region (Fc). This interaction facilitates uptake of the virus via phagocytosis of the virus-antibody complex by the immune cells. Usually the process of phagocytosis is accompanied by the virus degradation, however, if the virus is not neutralized, antibody binding might result in a virus escape and therefore, enhanced infection. Thus, phagocytosis can cause viral replication, with the subsequent death of immune cells. The virus “deceives” the process of phagocytosis of immune cells and uses the host's antibodies as a Trojan horse. ADE can be induced when the strength of antibody-antigen interaction is below the certain threshold. This phenomenon might lead to both increased virus infectivity and virulence. The viruses that can cause ADE frequently share some common features such as antigenic diversity, abilities to replicate and establish persistence in immune cells. ADE can occur during the development of a primary or secondary viral infection, as well as after vaccination with a subsequent virus challenge. It has been observed mainly with positive-strand RNA viruses. Among them are Flaviviruses such as Dengue virus, Yellow fever virus, Zika virus, Coronaviruses, including alpha- and betacoronaviruses, Orthomyxoviruses such as influenza, Retroviruses such as HIV, and Orthopneumoviruses such as RSV.

Middle East respiratory syndrome–related coronavirus species of virus

Middle East respiratory syndrome-related coronavirus (MERS-CoV), or EMC/2012 (HCoV-EMC/2012), is a species of coronavirus which infects humans, bats, and camels. The infecting virus is an enveloped, positive-sense, single-stranded RNA virus which enters its host cell by binding to the DPP4 receptor. The species is a member of the genus Betacoronavirus and subgenus Merbecovirus.

<i>Betacoronavirus</i> Genus of viruses in the subfamily Orthocoronavirinae

Betacoronavirus is one of four genera of coronaviruses. Member viruses are enveloped, positive-strand RNA viruses that infect mammals. 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 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.

Shi Zhengli is a Chinese virologist who researches SARS-like coronaviruses of bat origin. Shi directs the Center for Emerging Infectious Diseases at the Wuhan Institute of Virology (WIV), a biosafety level 4 (BSL-4) laboratory located in Jiangxia District, Wuhan. In 2017, Shi and her colleague Cui Jie discovered that the SARS coronavirus likely originated in a population of bats in a remote region of the Yunnan. She came to prominence in the popular press as "Batwoman" during the COVID-19 pandemic for her work with bat coronaviruses.

Coronavirus diseases Wikipedia list article

This article lists known coronavirus diseases caused by viruses in the coronavirus subfamily. The group of viruses 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.

Huanan Seafood Wholesale Market Market in Wuhan, Hubei, China

The Huanan Seafood Wholesale Market, also known as the Huanan Seafood Market, was a live animal and seafood market in Jianghan District, Wuhan, Hubei, China. The market gained media attention after being identified as a possible point of origin of COVID-19 and the resulting pandemic. The World Health Organization was notified on 31 December 2019 about an outbreak of pneumonia in Wuhan. Of the initial 41 people hospitalized with pneumonia who were officially identified as having laboratory-confirmed SARS-CoV-2 infection by 2 January 2020, two-thirds were exposed to the market. The market was closed on 1 January 2020 for sanitary procedures and disinfection. Thirty-three out of 585 environmental samples obtained from the market indicated evidence of coronavirus disease 2019 (COVID-19), according to the Chinese Center for Disease Control and Prevention.

The Wuhan Institute of Virology, Chinese Academy of Sciences is a research institute on virology administered by the Chinese Academy of Sciences (CAS). Located in Jiangxia District, Wuhan, Hubei, it opened mainland China's first biosafety level 4 (BSL–4) laboratory. The institute has strong ties to the Galveston National Laboratory in the United States, the Centre International de Recherche en Infectiologie in France and the National Microbiology Laboratory in Canada.

Coronavirus disease 2019 Disease caused by severe acute respiratory syndrome coronavirus 2

Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first case was identified in Wuhan, China in December 2019.

Susan R. Weiss is an American microbiologist who is a Professor of Microbiology at the Perelman School of Medicine at the University of Pennsylvania. Her research considers the biology of coronaviruses, including SARS, MERS and SARS-CoV-2. As of March 2020, Weiss serves as Co-Director of the University of Pennsylvania Coronavirus Research Center.

Karen Louise Mossman is a Canadian virologist who is a professor of Pathology and Molecular Medicine at McMaster University. Mossman looks to understand how viruses get around the defence mechanisms of cells. She was part of a team of Canadian researchers who first isolated SARS-CoV-2.

History of coronavirus

The history of coronaviruses is a reflection of the discovery of the diseases caused by coronaviruses and identification of the viruses. It starts with the first report of a new type of upper-respiratory tract disease among chickens in North Dakota, US, 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. The became known as infectious bronchitis virus (IBV), but later officially renamed as Avian coronavirus.

