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121-458: Severe acute respiratory syndrome coronavirus 2 ( SARS‑CoV‑2 ) is a strain of coronavirus that causes COVID-19 , the respiratory illness responsible for the COVID-19 pandemic . The virus previously had the provisional name 2019 novel coronavirus ( 2019-nCoV ), and has also been called human coronavirus 2019 ( HCoV-19 or hCoV-19 ). First identified in the city of Wuhan , Hubei, China,

242-620: A cloud seed . More and more water accumulates on the seed until a visible cloud is formed. In the case of ship tracks, the cloud seeds are stretched over a long narrow path where the wind has blown the ship's exhaust, so the resulting clouds resemble long strings over the ocean. The warming caused by human-produced greenhouse gases has been somewhat offset by the cooling effect of human-produced aerosols. In 2020, regulations on fuel significantly cut sulfur dioxide emissions from international shipping by approximately 80%, leading to an unexpected global geoengineering termination shock. Aerosols in

363-467: A common ancestor ", implying that the first human infection occurred in November or December 2019. Examination of the topology of the phylogenetic tree at the start of the pandemic also found high similarities between human isolates. As of 21 August 2021, 3,422 SARS‑CoV‑2 genomes, belonging to 19 strains, sampled on all continents except Antarctica were publicly available. On 11 February 2020,

484-439: A cross-species jump . Later in the 1890s, human coronavirus OC43 diverged from bovine coronavirus after another cross-species spillover event. It is speculated that the flu pandemic of 1890 may have been caused by this spillover event, and not by the influenza virus , because of the related timing, neurological symptoms, and unknown causative agent of the pandemic. Besides causing respiratory infections, human coronavirus OC43

605-409: A histogram with the area of each bar representing the proportion of particles in that size bin, usually normalised by dividing the number of particles in a bin by the width of the interval so that the area of each bar is proportionate to the number of particles in the size range that it represents. If the width of the bins tends to zero , the frequency function is: where Therefore, the area under

726-687: A mortality rate of approximately 34.5%. In December 2019, a pneumonia outbreak was reported in Wuhan , China. On 31 December 2019, the outbreak was traced to a novel strain of coronavirus, which was given the interim name 2019-nCoV by the World Health Organization, later renamed SARS-CoV-2 by the International Committee on Taxonomy of Viruses . As of 10 March 2023, there were at least 6,881,955 confirmed deaths and more than 676,609,955 confirmed cases in

847-435: A positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry. The genome size of coronaviruses ranges from approximately 26 to 32 kilobases , one of the largest among RNA viruses. They have characteristic club-shaped spikes that project from their surface, which in electron micrographs create an image reminiscent of the stellar corona , from which their name derives. The name "coronavirus"

968-495: A proofreading function which the RNA-dependent RNA polymerase lacks. Replication – One of the main functions of the complex is to replicate the viral genome. RdRp directly mediates the synthesis of negative-sense genomic RNA from the positive-sense genomic RNA. This is followed by the replication of positive-sense genomic RNA from the negative-sense genomic RNA. Transcription – The other important function of

1089-600: A slippery sequence (UUUAAAC) and a downstream RNA pseudoknot at the end of open reading frame ORF1a. The ribosomal frameshift allows for the continuous translation of ORF1a followed by ORF1b. The polyproteins have their own proteases , PLpro (nsp3) and 3CLpro (nsp5), which cleave the polyproteins at different specific sites. The cleavage of polyprotein pp1ab yields 16 nonstructural proteins (nsp1 to nsp16). Product proteins include various replication proteins such as RNA-dependent RNA polymerase ( nsp12 ), RNA helicase (nsp13), and exoribonuclease (nsp14). A number of

1210-411: A 5′ methylated cap and a 3′ polyadenylated tail, which allows it to act like a messenger RNA and be directly translated by the host cell's ribosomes . The host ribosomes translate the initial overlapping open reading frames ORF1a and ORF1b of the virus genome into two large overlapping polyproteins, pp1a and pp1ab. The larger polyprotein pp1ab is a result of a -1 ribosomal frameshift caused by

1331-632: A common ancestor with a bat coronavirus (ARCoV.2) between 1190 and 1449 CE. The human coronavirus 229E shared a common ancestor with a bat coronavirus (GhanaGrp1 Bt CoV) between 1686 and 1800 CE. More recently, alpaca coronavirus and human coronavirus 229E diverged sometime before 1960. MERS-CoV emerged in humans from bats through the intermediate host of camels. MERS-CoV, although related to several bat coronavirus species, appears to have diverged from these several centuries ago. The most closely related bat coronavirus and SARS-CoV diverged in 1986. The ancestors of SARS-CoV first infected leaf-nose bats of

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1452-589: A coronavirus infection in animals occurred in the late 1920s, when an acute respiratory infection of domesticated chickens emerged in North America. Arthur Schalk and M.C. Hawn in 1931 made the first detailed report which described a new respiratory infection of chickens in North Dakota . The infection of new-born chicks was characterized by gasping and listlessness with high mortality rates of 40–90%. Leland David Bushnell and Carl Alfred Brandly isolated

1573-515: A coronavirus is 5′-leader-UTR -replicase (ORF1ab)-spike (S)-envelope (E)-membrane (M)-nucleocapsid (N)- 3′UTR -poly (A) tail. The open reading frames 1a and 1b, which occupy the first two-thirds of the genome, encode the replicase polyprotein (pp1ab). The replicase polyprotein self cleaves to form 16 nonstructural proteins (nsp1–nsp16). The later reading frames encode the four major structural proteins: spike , envelope , membrane , and nucleocapsid . Interspersed between these reading frames are

1694-410: A distinct pair of electron-dense shells (shells that are relatively opaque to the electron beam used to scan the virus particle). The M protein is the main structural protein of the envelope that provides the overall shape and is a type III membrane protein . It consists of 218 to 263 amino acid residues and forms a layer 7.8 nm thick. It has three domains, a short N-terminal ectodomain ,