References

  1. 1 2 3 4 5 Giaimo C (1 April 2020). "The Spiky Blob Seen Around the World". The New York Times . Archived from the original on 2 April 2020. Retrieved 6 April 2020.
  2. 1 2 3 Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, et al. (March 2020). "The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2". Nature Microbiology . 5 (4): 536–544. doi:10.1038/s41564-020-0695-z. PMC   7095448 . PMID   32123347.
  3. "Coronavirus disease named Covid-19". BBC News Online . 11 February 2020. Archived from the original on 15 February 2020. Retrieved 15 February 2020.
  4. Surveillance case definitions for human infection with novel coronavirus (nCoV): interim guidance v1, January 2020 (Report). World Health Organization. January 2020. hdl: 10665/330376 . WHO/2019-nCoV/Surveillance/v2020.1.
  5. 1 2 "Healthcare Professionals: Frequently Asked Questions and Answers". United States Centers for Disease Control and Prevention (CDC). 11 February 2020. Archived from the original on 14 February 2020. Retrieved 15 February 2020.
  6. "About Novel Coronavirus (2019-nCoV)". United States Centers for Disease Control and Prevention (CDC). 11 February 2020. Archived from the original on 11 February 2020. Retrieved 25 February 2020.
  7. Harmon A (4 March 2020). "We Spoke to Six Americans with Coronavirus". The New York Times . Archived from the original on 13 March 2020. Retrieved 16 March 2020.
  8. 1 2 Wong, G.; Bi, Y. H.; Wang, Q. H.; Chen, X. W.; Zhang, Z. G.; Yao, Y. G. (2020). "Zoonotic origins of human coronavirus 2019 (HCoV-19 / SARS-CoV-2): Why is this work important?". Zoological Research. 41 (3): 213–219. doi:10.24272/j.issn.2095-8137.2020.031. PMC   7231470 . PMID   32314559.
  9. 1 2 3 4 5 6 7 Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF (17 March 2020). "Correspondence: The proximal origin of SARS-CoV-2". Nature Medicine . 26 (4): 450–452. doi:10.1038/s41591-020-0820-9. PMC   7095063 . PMID   32284615.
  10. 1 2 3 4 van Doremalen N, Bushmaker T, Morris DH, Holbrook MG, Gamble A, Williamson BN, et al. (17 March 2020). "Correspondence: Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1". The New England Journal of Medicine . 382 (16): 1564–1567. doi:10.1056/NEJMc2004973. PMC   7121658 . PMID   32182409.
  11. "hCoV-19 Database". China National GeneBank. Archived from the original on 17 June 2020. Retrieved 2 June 2020.
  12. 1 2 "Statement on the second meeting of the International Health Regulations (2005) Emergency Committee regarding the outbreak of novel coronavirus (2019-nCoV)". World Health Organization (WHO) (Press release). 30 January 2020. Archived from the original on 31 January 2020. Retrieved 30 January 2020.
  13. 1 2 "WHO Director-General's opening remarks at the media briefing on COVID-19 – 11 March 2020". World Health Organization (WHO) (Press release). 11 March 2020. Archived from the original on 11 March 2020. Retrieved 12 March 2020.
  14. Baltimore, D (1971). "Expression of animal virus genomes". Bacteriological Reviews. 35 (3): 235–241. doi: 10.1128/MMBR.35.3.235-241.1971 . PMC   378387 . PMID   4329869.
  15. 1 2 3 "CoV2020" . GISAID EpifluDB. Archived from the original on 12 January 2020. Retrieved 12 January 2020.
  16. 1 2 Chan JF, Yuan S, Kok KH, To KK, Chu H, Yang J, et al. (February 2020). "A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster". The Lancet . 395 (10223): 514–523. doi:10.1016/S0140-6736(20)30154-9. PMC   7159286 . PMID   31986261.
  17. "New coronavirus stable for hours on surfaces". National Institutes of Health (NIH). NIH.gov. 17 March 2020. Archived from the original on 23 March 2020. Retrieved 4 May 2020.
  18. 1 2 3 4 5 Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. (February 2020). "A pneumonia outbreak associated with a new coronavirus of probable bat origin". Nature . 579 (7798): 270–273. Bibcode:2020Natur.579..270Z. doi:10.1038/s41586-020-2012-7. PMC   7095418 . PMID   32015507.
  19. Perlman S (February 2020). "Another Decade, Another Coronavirus". The New England Journal of Medicine . 382 (8): 760–762. doi:10.1056/NEJMe2001126. PMC   7121143 . PMID   31978944.
  20. 1 2 Benvenuto D, Giovanetti M, Ciccozzi A, Spoto S, Angeletti S, Ciccozzi M (April 2020). "The 2019-new coronavirus epidemic: Evidence for virus evolution". Journal of Medical Virology . 92 (4): 455–459. doi:10.1002/jmv.25688. PMC   7166400 . PMID   31994738.
  21. 1 2 Novel Coronavirus (2019-nCoV): situation report, 22 (Report). World Health Organization. 11 February 2020. hdl: 10665/330991 .
  22. Shield C (7 February 2020). "Coronavirus: From bats to pangolins, how do viruses reach us?". Deutsche Welle. Archived from the original on 4 June 2020. Retrieved 13 March 2020.
  23. 1 2 3 4 Cohen J (January 2020). "Wuhan seafood market may not be source of novel virus spreading globally". Science . doi:10.1126/science.abb0611.
  24. Caspermeyer, Joseph (7 November 2020). "COVID-19 Patient Zero: Data Analysis Identifies the "Mother" of All SARS-CoV-2 Genomes". SciTechDaily . Archived from the original on 17 November 2020. Retrieved 7 November 2020.
  25. Kumar, Sudhir (29 September 2020). "An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic". bioRxiv . doi:10.1101/2020.09.24.311845. PMC   7523107 . PMID   32995781. Archived from the original on 17 November 2020. Retrieved 7 November 2020.
  26. 1 2 Sanche, S.; Lin, Y. T.; Xu, C.; Romero-Severson, E.; Hengartner, E.; Ke, R. (July 2020). "High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2". Emerging Infectious Diseases. 26 (7): 1470–1477. doi:10.3201/eid2607.200282. PMC   7323562 . PMID   32255761.
  27. "Q&A on coronaviruses (COVID-19)". World Health Organization (WHO). 11 February 2020. Archived from the original on 20 January 2020. Retrieved 24 February 2020.
  28. 1 2 "How COVID-19 Spreads". U.S. Centers for Disease Control and Prevention (CDC). 27 January 2020. Archived from the original on 28 January 2020. Retrieved 29 January 2020.
  29. 1 2 Letko M, Marzi A, Munster V (February 2020). "Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses". Nature Microbiology . 5 (4): 562–569. doi:10.1038/s41564-020-0688-y. PMC   7095430 . PMID   32094589.
  30. 1 2 Hoffman M, Kliene-Weber H, Krüger N, Herrler T, Erichsen S, Schiergens TS, et al. (16 April 2020). "SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor". Cell . 181 (2): 271–280.e8. doi:10.1016/j.cell.2020.02.052. PMC   7102627 . PMID   32142651.
  31. Wu, Katherine J. (15 April 2020). "There are more viruses than stars in the universe. Why do only some infect us? – More than a quadrillion quadrillion individual viruses exist on Earth, but most are not poised to hop into humans. Can we find the ones that are?". National Geographic Society . Archived from the original on 23 April 2020. Retrieved 18 May 2020.
  32. Huang P (22 January 2020). "How Does Wuhan Coronavirus Compare with MERS, SARS and the Common Cold?". NPR . Archived from the original on 2 February 2020. Retrieved 3 February 2020.
  33. 1 2 Fox D (24 January 2020). "What you need to know about the Wuhan coronavirus". Nature . doi:10.1038/d41586-020-00209-y.
  34. World Health Organization (30 January 2020). Novel Coronavirus (2019-nCoV): situation report, 10 (Report). World Health Organization. hdl: 10665/330775 .
  35. "World Health Organization Best Practices for the Naming of New Human Infectious Diseases" (PDF). WHO. May 2015. Archived (PDF) from the original on 12 February 2020.
  36. "Novel coronavirus named 'Covid-19': WHO". TODAYonline. Archived from the original on 21 March 2020. Retrieved 11 February 2020.
  37. "The coronavirus spreads racism against—and among—ethnic Chinese". The Economist . 17 February 2020. Archived from the original on 17 February 2020. Retrieved 17 February 2020.
  38. Hui M (18 March 2020). "Why won't the WHO call the coronavirus by its name, SARS-CoV-2?". Quartz . Archived from the original on 25 March 2020. Retrieved 26 March 2020.
  39. "Naming the coronavirus disease (COVID-2019) and the virus that causes it". World Health Organization. Archived from the original on 28 February 2020. Retrieved 24 February 2020. From a risk communications perspective, using the name SARS can have unintended consequences in terms of creating unnecessary fear for some populations. ... For that reason and others, WHO has begun referring to the virus as "the virus responsible for COVID-19" or "the COVID-19 virus" when communicating with the public. Neither of these designations are [sic] intended as replacements for the official name of the virus as agreed by the ICTV.
  40. Gstalter, Morgan (19 March 2020). "WHO official warns against calling it 'Chinese virus', says 'there is no blame in this'". The Hill . Archived from the original on 18 April 2020. Retrieved 21 March 2020.
  41. Shinkman, Paul (17 March 2020). "Trump Fires Back at Complaints He's Stigmatizing China Over Coronavirus". US News . Archived from the original on 29 March 2020. Retrieved 21 March 2020.
  42. Will Steakin (20 June 2020). "Trump heads to Tulsa for return rally amid pandemic, despite mounting warnings from health experts". Archived from the original on 20 June 2020. Retrieved 20 June 2020.
  43. Li J, You Z, Wang Q, Zhou Z, Qiu Y, Luo R, et al. (March 2020). "The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future". Microbes and Infection. 22 (2): 80–85. doi:10.1016/j.micinf.2020.02.002. PMC   7079563 . PMID   32087334. Archived from the original on 14 April 2020. Retrieved 19 April 2020.