1815-677: A global alert soon after. The WHO update on 28 September 2012 said the virus did not seem to pass easily from person to person. However, on 12 May 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 were reported by the Ministry of Health in Tunisia . Two confirmed cases involved people who seemed to have caught

1936-408: A large number of animal coronaviruses identified since the 1960s. Coronaviruses are large, roughly spherical particles with unique surface projections. Their size is highly variable with average diameters of 80 to 120  nm . Extreme sizes are known from 50 to 200 nm in diameter. The total molecular mass is on average 40,000  kDa . They are enclosed in an envelope embedded with

2057-633: A membrane protein that regulates the renin–angiotensin system. 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". In January 2020, the World Health Organization (WHO) recommended "2019 novel coronavirus" (2019-nCoV) as the provisional name for the virus. This was in accordance with WHO's 2015 guidance against using geographical locations, animal species, or groups of people in disease and virus names. On 11 February 2020,

2178-407: A mink euthanasia campaign rendering it virtually extinct. Each SARS-CoV-2 virion is 60–140 nanometres (2.4 × 10–5.5 × 10 in) in diameter; its mass within the global human populace has been estimated as being between 0.1 and 10 kilograms. Like other coronaviruses, SARS-CoV-2 has four structural proteins, known as the S ( spike ), E ( envelope ), M ( membrane ), and N ( nucleocapsid ) proteins;

2299-399: A number of protein molecules. The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell. The viral envelope is made up of a lipid bilayer in which the membrane (M), envelope (E) and spike (S) structural proteins are anchored. The molar ratio of E:S:M in the lipid bilayer is approximately 1:20:300. The E and M protein are

2420-416: 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. Some institutions have advised that those infected with SARS‑CoV‑2 restrict their contact with animals. On 1   February 2020, the World Health Organization (WHO) indicated that "transmission from asymptomatic cases

2541-489: A seasonal incidence occurring in the winter months in temperate climates . There is no preponderance in any season in tropical climates . In 2003, following the outbreak of severe acute respiratory syndrome (SARS) which had begun the prior year in Asia, and secondary cases elsewhere in the world, the World Health Organization (WHO) issued a press release stating that a novel coronavirus identified by several laboratories

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2662-419: A short carboxy terminal end and has a net negative charge due to excess of acidic over basic amino acid residues. Coronaviruses contain a positive-sense, single-stranded RNA genome. The genome size for coronaviruses ranges from 26.4 to 31.7 kilobases . The genome size is one of the largest among RNA viruses. The genome has a 5′ methylated cap and a 3′ polyadenylated tail . The genome organization for

2783-506: A significant effect on Earth's climate: volcanic, desert dust, sea-salt, that originating from biogenic sources and human-made. Volcanic aerosol forms in the stratosphere after an eruption as droplets of sulfuric acid that can prevail for up to two years, and reflect sunlight, lowering temperature. Desert dust, mineral particles blown to high altitudes, absorb heat and may be responsible for inhibiting storm cloud formation. Human-made sulfate aerosols , primarily from burning oil and coal, affect

2904-429: A significant settling speed make the mixture a suspension , but the distinction is not clear. In everyday language, aerosol often refers to a dispensing system that delivers a consumer product from a spray can . Diseases can spread by means of small droplets in the breath , sometimes called bioaerosols . Aerosol is defined as a suspension system of solid or liquid particles in a gas. An aerosol includes both

3025-558: 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; the number of genomes increased to 42 by 30 January 2020. A phylogenetic analysis of those samples showed they were "highly related with at most seven mutations relative to

3146-529: A triple-spanning transmembrane domain , and a C-terminal endodomain . The C-terminal domain forms a matrix-like lattice that adds to the extra-thickness of the envelope. Different species can have either N - or O -linked glycans in their protein amino-terminal domain. The M protein is crucial during the assembly, budding , envelope formation, and pathogenesis stages of the virus lifecycle. The E proteins are minor structural proteins and highly variable in different species. There are only about 20 copies of

3267-482: A unique pathogenesis because it causes both upper and lower respiratory tract infections . Six species of human coronaviruses are known, with one species subdivided into two different strains, making seven strains of human coronaviruses altogether. Four human coronaviruses produce symptoms that are generally mild, even though it is contended they might have been more aggressive in the past: Three human coronaviruses produce potentially severe symptoms: These cause

3388-403: A virus of Severe acute respiratory syndrome–related coronavirus . 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. Coronavirus genomes and subgenomes encode six open reading frames (ORFs). In October 2020, researchers discovered a possible overlapping gene named ORF3d , in

3509-435: Is also capable of genetic recombination when at least two viral genomes are present in the same infected cell. RNA recombination appears to be a major driving force in determining genetic variability within a coronavirus species, the capability of a coronavirus species to jump from one host to another and, infrequently, in determining the emergence of novel coronaviruses. The exact mechanism of recombination in coronaviruses

3630-594: Is also suspected of playing a role in neurological diseases . In the 1950s, the human coronavirus OC43 began to diverge into its present genotypes . Phylogenetically, mouse hepatitis virus ( Murine coronavirus ), which infects the mouse's liver and central nervous system , is related to human coronavirus OC43 and bovine coronavirus. Human coronavirus HKU1, like the aforementioned viruses, also has its origins in rodents. Coronaviruses vary significantly in risk factor. Some can kill more than 30% of those infected, such as MERS-CoV , and some are relatively harmless, such as

3751-471: Is another possible cause of infection. Preliminary research indicates that the virus may remain viable on plastic ( polypropylene ) and stainless steel ( AISI 304 ) for up to three days, but it does not survive on cardboard for more than one day or on copper for more than four hours. The virus is inactivated by soap, which destabilizes its lipid bilayer . Viral RNA has also been found in stool samples and semen from infected individuals. The degree to which

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3872-461: Is any amino acid . 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 . 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. Although such sites are a common naturally-occurring feature of other viruses within

3993-409: Is derived from Latin corona , meaning "crown" or "wreath", itself a borrowing from Greek κορώνη korṓnē , "garland, wreath". The name was coined by June Almeida and David Tyrrell who first observed and studied human coronaviruses. The word was first used in print in 1968 by an informal group of virologists in the journal Nature to designate the new family of viruses. The name refers to

4114-406: Is estimated to have existed as recently as 8000  BCE , although some models place the common ancestor as far back as 55 million years or more, implying long term coevolution with bat and avian species. The most recent common ancestor of the alphacoronavirus line has been placed at about 2400 BCE, of the betacoronavirus line at 3300 BCE, of the gammacoronavirus line at 2800 BCE, and

4235-450: Is generally by copy-choice replication, in which gene material switches from one RNA template molecule to another during replication. The SARS-CoV-2 RNA sequence is approximately 30,000 bases in length, relatively long for a coronavirus—which in turn carry the largest genomes among all RNA families. Its genome consists nearly entirely of protein-coding sequences, a trait shared with other coronaviruses. A distinguishing feature of SARS‑CoV‑2

4356-476: Is in turn composed of an S1 and S2 subunit . The homotrimeric S   protein is a class I fusion protein which mediates the receptor binding and membrane fusion between the virus and host cell. The S1 subunit forms the head of the spike and has the receptor-binding domain (RBD). The S2 subunit forms the stem which anchors the spike in the viral envelope and on protease activation enables fusion. The two subunits remain noncovalently linked as they are exposed on

4477-471: Is its incorporation of a polybasic site cleaved by furin , which appears to be an important element enhancing its virulence. 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. The furin protease recognizes the canonical peptide sequence R X[ R / K ] R ↓X where the cleavage site is indicated by a down arrow and X

4598-451: Is likely not a major driver of transmission". One meta-analysis found that 17% of infections are asymptomatic, and asymptomatic individuals were 42% less likely to transmit the virus. 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

4719-675: Is likely to have occurred in late 2019. Epidemiological studies estimate that in the period between December 2019 and September 2020 each infection resulted in an average of 2.4–3.4 new infections when no members of the community were immune and no preventive measures were taken. However, some subsequent variants have become more infectious. The virus is airborne and primarily spreads between people through close contact and via aerosols and respiratory droplets that are exhaled when talking, breathing, or otherwise exhaling, as well as those produced from coughs and sneezes. It enters human cells by binding to angiotensin-converting enzyme 2 (ACE2),

4840-503: Is the protein responsible for allowing the virus to attach to and fuse with the membrane of a host cell; specifically, its S1 subunit catalyzes attachment, the S2 subunit fusion. Coronavirus 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

4961-421: Is unclear, but likely involves template switching during genome replication. The replicated positive-sense genomic RNA becomes the genome of the progeny viruses . The mRNAs are gene transcripts of the last third of the virus genome after the initial overlapping reading frame. These mRNAs are translated by the host's ribosomes into the structural proteins and many accessory proteins. RNA translation occurs inside

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5082-511: The mass concentration ( M ), defined as the mass of particulate matter per unit volume, in units such as μg/m . Also commonly used is the number concentration ( N ), the number of particles per unit volume, in units such as number per m or number per cm . Particle size has a major influence on particle properties, and the aerosol particle radius or diameter ( d p ) is a key property used to characterise aerosols. Aerosols vary in their dispersity . A monodisperse aerosol, producible in

5203-558: The COVID-19 pandemic . The Wuhan strain has been identified as a new strain of Betacoronavirus from group 2B with approximately 70% genetic similarity to the SARS-CoV. The virus has a 96% similarity to a bat coronavirus, so it is widely suspected to originate from bats as well. Aerosols Several types of atmospheric aerosol have a significant effect on Earth's climate: volcanic, desert dust, sea-salt, that originating from biogenic sources and human-made. Volcanic aerosol forms in

5324-641: The International Committee on Taxonomy of Viruses adopted the official name "severe acute respiratory syndrome coronavirus 2" (SARS‑CoV‑2). To avoid confusion with the disease SARS , the WHO sometimes refers to SARS‑CoV‑2 as "the COVID-19 virus" in public health communications and the name HCoV-19 was included in some research articles. Referring to COVID-19 as the "Wuhan virus" has been described as dangerous by WHO officials, and as xenophobic by many journalists and academics. Human-to-human transmission of SARS‑CoV‑2

5445-403: The International Committee on Taxonomy of Viruses announced that according to existing rules that compute hierarchical relationships among coronaviruses based on five conserved sequences of nucleic acids, the differences between what was then called 2019-nCoV and the virus from the 2003 SARS outbreak were insufficient to make them separate viral species . Therefore, they identified 2019-nCoV as

5566-478: The National Institute of Health the same year was able to isolate another member of this new group of viruses using organ culture and named one of the samples OC43 (OC for organ culture). Like B814, 229E, and IBV, the novel cold virus OC43 had distinctive club-like spikes when observed with the electron microscope. The IBV-like novel cold viruses were soon shown to be also morphologically related to

5687-474: The World Health Organization designated the outbreak a public health emergency of international concern from January 30, 2020, to May 5, 2023. SARS‑CoV‑2 is a positive-sense single-stranded RNA virus that is contagious in humans. SARS‑CoV‑2 is a strain of the species Betacoronavirus pandemicum (SARSr-CoV), as is SARS-CoV-1 , the virus that caused the 2002–2004 SARS outbreak . There are animal-borne coronavirus strains more closely related to SARS-CoV-2,

5808-442: The common cold (which is also caused by other viruses, predominantly rhinoviruses ), 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 . Coronaviruses constitute the subfamily Orthocoronavirinae , in the family Coronaviridae , order Nidovirales and realm Riboviria . They are enveloped viruses with