  44. Kessler, Glenn (17 April 2020). "Trump's false claim that the WHO said the coronavirus was 'not communicable'". The Washington Post. Archived from the original on 17 April 2020. Retrieved 17 April 2020.
  45. Kuo, Lily (21 January 2020). "China confirms human-to-human transmission of coronavirus". The Guardian . Archived from the original on 22 March 2020. Retrieved 18 April 2020.
  46. Edwards E (25 January 2020). "How does coronavirus spread?". NBC News. Archived from the original on 28 January 2020. Retrieved 13 March 2020.
  47. Anfinrud P, Stadnytskyi V, Bax CE, Bax A (May 2020). "Visualizing Speech-Generated Oral Fluid Droplets with Laser Light Scattering". The New England Journal of Medicine. 382 (21): 2061–2063. doi:10.1056/NEJMc2007800. PMC   7179962 . PMID   32294341.
  48. Stadnytskyi V, Bax CE, Bax A, Anfinrud P (June 2020). "The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission". Proceedings of the National Academy of Sciences of the United States of America. 117 (22): 11875–11877. doi:10.1073/pnas.2006874117. PMC   7275719 . PMID   32404416.
  49. Mandavilli, Apoorva]] (4 July 2020). "239 Experts With One Big Claim: The Coronavirus Is Airborne – The W.H.O. has resisted mounting evidence that viral particles floating indoors are infectious, some scientists say. The agency maintains the research is still inconclusive". The New York Times . Archived from the original on 17 November 2020. Retrieved 5 July 2020.
  50. Zeynep Tufekci (30 July 2020). "We Need to Talk About Ventilation". The Atlantic. Archived from the original on 17 November 2020. Retrieved 8 September 2020.
  51. Lewis, Dyani (July 2020). "Mounting evidence suggests coronavirus is airborne — but health advice has not caught up". Nature. 583 (7817): 510–513. Bibcode:2020Natur.583..510L. doi: 10.1038/d41586-020-02058-1 . PMID   32647382. S2CID   220470431. Archived from the original on 14 September 2020. Retrieved 9 October 2020.
  52. "Getting your workplace ready for COVID-19" (PDF). World Health Organization. 27 February 2020. Archived (PDF) from the original on 2 March 2020. Retrieved 3 March 2020.
  53. Yong E (20 March 2020). "Why the Coronavirus Has Been So Successful". The Atlantic. Archived from the original on 20 March 2020. Retrieved 20 March 2020.
  54. Gibbens S (18 March 2020). "Why soap is preferable to bleach in the fight against coronavirus". National Geographic . Archived from the original on 2 April 2020. Retrieved 2 April 2020.
  55. Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H, et al. (March 2020). "First Case of 2019 Novel Coronavirus in the United States". The New England Journal of Medicine . 382 (10): 929–936. doi:10.1056/NEJMoa2001191. PMC   7092802 . PMID   32004427.
  56. Li D, Jin M, Bao P, Zhao W, Zhang S (7 May 2020). "Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease 2019". JAMA Network Open. 3 (5): e208292. doi:10.1001/jamanetworkopen.2020.8292. PMC   7206502 . PMID   32379329.
  57. Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Müller MA, et al. (April 2020). "Virological assessment of hospitalized patients with COVID-2019". Nature. 581 (7809): 465–469. Bibcode:2020Natur.581..465W. doi: 10.1038/s41586-020-2196-x . PMID   32235945.
  58. Kupferschmidt K (February 2020). "Study claiming new coronavirus can be transmitted by people without symptoms was flawed". Science . doi:10.1126/science.abb1524.
  59. To KK, Tsang OT, Leung W, Tam AR, Wu T, Lung DC, et al. (March 2020). "Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study". The Lancet Infectious Diseases. 20 (5): 565–574. doi:10.1016/S1473-3099(20)30196-1. PMC   7158907 . PMID   32213337. Archived from the original on 17 April 2020. Retrieved 21 April 2020.
  60. World Health Organization (1 February 2020). Novel Coronavirus (2019-nCoV): situation report, 12 (Report). World Health Organization. hdl: 10665/330777 .
  61. Li R, Pei S, Chen B, Song Y, Zhang T, Yang W, et al. (16 March 2020). "Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2)". Science . 368 (6490): 489–493. Bibcode:2020Sci...368..489L. doi:10.1126/science.abb3221. PMC   7164387 . PMID   32179701.
  62. Daily Telegraph , Thursday 28 May 2020, page 2 column 1, which refers to the medical journal Thorax; Thorax May 2020 article COVID-19: in the footsteps of Ernest Shackleton Archived 30 May 2020 at the Wayback Machine
  63. He X, Lau EH, Wu P, Deng X, Wang J, Hao X, et al. (15 April 2020). "Temporal dynamics in viral shedding and transmissibility of COVID-19". Nature Medicine. 26 (5): 672–675. doi: 10.1038/s41591-020-0869-5 . PMID   32296168. Archived from the original on 19 April 2020. Retrieved 21 April 2020.