5929-591: The common cold to more severe diseases such as Middle East respiratory syndrome (MERS, fatality rate ~34%). SARS-CoV-2 is the seventh known coronavirus to infect people, after 229E , NL63 , OC43 , HKU1 , MERS-CoV , and the original SARS-CoV . Like the SARS-related coronavirus implicated in the 2003 SARS outbreak, SARS‑CoV‑2 is a member of the subgenus Sarbecovirus ( beta-CoV lineage B). Coronaviruses undergo frequent recombination. The mechanism of recombination in unsegmented RNA viruses such as SARS-CoV-2

6050-460: The endoplasmic reticulum . The viral structural proteins S, E, and M move along the secretory pathway into the Golgi intermediate compartment . There, the M   proteins direct most protein-protein interactions required for the assembly of viruses following its binding to the nucleocapsid . Progeny viruses are then released from the host cell by exocytosis through secretory vesicles. Once released

6171-465: The index case ". The authors later published a correction that showed that shedding began earlier than first estimated, four to five days before symptoms appear. There is uncertainty about reinfection and long-term immunity. It is not known how common reinfection is, but reports have indicated that it is occurring with variable severity. The first reported case of reinfection was a 33-year-old man from Hong Kong who first tested positive on 26 March 2020,

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6292-481: 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. 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. Studies have identified

6413-522: The power function distribution , occasionally applied to atmospheric aerosols; the exponential distribution , applied to powdered materials; and for cloud droplets, the Khrgian–Mazin distribution. For low values of the Reynolds number (<1), true for most aerosol motion, Stokes' law describes the force of resistance on a solid spherical particle in a fluid. However, Stokes' law is only valid when

6534-427: The skewness associated with a long tail of larger particles. Also for a quantity that varies over a large range, as many aerosol sizes do, the width of the distribution implies negative particles sizes, which is not physically realistic. However, the normal distribution can be suitable for some aerosols, such as test aerosols, certain pollen grains and spores . A more widely chosen log-normal distribution gives

6655-514: The terminal velocity of a particle undergoing gravitational settling in still air. Neglecting buoyancy effects, we find: where The terminal velocity can also be derived for other kinds of forces. If Stokes' law holds, then the resistance to motion is directly proportional to speed. The constant of proportionality is the mechanical mobility ( B ) of a particle: A particle traveling at any reasonable initial velocity approaches its terminal velocity exponentially with an e -folding time equal to

6776-417: The virus to enter the host cell by endocytosis or direct fusion of the viral envelope with the host membrane . Coronaviruses can enter cells by either fusing to their lipid envelope with the cell membrane on the cell surface or by internalization via endocytosis. On entry into the host cell , the virus particle is uncoated , and its genome enters the cell cytoplasm . The coronavirus RNA genome has

6897-435: The 20 μm range show a particularly long persistence time in air conditioned rooms due to their "jet rider" behaviour (move with air jets, gravitationally fall out in slowly moving air); as this aerosol size is most effectively adsorbed in the human nose, the primordial infection site in COVID-19 , such aerosols may contribute to the pandemic. Aerosol particles with an effective diameter smaller than 10 μm can enter

7018-417: The E protein molecule in a coronavirus particle. They are 8.4 to 12 kDa in size and are composed of 76 to 109 amino acids. They are integral proteins (i.e. embedded in the lipid layer) and have two domains namely a transmembrane domain and an extramembrane C-terminal domain. They are almost fully α-helical, with a single α-helical transmembrane domain, and form pentameric (five-molecular) ion channels in

7139-455: The Earth's atmosphere can influence its climate, as well as human health. Volcanic eruptions release large amounts of sulphuric acid , hydrogen sulfide and hydrochloric acid into the atmosphere. These gases represent aerosols and eventually return to earth as acid rain , having a number of adverse effects on the environment and human life. When aerosols absorb pollutants, it facilitates

7260-632: The International Committee for the Nomenclature of Viruses (later renamed International Committee on Taxonomy of Viruses ) in 1971. As the number of new species increased, the genus was split into four genera, namely Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus in 2009. The common name coronavirus is used to refer to any member of the subfamily Orthocoronavirinae . As of 2020, 45 species are officially recognised. The earliest reports of

7381-492: The N protein holds the RNA genome, and the S, E, and M proteins together create the viral envelope . Coronavirus S proteins are glycoproteins and also type I membrane proteins (membranes containing a single transmembrane domain oriented on the extracellular side). They are divided into two functional parts (S1 and S2). In SARS-CoV-2, the spike protein, which has been imaged at the atomic level using cryogenic electron microscopy ,

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7502-1620: 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 . A phylogenetic tree based on whole-genome sequences of SARS-CoV-2 and related coronaviruses is: ( Bat ) Rc-o319 , 81% to SARS-CoV-2, Rhinolophus cornutus , Iwate , Japan Bat SL-ZXC21 , 88% to SARS-CoV-2, Rhinolophus pusillus , Zhoushan , Zhejiang Bat SL-ZC45 , 88% to SARS-CoV-2, Rhinolophus pusillus , Zhoushan, Zhejiang Pangolin SARSr-CoV-GX, 85.3% to SARS-CoV-2, Manis javanica , smuggled from Southeast Asia Pangolin SARSr-CoV-GD, 90.1% to SARS-CoV-2, Manis javanica , smuggled from Southeast Asia Bat RshSTT182, 92.6% to SARS-CoV-2, Rhinolophus shameli , Steung Treng , Cambodia Bat RshSTT200, 92.6% to SARS-CoV-2, Rhinolophus shameli , Steung Treng, Cambodia (Bat) RacCS203 , 91.5% to SARS-CoV-2, Rhinolophus acuminatus , Chachoengsao , Thailand (Bat) RmYN02 , 93.3% to SARS-CoV-2, Rhinolophus malayanus , Mengla , Yunnan (Bat) RpYN06 , 94.4% to SARS-CoV-2, Rhinolophus pusillus , Xishuangbanna , Yunnan (Bat) RaTG13 , 96.1% to SARS-CoV-2, Rhinolophus affinis , Mojiang , Yunnan (Bat) BANAL-52 , 96.8% to SARS-CoV-2, Rhinolophus malayanus , Vientiane , Laos SARS-CoV-2 SARS-CoV-1 , 79% to SARS-CoV-2 There are many thousands of variants of SARS-CoV-2, which can be grouped into

7623-598: The SARS‑CoV‑2 genome (matches above 90 percent may sound high, but in genomic terms it is a wide evolutionary gap). In addition, despite similarities in a few critical amino acids, pangolin virus samples exhibit poor binding to the human ACE2 receptor. SARS‑CoV‑2 belongs to the broad family of viruses known as coronaviruses . It is a positive-sense single-stranded RNA (+ssRNA) virus, with a single linear RNA segment. Coronaviruses infect humans, other mammals, including livestock and companion animals, and avian species. Human coronaviruses are capable of causing illnesses ranging from

7744-573: The Subfamily Orthocoronavirinae, it appears in few other viruses from the Beta-CoV genus, and it is unique among members of its subgenus for such a site. The furin cleavage site PRRAR↓ is highly similar to that of the feline coronavirus , an alphacoronavirus 1 strain. Viral genetic sequence data can provide critical information about whether viruses separated by time and space are likely to be epidemiologically linked. With

7865-451: The behavior of clouds. Although all hydrometeors , solid and liquid, can be described as aerosols, a distinction is commonly made between such dispersions (i.e. clouds) containing activated drops and crystals, and aerosol particles. The atmosphere of Earth contains aerosols of various types and concentrations, including quantities of: Aerosols can be found in urban ecosystems in various forms, for example: The presence of aerosols in

7986-439: The bronchi, while the ones with an effective diameter smaller than 2.5 μm can enter as far as the gas exchange region in the lungs, which can be hazardous to human health. For a monodisperse aerosol, a single number—the particle diameter—suffices to describe the size of the particles. However, more complicated particle-size distributions describe the sizes of the particles in a polydisperse aerosol. This distribution defines

8107-403: The characteristic appearance of virions (the infective form of the virus) by electron microscopy , which have a fringe of large, bulbous surface projections creating an image reminiscent of the solar corona or halo. This morphology is created by the viral spike peplomers , which are proteins on the surface of the virus. The scientific name Coronavirus was accepted as a genus name by

8228-435: The common cold. Coronaviruses can cause colds with major symptoms, such as fever, and a sore throat from swollen adenoids . Coronaviruses can cause pneumonia (either direct viral pneumonia or secondary bacterial pneumonia ) and bronchitis (either direct viral bronchitis or secondary bacterial bronchitis). The human coronavirus discovered in 2003, SARS-CoV , which causes severe acute respiratory syndrome (SARS), has

8349-468: The complex is to transcribe the viral genome. RdRp directly mediates the synthesis of negative-sense subgenomic RNA molecules from the positive-sense genomic RNA. This process is followed by the transcription of these negative-sense subgenomic RNA molecules to their corresponding positive-sense mRNAs . The subgenomic mRNAs form a " nested set " which have a common 5'-head and partially duplicate 3'-end. Recombination – The replicase-transcriptase complex

8470-486: The coronavirus species, by either an aerosol , fomite , or fecal-oral route . Human coronaviruses infect the epithelial cells of the respiratory tract , while animal coronaviruses generally infect the epithelial cells of the digestive tract . SARS coronavirus , for example, infects the human epithelial cells of the lungs via an aerosol route by binding to the angiotensin-converting enzyme 2 (ACE2) receptor. Transmissible gastroenteritis coronavirus (TGEV) infects

8591-556: The deltacoronavirus line at about 3000 BCE. Bats and birds, as warm-blooded flying vertebrates, are an ideal natural reservoir for the coronavirus gene pool (with bats the reservoir for alphacoronaviruses and betacoronavirus – and birds the reservoir for gammacoronaviruses and deltacoronaviruses). The large number and global range of bat and avian species that host viruses have enabled extensive evolution and dissemination of coronaviruses. Many human coronaviruses have their origin in bats. The human coronavirus NL63 shared

8712-409: The deposition of pollutants to the surface of the earth as well as to bodies of water. This has the potential to be damaging to both the environment and human health. Ship tracks are clouds that form around the exhaust released by ships into the still ocean air. Water molecules collect around the tiny particles ( aerosols ) from exhaust to form a cloud seed . More and more water accumulates on

8833-500: The deposition of pollutants to the surface of the earth as well as to bodies of water. This has the potential to be damaging to both the environment and human health. Aerosols interact with the Earth's energy budget in two ways, directly and indirectly. Ship tracks are clouds that form around the exhaust released by ships into the still ocean air. Water molecules collect around the tiny particles ( aerosols ) from exhaust to form

8954-444: The diameter of the spherical particle with a density of 1000 kg/m and the same settling velocity as the irregular particle. Neglecting the slip correction, the particle settles at the terminal velocity proportional to the square of the aerodynamic diameter, d a : where This equation gives the aerodynamic diameter: One can apply the aerodynamic diameter to particulate pollutants or to inhaled drugs to predict where in

9075-624: The disease from their late father, who became ill after a visit to Qatar and Saudi Arabia. Despite this, it appears the virus had trouble spreading from human to human, as most individuals who are infected do not transmit the virus. By 30 October 2013, there were 124 cases and 52 deaths in Saudi Arabia. After the Dutch Erasmus Medical Centre sequenced the virus, the virus was given a new name, Human Coronavirus–Erasmus Medical Centre (HCoV-EMC). The final name for