  64. 1 2 Hou YJ, Okuda K, Edwards CE, Martinez DR, Asakura T, Dinnon KH, et al. (July 2020). "SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract". Cell. 182 (2): 429–446.e14. doi: 10.1016/j.cell.2020.05.042 . PMC   7250779 . PMID   32526206.
  65. "Questions and Answers on the COVID-19: OIE – World Organisation for Animal Health". www.oie.int. Archived from the original on 31 March 2020. Retrieved 16 April 2020.
  66. Goldstein J (6 April 2020). "Bronx Zoo Tiger Is Sick with the Coronavirus". The New York Times . Archived from the original on 9 April 2020. Retrieved 10 April 2020.
  67. "USDA Statement on the Confirmation of COVID-19 in a Tiger in New York". United States Department of Agriculture . 5 April 2020. Archived from the original on 15 April 2020. Retrieved 16 April 2020.
  68. "If You Have Animals—Coronavirus Disease 2019 (COVID-19)". Centers for Disease Control and Prevention (CDC). 13 April 2020. Archived from the original on 1 April 2020. Retrieved 16 April 2020.
  69. 1 2 Ledford, Heidi (4 September 2020). "Coronavirus reinfections: three questions scientists are asking". Nature. 585 (7824): 168–169. doi: 10.1038/d41586-020-02506-y . PMID   32887957. S2CID   221501940. Archived from the original on 17 November 2020. Retrieved 9 October 2020.
  70. 1 2 To, Kelvin Kai-Wang; Hung, Ivan Fan-Ngai; Ip, Jonathan Daniel; Chu, Allen Wing-Ho; Chan, Wan-Mui; Tam, Anthony Raymond; et al. (25 August 2020). "Coronavirus Disease 2019 (COVID-19) Re-infection by a Phylogenetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2 Strain Confirmed by Whole Genome Sequencing". Clinical Infectious Diseases: ciaa1275. doi:10.1093/cid/ciaa1275. PMC   7499500 . PMID   32840608. S2CID   221308584.
  71. 1 2 Tillett, Richard L; Sevinsky, Joel R; Hartley, Paul D; Kerwin, Heather; Crawford, Natalie; Gorzalski, Andrew; et al. (October 2020). "Genomic evidence for reinfection with SARS-CoV-2: a case study". The Lancet Infectious Diseases: S1473309920307647. doi: 10.1016/S1473-3099(20)30764-7 . PMC   7550103 . PMID   33058797.
  72. Eschner K (28 January 2020). "We're still not sure where the Wuhan coronavirus really came from". Popular Science . Archived from the original on 30 January 2020. Retrieved 30 January 2020.
  73. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. (15 February 2020). "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China". The Lancet . 395 (10223): 497–506. doi:10.1016/S0140-6736(20)30183-5. PMC   7159299 . PMID   31986264. Archived from the original on 31 January 2020. Retrieved 26 March 2020.
  74. 1 2 Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, et al. (15 February 2020). "Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study". The Lancet . 395 (10223): 507–513. doi:10.1016/S0140-6736(20)30211-7. PMC   7135076 . PMID   32007143. Archived from the original on 31 January 2020. Retrieved 9 March 2020.
  75. 1 2 Cyranoski D (26 February 2020). "Mystery deepens over animal source of coronavirus". Nature . 579 (7797): 18–19. Bibcode:2020Natur.579...18C. doi: 10.1038/d41586-020-00548-w . PMID   32127703.
  76. Yu WB, Tang GD, Zhang L, Corlett RT (21 February 2020). "Decoding evolution and transmissions of novel pneumonia coronavirus using the whole genomic data". ChinaXiv. doi:10.12074/202002.00033 (inactive 11 November 2020). Archived from the original on 23 February 2020. Retrieved 25 February 2020.CS1 maint: DOI inactive as of November 2020 (link)
  77. Forster P, Forster L, Renfrew C, Forster M (8 April 2020). "Phylogenetic network analysis of SARS-CoV-2 genomes" (PDF). PNAS. 117 (17): 9241–9243. doi:10.1073/pnas.2004999117. PMC   7196762 . PMID   32269081. Archived (PDF) from the original on 16 April 2020. Retrieved 17 April 2020.
  78. "COVID-19: genetic network analysis provides 'snapshot' of pandemic origins". Cambridge University. 9 April 2020. Archived from the original on 16 April 2020. Retrieved 17 April 2020.
  79. "Bat SARS-like coronavirus isolate bat-SL-CoVZC45, complete genome". National Center for Biotechnology Information (NCBI). 15 February 2020. Archived from the original on 4 June 2020. Retrieved 15 February 2020.
  80. "Bat SARS-like coronavirus isolate bat-SL-CoVZXC21, complete genome". National Center for Biotechnology Information (NCBI). 15 February 2020. Archived from the original on 4 June 2020. Retrieved 15 February 2020.
  81. "Bat coronavirus isolate RaTG13, complete genome". National Center for Biotechnology Information (NCBI). 10 February 2020. Archived from the original on 15 May 2020. Retrieved 5 March 2020.