9196-435: The diseases commonly called SARS , MERS , and COVID-19 respectively. Although the common cold is usually caused by rhinoviruses , in about 15% of cases the cause is a coronavirus. The human coronaviruses HCoV-OC43, HCoV-HKU1, HCoV-229E, and HCoV-NL63 continually circulate in the human population in adults and children worldwide and produce the generally mild symptoms of the common cold. The four mild coronaviruses have

9317-472: The envelope, there is the nucleocapsid , which is formed from multiple copies of the nucleocapsid (N) protein, which are bound to the positive-sense single-stranded RNA genome in a continuous beads -on-a-string type conformation. N protein is a phosphoprotein of 43 to 50 kDa in size, and is divided into three conserved domains. The majority of the protein is made up of domains 1 and 2, which are typically rich in arginines and lysines . Domain 3 has

9438-543: The first infection, but the mechanisms that could account for this are not known. No natural reservoir for SARS-CoV-2 has been identified. Prior to the emergence of SARS-CoV-2 as a pathogen infecting humans, there had been two previous zoonosis -based coronavirus epidemics, those caused by SARS-CoV-1 and MERS-CoV . The first known infections from SARS‑CoV‑2 were discovered in Wuhan, China. The original source of viral transmission to humans remains unclear, as does whether

9559-558: The frequency curve between two sizes a and b represents the total fraction of the particles in that size range: It can also be formulated in terms of the total number density N : Assuming spherical aerosol particles, the aerosol surface area per unit volume ( S ) is given by the second moment : And the third moment gives the total volume concentration ( V ) of the particles: The particle size distribution can be approximated. The normal distribution usually does not suitably describe particle size distributions in aerosols because of

9680-420: The genus Hipposideridae ; subsequently, they spread to horseshoe bats in the species Rhinolophidae , then to Asian palm civets , and finally to humans. Unlike other betacoronaviruses, bovine coronavirus of the species Betacoronavirus 1 and subgenus Embecovirus is thought to have originated in rodents and not in bats. In the 1790s, equine coronavirus diverged from the bovine coronavirus after

9801-403: The laboratory, contains particles of uniform size. Most aerosols, however, as polydisperse colloidal systems, exhibit a range of particle sizes. Liquid droplets are almost always nearly spherical, but scientists use an equivalent diameter to characterize the properties of various shapes of solid particles, some very irregular. The equivalent diameter is the diameter of a spherical particle with

9922-407: The lipid bilayer. They are responsible for virion assembly, intracellular trafficking and morphogenesis (budding). The spikes are the most distinguishing feature of coronaviruses and are responsible for the corona- or halo-like surface. On average a coronavirus particle has 74 surface spikes. Each spike is about 20 nm long and is composed of a trimer of the S   protein. The S protein

10043-415: The members of betacoronavirus subgroup A ) also has a shorter spike-like surface protein called hemagglutinin esterase (HE). The HE proteins occur as homodimers composed of about 400 amino acid residues and are 40 to 50 kDa in size. They appear as tiny surface projections of 5 to 7 nm long embedded in between the spikes. They help in the attachment to and detachment from the host cell. Inside

10164-494: The most closely known relative being the BANAL-52 bat coronavirus. SARS-CoV-2 is of zoonotic origin; its close genetic similarity to bat coronaviruses suggests it emerged from such a bat-borne virus . Research is ongoing as to whether SARS‑CoV‑2 came directly from bats or indirectly through any intermediate hosts. The virus shows little genetic diversity , indicating that the spillover event introducing SARS‑CoV‑2 to humans

10285-708: The most variable components as they are responsible for host cell specificity. They possess two major domains named N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), both of which serve as the receptor-binding domains. The NTDs recognize and bind sugars on the surface of the host cell. An exception is the MHV NTD that binds to a protein receptor carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). S1-CTDs are responsible for recognizing different protein receptors such as angiotensin-converting enzyme 2 (ACE2), aminopeptidase N (APN), and dipeptidyl peptidase 4 (DPP4). A subset of coronaviruses (specifically

10406-572: The mouse hepatitis virus. This new group of viruses were named coronaviruses after their distinctive morphological appearance. Human coronavirus 229E and human coronavirus OC43 continued to be studied in subsequent decades. The coronavirus strain B814 was lost. It is not known which present human coronavirus it was. Other human coronaviruses have since been identified, including SARS-CoV in 2003, HCoV NL63 in 2003, HCoV HKU1 in 2004, MERS-CoV in 2013, and SARS-CoV-2 in 2019. There have also been

10527-614: The much larger clades . Several different clade nomenclatures have been proposed. Nextstrain divides the variants into five clades (19A, 19B, 20A, 20B, and 20C), while GISAID divides them into seven (L, O, V, S, G, GH, and GR). Several notable variants of SARS-CoV-2 emerged in late 2020. The World Health Organization has currently declared five variants of concern , which are as follows: Other notable variants include 6 other WHO-designated variants under investigation and Cluster 5 , which emerged among mink in Denmark and resulted in

10648-624: The natural reservoir of the virus that caused the 2002–2004 SARS outbreak has resulted in the discovery of many SARS-like bat coronaviruses , most originating in horseshoe bats . The closest match by far, published in Nature (journal) in February 2022, were viruses BANAL-52 (96.8% resemblance to SARS‑CoV‑2), BANAL-103 and BANAL-236, collected in three different species of bats in Feuang , Laos. An earlier source published in February 2020 identified

10769-558: The nonstructural proteins coalesce to form a multi-protein replicase-transcriptase complex (RTC). The main replicase-transcriptase protein is the RNA-dependent RNA polymerase (RdRp). It is directly involved in the replication and transcription of RNA from an RNA strand. The other nonstructural proteins in the complex assist in the replication and transcription process. The exoribonuclease nonstructural protein, for instance, provides extra fidelity to replication by providing