  82. Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) (PDF) (Report). World Health Organization (WHO). 24 February 2020. Archived (PDF) from the original on 29 February 2020. Retrieved 5 March 2020.
  83. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. (February 2020). "Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding". The Lancet . 395 (10224): 565–574. doi:10.1016/S0140-6736(20)30251-8. PMC   7159086 . PMID   32007145.
  84. Wu D, Wu T, Liu Q, Yang Z (12 March 2020). "The SARS-CoV-2 outbreak: what we know". International Journal of Infectious Diseases. 94: 44–48. doi:10.1016/j.ijid.2020.03.004. ISSN   1201-9712. PMC   7102543 . PMID   32171952. Archived from the original on 9 April 2020. Retrieved 16 April 2020.
  85. Paraskevis D, Kostaki EG, Magiorkinis G, Panayiotakopoulos G, Sourvinos G, Tsiodras S (April 2020). "Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event". Infection, Genetics and Evolution . 79: 104212. doi:10.1016/j.meegid.2020.104212. PMC   7106301 . PMID   32004758. Archived from the original on 17 November 2020. Retrieved 9 April 2020.
  86. 1 2 Zhang T, Wu Q, Zhang Z (19 March 2020). "Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak". Current Biology . 30 (7): 1346–1351.e2. doi:10.1016/j.cub.2020.03.022. PMC   7156161 . PMID   32197085.
  87. 1 2 Beeching NJ, Fletcher TE, Fowler R (22 May 2020). "BMJ Best Practice: Coronavirus Disease 2019 (COVID-19)" (PDF). BMJ . Archived (PDF) from the original on 13 June 2020. Retrieved 25 May 2020.
  88. Ortiz-Prado E, Simbaña-Rivera K, Gómez- Barreno L, Rubio-Neira M, Guaman LP, Kyriakidis NC, et al. (September 2020). "Clinical, molecular, and epidemiological characterization of the SARS-CoV-2 virus and the Coronavirus Disease 2019 (COVID-19), a comprehensive literature review". Diagnostic Microbiology and Infectious Disease. 98 (1): 115094. doi:10.1016/j.diagmicrobio.2020.115094. ISSN   0732-8893. PMC   7260568 . PMID   32623267.
  89. Liu P, Chen W, Chen JP (October 2019). "Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)". Viruses . 11 (11): 979. doi:10.3390/v11110979. PMC   6893680 . PMID   31652964.
  90. Cyranoski D (7 February 2020). "Did pangolins spread the China coronavirus to people?". Nature . doi:10.1038/d41586-020-00364-2. S2CID   212825975. Archived from the original on 7 February 2020. Retrieved 12 February 2020.
  91. Xiao K, Zhai J, Feng Y (February 2020). "Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins" (PDF). bioRxiv (preprint). doi:10.1101/2020.02.17.951335. S2CID   213920763. Archived (PDF) from the original on 22 April 2020. Retrieved 5 May 2020.
  92. Wong MC, Cregeen SJ, Ajami NJ, Petrosino JF (February 2020). "Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019" (PDF). bioRxiv (preprint). doi:10.1101/2020.02.07.939207. PMC   7217297 . PMID   32511310. Archived (PDF) from the original on 22 April 2020. Retrieved 5 May 2020.
  93. Stawicki SP, Jeanmonod R, Miller AC, Paladino L, Gaieski DF, Yaffee AQ, et al. (22 May 2020). "The 2019–2020 Novel Coronavirus (Severe Acute Respiratory Syndrome Coronavirus 2) Pandemic: A Joint American College of Academic International Medicine-World Academic Council of Emergency Medicine Multidisciplinary COVID-19 Working Group Consensus Paper". Journal of Global Infectious Diseases. 12 (2): 47–93. doi:10.4103/jgid.jgid_86_20. ISSN   0974-777X. PMC   7384689 . PMID   32773996.
  94. Timmer, John (1 June 2020). "SARS-CoV-2 looks like a hybrid of viruses from two different species". Ars Technica. Archived from the original on 5 June 2020. Retrieved 6 June 2020.
  95. 1 2 Li X, Giorgi EE, Marichannegowda MH, Foley B, Xiao C, Kong X, et al. (July 2020). "Emergence of SARS-CoV-2 through recombination and strong purifying selection". Science Advances. 6 (27): eabb9153. Bibcode:2020SciA....6B9153L. doi:10.1126/sciadv.abb9153. ISSN   2375-2548. PMC   7458444 . PMID   32937441.
  96. Rehman Su, Shafique L, Ihsan A, Liu Q (23 March 2020). "Evolutionary Trajectory for the Emergence of Novel Coronavirus SARS-CoV-2". Pathogens. 9 (3): 240. doi:10.3390/pathogens9030240. ISSN   2076-0817. PMC   7157669 . PMID   32210130.
  97. Yan, Renhong; Zhang, Yuanyuan; Li, Yaning; Xia, Lu; Guo, Yingying; Zhou, Qiang (27 March 2020). "Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2". Science. 367 (6485): 1444–1448. Bibcode:2020Sci...367.1444Y. doi:10.1126/science.abb2762. ISSN   1095-9203. PMC   7164635 . PMID   32132184.
  98. 1 2 Ho, Mitchell (30 April 2020). "Perspectives on the development of neutralizing antibodies against SARS-CoV-2". Antibody Therapeutics. 3 (2): 109–114. doi:10.1093/abt/tbaa009. PMC   7291920 . PMID   32566896. S2CID   219476100. Archived from the original on 14 June 2020. Retrieved 14 June 2020.