10890-521: The novel virus by serially passing it through organ culture of human embryonic trachea . The new cultivating method was introduced to the lab by Bertil Hoorn. The isolated virus when intranasally inoculated into volunteers caused a cold and was inactivated by ether which indicated it had a lipid envelope . Dorothy Hamre and John Procknow at the University of Chicago isolated a novel cold from medical students in 1962. They isolated and grew

11011-542: The number frequency as: where: The log-normal distribution has no negative values, can cover a wide range of values, and fits many observed size distributions reasonably well. Other distributions sometimes used to characterise particle size include: the Rosin-Rammler distribution , applied to coarsely dispersed dusts and sprays; the Nukiyama–Tanasawa distribution, for sprays of extremely broad size ranges;

11132-519: The particles and the suspending gas, which is usually air. Meteorologists and climatologists often refer to them as particle matter, while the classification in sizes ranges like PM2.5 or PM10, is useful in the field of atmospheric pollution as these size range play a role in ascertain the harmful effects in human health. Frederick G. Donnan presumably first used the term aerosol during World War I to describe an aero- solution , clouds of microscopic particles in air. This term developed analogously to

11253-624: The pig epithelial cells of the digestive tract via a fecal–oral route by binding to the alanine aminopeptidase (APN) receptor. Coronaviruses form the subfamily Orthocoronavirinae, which is one of two subfamilies in the family Coronaviridae , order Nidovirales , and realm Riboviria . They are divided into the four genera: Alphacoronavirus , Betacoronavirus , Gammacoronavirus and Deltacoronavirus . Alphacoronaviruses and betacoronaviruses infect mammals, while gammacoronaviruses and deltacoronaviruses primarily infect birds. The most recent common ancestor (MRCA) of all coronaviruses

11374-433: The reading frames for the accessory proteins. The number of accessory proteins and their function is unique depending on the specific coronavirus. Infection begins when the viral spike protein attaches to its complementary host cell receptor. After attachment, a protease of the host cell cleaves and activates the receptor-attached spike protein. Depending on the host cell protease available, cleavage and activation allows

11495-436: The relative amounts of particles, sorted according to size. One approach to defining the particle size distribution uses a list of the sizes of every particle in a sample. However, this approach proves tedious to ascertain in aerosols with millions of particles and awkward to use. Another approach splits the size range into intervals and finds the number (or proportion) of particles in each interval. These data can be presented in

11616-401: The relaxation time: where: To account for the effect of the shape of non-spherical particles, a correction factor known as the dynamic shape factor is applied to Stokes' law. It is defined as the ratio of the resistive force of the irregular particle to that of a spherical particle with the same volume and velocity: where: The aerodynamic diameter of an irregular particle is defined as

11737-461: The respiratory tract such particles deposit. Pharmaceutical companies typically use aerodynamic diameter, not geometric diameter, to characterize particles in inhalable drugs. The previous discussion focused on single aerosol particles. In contrast, aerosol dynamics explains the evolution of complete aerosol populations. The concentrations of particles will change over time as a result of many processes. External processes that move particles outside

11858-576: The role of pangolins as an intermediate host was initially posited (a study published in July 2020 suggested that pangolins are an intermediate host of SARS‑CoV‑2-like coronaviruses), subsequent studies have not substantiated their contribution to the spillover. Evidence against this hypothesis includes the fact that pangolin virus samples are too distant to SARS-CoV-2: isolates obtained from pangolins seized in Guangdong were only 92% identical in sequence to

11979-421: The same value of some physical property as the irregular particle. The equivalent volume diameter ( d e ) is defined as the diameter of a sphere of the same volume as that of the irregular particle. Also commonly used is the aerodynamic diameter ,  d a . People generate aerosols for various purposes, including: Some devices for generating aerosols are: Several types of atmospheric aerosol have

12100-666: The seed until a visible cloud is formed. In the case of ship tracks, the cloud seeds are stretched over a long narrow path where the wind has blown the ship's exhaust, so the resulting clouds resemble long strings over the ocean. The warming caused by human-produced greenhouse gases has been somewhat offset by the cooling effect of human-produced aerosols. In 2020, regulations on fuel significantly cut sulfur dioxide emissions from international shipping by approximately 80%, leading to an unexpected global geoengineering termination shock. The liquid or solid particles in an aerosol have diameters typically less than 1 μm . Larger particles with

12221-507: The source of a majority of infections. That may explain how out of 217 on board a cruise liner that docked at Montevideo , only 24 of 128 who tested positive for viral RNA showed symptoms. Similarly, a study of ninety-four patients hospitalized in January and February 2020 estimated patients began shedding virus two to three days before symptoms appear and that "a substantial proportion of transmission probably occurred before first symptoms in

12342-551: The source. For a virus recently acquired through a cross-species transmission, rapid evolution is expected. The mutation rate estimated from early cases of SARS-CoV-2 was of 6.54 × 10 per site per year. Coronaviruses in general have high genetic plasticity , but SARS-CoV-2's viral evolution is slowed by the RNA proofreading capability of its replication machinery. For comparison, the viral mutation rate in vivo of SARS-CoV-2 has been found to be lower than that of influenza. Research into

12463-424: The stratosphere after an eruption as droplets of sulfuric acid that can prevail for up to two years, and reflect sunlight, lowering temperature. Desert dust, mineral particles blown to high altitudes, absorb heat and may be responsible for inhibiting storm cloud formation. Human-made sulfate aerosols , primarily from burning oil and coal, affect the behavior of clouds. When aerosols absorb pollutants, it facilitates

12584-403: The structural proteins that combined with the lipid bilayer to shape the viral envelope and maintain its size. S proteins are needed for interaction with the host cells. But human coronavirus NL63 is peculiar in that its M protein has the binding site for the host cell, and not its S protein. The diameter of the envelope is 85 nm. The envelope of the virus in electron micrographs appears as