  99. Kelly G (1 January 2015). "Pangolins: 13 facts about the world's most hunted animal". The Telegraph. Archived from the original on 24 December 2019. Retrieved 9 March 2020.
  100. Gorman J (27 February 2020). "China's Ban on Wildlife Trade a Big Step, but Has Loopholes, Conservationists Say". The New York Times . Archived from the original on 13 March 2020. Retrieved 23 March 2020.
  101. Carrington, Damian (27 April 2020). "Halt destruction of nature or suffer even worse pandemics, say world's top scientists". The Guardian. ISSN   0261-3077. Archived from the original on 15 May 2020. Retrieved 31 May 2020.
  102. Pontes, Nadia (29 April 2020). "How deforestation can lead to more infectious diseases". DW.COM. Archived from the original on 5 May 2020. Retrieved 31 May 2020.
  103. Cheng, Vincent C. C.; Lau, Susanna K. P.; Woo, Patrick C. Y.; Yuen, Kwok Yung (October 2007). "Severe Acute Respiratory Syndrome Coronavirus as an Agent of Emerging and Reemerging Infection". Clinical Microbiology Reviews. 20 (4): 660–694. doi:10.1128/CMR.00023-07. ISSN   0893-8512. PMC   2176051 . PMID   17934078.
  104. "Escaping the 'Era of Pandemics': experts warn worse crises to come; offer options to reduce risk". EurekAlert!. 29 October 2020. Archived from the original on 17 November 2020. Retrieved 30 October 2020.
  105. "Origin of SARS-CoV-2". www.who.int. Archived from the original on 17 November 2020. Retrieved 14 October 2020.
  106. Segreto, Rossana; Deigin, Yuri. "The genetic structure of SARS-CoV-2 does not rule out a laboratory origin". BioEssays. n/a (n/a): 2000240. doi: 10.1002/bies.202000240 .
  107. "The COVID-19 coronavirus epidemic has a natural origin, scientists say—Scripps Research's analysis of public genome sequence data from SARS‑CoV‑2 and related viruses found no evidence that the virus was made in a laboratory or otherwise engineered". EurekAlert! . Scripps Research Institute. 17 March 2020. Archived from the original on 3 April 2020. Retrieved 15 April 2020.
  108. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. (February 2020). "A Novel Coronavirus from Patients with Pneumonia in China, 2019". The New England Journal of Medicine . 382 (8): 727–733. doi:10.1056/NEJMoa2001017. PMC   7092803 . PMID   31978945.
  109. "Phylogeny of SARS-like betacoronaviruses". nextstrain. Archived from the original on 20 January 2020. Retrieved 18 January 2020.
  110. Wong AC, Li X, Lau SK, Woo PC (February 2019). "Global Epidemiology of Bat Coronaviruses". Viruses . 11 (2): 174. doi:10.3390/v11020174. PMC   6409556 . PMID   30791586.
  111. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D (9 March 2020). "Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein". Cell . 181 (2): 281–292.e6. doi:10.1016/j.cell.2020.02.058. PMC   7102599 . PMID   32155444.
  112. Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG, Decroly E (February 2020). "The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade". Antiviral Research . 176: 104742. doi:10.1016/j.antiviral.2020.104742. PMC   7114094 . PMID   32057769.
  113. "Initial genome release of novel coronavirus". Virological. 11 January 2020. Archived from the original on 12 January 2020. Retrieved 12 January 2020.
  114. 1 2 Bedford T, Neher R, Hadfield N, Hodcroft E, Ilcisin M, Müller N. "Genomic analysis of nCoV spread: Situation report 2020-01-30". nextstrain.org. Archived from the original on 15 March 2020. Retrieved 18 March 2020.
  115. "Genomic epidemiology of novel coronavirus - Global subsampling". Nextstrain. Archived from the original on 20 April 2020. Retrieved 7 May 2020.
  116. "New, more infectious strain of COVID-19 now dominates global cases of virus: study". medicalxpress.com. Archived from the original on 17 November 2020. Retrieved 16 August 2020.
  117. Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. (2 July 2020). "Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus". Cell. 182 (4): 812–827.e19. doi: 10.1016/j.cell.2020.06.043 . ISSN   0092-8674. PMC   7332439 . PMID   32697968.
  118. Dockrill, Peter (11 November 2020). "Scientists Just Found a Mysteriously Hidden 'Gene Within a Gene' in SARS-CoV-2". ScienceAlert . Archived from the original on 17 November 2020. Retrieved 11 November 2020.
  119. Nelson, Chase W; et al. (1 October 2020). "Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic". eLife . 9. doi:10.7554/eLife.59633. PMC   7655111 . PMID   33001029. Archived from the original on 17 November 2020. Retrieved 11 November 2020.
  120. 1 2 3 Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, et al. (February 2020). "Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods". Acta Pharmaceutica Sinica B. 10 (5): 766–788. doi:10.1016/j.apsb.2020.02.008. PMC   7102550 . PMID   32292689.
  121. 1 2 Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, et al. (February 2020). "Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation". Science . 367 (6483): 1260–1263. Bibcode:2020Sci...367.1260W. doi:10.1126/science.abb2507. PMC   7164637 . PMID   32075877.
  122. Mandelbaum RF (19 February 2020). "Scientists Create Atomic-Level Image of the New Coronavirus's Potential Achilles Heel". Gizmodo . Archived from the original on 8 March 2020. Retrieved 13 March 2020.
  123. 1 2 3 Aronson JK (25 March 2020). "Coronaviruses – a general introduction". Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford. Archived from the original on 22 May 2020. Retrieved 24 May 2020.
  124. Xu X, Chen P, Wang J, Feng J, Zhou H, Li X, et al. (March 2020). "Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission". Science China Life Sciences . 63 (3): 457–460. doi:10.1007/s11427-020-1637-5. PMC   7089049 . PMID   32009228.
  125. Letko M, Munster V (January 2020). "Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV" (PDF). bioRxiv (preprint). doi:10.1101/2020.01.22.915660. PMC   7217099 . PMID   32511294. Archived (PDF) from the original on 22 April 2020. Retrieved 5 May 2020.
  126. El Sahly HM. "Genomic Characterization of the 2019 Novel Coronavirus". The New England Journal of Medicine . Archived from the original on 17 February 2020. Retrieved 9 February 2020.
  127. "Novel coronavirus structure reveals targets for vaccines and treatments". National Institutes of Health (NIH). 2 March 2020. Archived from the original on 1 April 2020. Retrieved 3 April 2020.
  128. Wang K, Chen W, Zhou YS, Lian JQ, Zhang Z, Du P, et al. (14 March 2020). "SARS-CoV-2 invades host cells via a novel route: CD147-spike protein" (PDF). bioRxiv (preprint). doi:10.1101/2020.03.14.988345. S2CID   214725955. Archived (PDF) from the original on 11 May 2020. Retrieved 5 May 2020.
  129. "Anatomy of a Killer: Understanding SARS-CoV-2 and the drugs that might lessen its power". The Economist . 12 March 2020. Archived from the original on 14 March 2020. Retrieved 14 March 2020.
  130. Oberholzer M, Febbo P (19 February 2020). "What We Know Today about Coronavirus SARS-CoV-2 and Where Do We Go from Here". Genetic Engineering and Biotechnology News . Archived from the original on 14 March 2020. Retrieved 13 March 2020.
  131. Ma J (13 March 2020). "Coronavirus: China's first confirmed Covid-19 case traced back to November 17". South China Morning Post . Archived from the original on 13 March 2020. Retrieved 16 March 2020.
  132. 1 2 3 4 5 6 "COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU)". ArcGIS . Johns Hopkins University . Retrieved 29 November 2020.
  133. Coronavirus disease 2019 (COVID-19) Situation Report – 69 (Report). World Health Organization. 29 March 2020. hdl: 10665/331615 .
  134. Wee SL, McNeil Jr. DG, Hernández JC (30 January 2020). "W.H.O. Declares Global Emergency as Wuhan Coronavirus Spreads". The New York Times . Archived from the original on 30 January 2020. Retrieved 30 January 2020.
  135. McKay B, Calfas J, Ansari T (11 March 2020). "Coronavirus Declared Pandemic by World Health Organization". The Wall Street Journal . Archived from the original on 11 March 2020. Retrieved 12 March 2020.
  136. Rocklöv J, Sjödin H, Wilder-Smith A (February 2020). "COVID-19 outbreak on the Diamond Princess cruise ship: estimating the epidemic potential and effectiveness of public health countermeasures". Journal of Travel Medicine. 27 (3). doi:10.1093/jtm/taaa030. PMC   7107563 . PMID   32109273.
  137. Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, et al. (24 June 2020). "Coronavirus Disease 2019–COVID-19". Clinical Microbiology Reviews. 33 (4). doi:10.1128/CMR.00028-20. ISSN   0893-8512. PMC   7405836 . PMID   32580969.
  138. Branswell H (30 January 2020). "Limited data on coronavirus may be skewing assumptions about severity". STAT. Archived from the original on 1 February 2020. Retrieved 13 March 2020.
  139. Wu JT, Leung K, Leung GM (February 2020). "Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study". The Lancet . 395 (10225): 689–697. doi:10.1016/S0140-6736(20)30260-9. PMC   7159271 . PMID   32014114.
  140. Boseley S, McCurry J (30 January 2020). "Coronavirus deaths leap in China as countries struggle to evacuate citizens". The Guardian . Archived from the original on 6 February 2020. Retrieved 10 March 2020.
  141. Paulinus A (25 February 2020). "Coronavirus: China to repay Africa in safeguarding public health". The Sun . Archived from the original on 9 March 2020. Retrieved 10 March 2020.

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