12705-625: The term hydrosol , a colloid system with water as the dispersed medium. Primary aerosols contain particles introduced directly into the gas; secondary aerosols form through gas-to-particle conversion. Key aerosol groups include sulfates, organic carbon, black carbon, nitrates, mineral dust, and sea salt, they usually clump together to form a complex mixture. Various types of aerosol, classified according to physical form and how they were generated, include dust, fume, mist, smoke and fog. There are several measures of aerosol concentration. Environmental science and environmental health often use

12826-469: The velocity of the gas at the surface of the particle is zero. For small particles (< 1 μm) that characterize aerosols, however, this assumption fails. To account for this failure, one can introduce the Cunningham correction factor , always greater than 1. Including this factor, one finds the relation between the resisting force on a particle and its velocity: where This allows us to calculate

12947-451: The viral surface until they attach to the host cell membrane. In a functionally active state, three S1 are attached to two S2 subunits. The subunit complex is split into individual subunits when the virus binds and fuses with the host cell under the action of proteases such as cathepsin family and transmembrane protease serine 2 (TMPRSS2) of the host cell. S1 proteins are the most critical components in terms of infection. They are also

13068-490: The virus RaTG13 , collected in bats in Mojiang , Yunnan, China to be the closest to SARS‑CoV‑2, with 96.1% resemblance. None of the above are its direct ancestor. Bats are considered the most likely natural reservoir of SARS‑CoV‑2. Differences between the bat coronavirus and SARS‑CoV‑2 suggest that humans may have been infected via an intermediate host; although the source of introduction into humans remains unknown. Although

13189-541: The virus became pathogenic before or after the spillover event . Because many of the early infectees were workers at the Huanan Seafood Market , it has been suggested that the virus might have originated from the market. However, other research indicates that visitors may have introduced the virus to the market, which then facilitated rapid expansion of the infections. A March 2021 WHO-convened report stated that human spillover via an intermediate animal host

13310-524: The virus in kidney tissue culture , designating it 229E. The novel virus caused a cold in volunteers and, like B814, was inactivated by ether. Scottish virologist June Almeida at St Thomas' Hospital in London, collaborating with Tyrrell, compared the structures of IBV, B814 and 229E in 1967. Using electron microscopy the three viruses were shown to be morphologically related by their general shape and distinctive club-like spikes . A research group at

13431-735: The virus is Middle East respiratory syndrome coronavirus (MERS-CoV). The only U.S. cases (both survived) were recorded in May 2014. In May 2015, an outbreak of MERS-CoV occurred in the Republic of Korea , when a man who had traveled to the Middle East, visited four hospitals in the Seoul area to treat his illness. This caused one of the largest outbreaks of MERS-CoV outside the Middle East. As of December 2019, 2,468 cases of MERS-CoV infection had been confirmed by laboratory tests, 851 of which were fatal,

13552-422: 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 or in the first week of symptoms and declines thereafter. The duration of SARS-CoV-2 RNA shedding is generally between 3 and 46 days after symptom onset. A study by a team of researchers from the University of North Carolina found that

13673-580: The virus may be airborne as well, with aerosols potentially being able to transmit the virus. During human-to-human transmission, between 200 and 800 infectious SARS‑CoV‑2 virions are thought to initiate a new infection. If confirmed, aerosol transmission has biosafety implications because a major concern associated with the risk of working with emerging viruses in the laboratory is the generation of aerosols from various laboratory activities which are not immediately recognizable and may affect other scientific personnel. Indirect contact via contaminated surfaces

13794-503: The virus that caused the infection in 1933. The virus was then known as infectious bronchitis virus (IBV). Charles D. Hudson and Fred Robert Beaudette cultivated the virus for the first time in 1937. The specimen came to be known as the Beaudette strain. In the late 1940s, two more animal coronaviruses, JHM that causes brain disease (murine encephalitis) and mouse hepatitis virus (MHV) that causes hepatitis in mice were discovered. It

13915-420: The virus. 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. The man's second infection was symptomatically more severe than

14036-422: The viruses can infect other host cells. Infected carriers are able to shed viruses into the environment. The interaction of the coronavirus spike protein with its complementary cell receptor is central in determining the tissue tropism , infectivity , and species range of the released virus. Coronaviruses mainly target epithelial cells . They are transmitted from one host to another host, depending on

14157-403: Was confirmed on 20 January 2020 during the COVID-19 pandemic . Transmission was initially assumed to occur primarily via respiratory droplets from coughs and sneezes within a range of about 1.8 metres (6 ft). Laser light scattering experiments suggest that speaking is an additional mode of transmission and a far-reaching one, indoors, with little air flow. Other studies have suggested that

14278-451: 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 . 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

14399-891: Was not realized at the time that these three different viruses were related. Human coronaviruses were discovered in the 1960s using two different methods in the United Kingdom and the United States. E.C. Kendall, Malcolm Bynoe, and David Tyrrell working at the Common Cold Unit of the British Medical Research Council collected a unique common cold virus designated B814 in 1961. The virus could not be cultivated using standard techniques which had successfully cultivated rhinoviruses , adenoviruses and other known common cold viruses. In 1965, Tyrrell and Bynoe successfully cultivated

14520-470: Was the causative agent for SARS. The virus was officially named the SARS coronavirus (SARS-CoV). More than 8,000 people from 29 countries and territories were infected, and at least 774 died. In September 2012, a new type of coronavirus was identified, initially called Novel Coronavirus 2012, and now officially named Middle East respiratory syndrome coronavirus (MERS-CoV). The World Health Organization issued

14641-540: Was the most likely explanation, with direct spillover from bats next most likely. Introduction through the food supply chain and the Huanan Seafood Market was considered another possible, but less likely, explanation. An analysis in November 2021, however, said that the earliest-known case had been misidentified and that the preponderance of early cases linked to the Huanan Market argued for it being

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