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40-752: Bat coronavirus RaTG13 is a SARS-like betacoronavirus identified in the droppings of the horseshoe bat Rhinolophus affinis . It was discovered in 2013 in bat droppings from a mining cave near the town of Tongguan in Mojiang county in Yunnan , China . In February 2020, it was identified as the closest known relative of SARS-CoV-2 , the virus that causes COVID-19 , sharing 96.1% nucleotide identity . However, in 2022, scientists found three closer matches in bats found 530 km south, in Feuang , Laos, designated as BANAL-52 (96.8% identity), BANAL-103 and BANAL-236 . In
80-460: A hawthorn tree, and migrates during the summer to its secondary host, a plant in the carrot family . The host range is the set of hosts that a parasite can use as a partner. In the case of human parasites, the host range influences the epidemiology of the parasitism or disease. For instance, the production of antigenic shifts in Influenza A virus can result from pigs being infected with
120-461: A host is a larger organism that harbours a smaller organism ; whether a parasitic , a mutualistic , or a commensalist guest ( symbiont ). The guest is typically provided with nourishment and shelter. Examples include animals playing host to parasitic worms (e.g. nematodes ), cells harbouring pathogenic (disease-causing) viruses , or a bean plant hosting mutualistic (helpful) nitrogen-fixing bacteria . More specifically in botany ,
160-403: A deep sea giant tubeworm, has an obligate mutualistic association with internal, sulfide-oxidizing, bacterial symbionts. The tubeworm extracts the chemicals that the bacteria need from the sediment, and the bacteria supply the tubeworm, which has no mouth, with nutrients. Some hermit crabs place pieces of sponge on the shell in which they are living. These grow over and eventually dissolve away
200-420: A host and only become parasitic when environmental conditions deteriorate. A parasite may have a long-term relationship with its host, as is the case with all endoparasites. The guest seeks out the host and obtains food or another service from it, but does not usually kill it. In contrast, a parasitoid spends a large part of its life within or on a single host, ultimately causing the host's death, with some of
240-424: A host plant supplies food resources to micropredators, which have an evolutionarily stable relationship with their hosts similar to ectoparasitism . The host range is the collection of hosts that an organism can use as a partner. Symbiosis spans a wide variety of possible relationships between organisms, differing in their permanence and their effects on the two parties. If one of the partners in an association
280-464: A limited host range is oligophagous, being restricted to a few closely related species, usually in the same plant family. The diamondback moth is an example of this, feeding exclusively on brassicas , and the larva of the potato tuber moth feeds on potatoes, tomatoes and tobacco, all members of the same plant family, Solanaceae . Herbivorous insects with a wide range of hosts in various different plant families are known as polyphagous . One example
320-543: A novel sequence of ribonucleic acids later identified as "RaTG13". In 2020, Shi and her group retested the serum samples from the miners for SARS-CoV-2. The samples tested negative. In 2020, the strain identified in the sample was renamed from the original Ra4991 (4991st sample collected from Rhinolophus affinis ) to "RaTG13", to reflect the originating bat species (Ra from Rhinolophus affinis ), geographic location (TG from Tongguan), and year collected (13 from 2013). The name change has been considered innuendo by advocates of
360-418: A possible cause of the infection, different animals (including bats, rats, and musk shrews ) were also sampled in and around the mining cave. Between 2012 and 2015, Shi Zhengli and her group isolated 293 different coronaviruses (284 alpha- and 9 beta-coronaviruses ) from bat feces samples in the cave. One of the samples collected in 2013 from Rhinolophus affinis (the intermediate horseshoe bat) contained
400-428: A small predator lives parasitically on a much larger host plant, eating parts of it. The range of plants on which a herbivorous insect feeds is known as its host range. This can be wide or narrow, but it never includes all plants. A small number of insects are monophagous , feeding on a single plant. The silkworm larva is one of these, with mulberry leaves being the only food consumed. More often, an insect with
440-401: Is cleaved into 16 nonstructural proteins (see UniProt annotation of SARS rep , P0C6X7 ). As of May 2013, GenBank has 46 published complete genomes of the α- (group 1), β- (group 2), γ- (group 3), and δ- (group 4) CoVs. Genetic recombination can occur when two or more viral genomes are present in the same host cell. The dromedary camel Beta-CoV HKU23 exhibits genetic diversity in
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#1732801386913480-470: Is created by the viral spike (S) peplomers , which are proteins that populate the surface of the virus and determine host tropism . The order Nidovirales is named for the Latin nidus , which means 'nest'. It refers to this order's production of a 3′-coterminal nested set of subgenomic mRNAs during infection. Several structures of the spike proteins have been resolved. The receptor binding domain in
520-499: Is much larger than the other, it is generally known as the host. In parasitism , the parasite benefits at the host's expense. In commensalism , the two live together without harming each other, while in mutualism , both parties benefit. Most parasites are only parasitic for part of their life cycle. By comparing parasites with their closest free-living relatives, parasitism has been shown to have evolved on at least 233 separate occasions. Some organisms live in close association with
560-445: Is not always easy or even possible to identify which host is definitive and which secondary. The life cycles of many parasites are not well understood, and the subjectively or economically more important organism may initially be designated incorrectly as primary. Mislabelling may continue even after the error becomes known. For example trout and salmon are sometimes said to be "primary hosts" for salmonid whirling disease , even though
600-456: Is one of four genera ( Alpha -, Beta- , Gamma- , and Delta- ) of coronaviruses . Member viruses are enveloped , positive-strand RNA viruses that infect mammals , including humans . 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. The coronavirus genera are each composed of varying viral lineages with
640-561: Is the buff ermine moth whose larvae feed on alder , mint , plantain , oak , rhubarb , currant , blackberry , dock , ragwort , nettle and honeysuckle . Plants often produce toxic or unpalatable secondary metabolites to deter herbivores from feeding on them. Monophagous insects have developed specific adaptations to overcome those in their specialist hosts, giving them an advantage over polyphagous species. However, this puts them at greater risk of extinction if their chosen hosts suffer setbacks. Monophagous species are able to feed on
680-455: Is the first betacoronavirus belonging to lineage C that is known to infect humans. The name "betacoronavirus" is derived from Ancient Greek βῆτα ( bē̂ta , "the second letter of the Greek alphabet "), and κορώνη (korṓnē, “garland, wreath”), meaning crown, which describes the appearance of the surface projections seen under electron microscopy that resemble a solar corona . This morphology
720-643: The Hippocratic Corpus describes human bladder worm . The medieval Persian physician Avicenna recorded human and animal parasites including roundworms, threadworms, the Guinea worm and tapeworms. In Early Modern times, Francesco Redi recorded animal parasites, while the microscopist Antonie van Leeuwenhoek observed and illustrated the protozoan Giardia lamblia from "his own loose stools". Hosts to mutualistic symbionts were recognised more recently, when in 1877 Albert Bernhard Frank described
760-533: The SARS-CoV-2 genome (it shares 96.1% nucleotide similarity), and its identification in animal droppings is a supporting piece of evidence for SARS-CoV-2's natural origin. The main area of divergence between RaTG13 and SARS-CoV-2 is in the receptor-binding domain (RBD) of the spike protein (S), which is the portion that binds to the receptor protein on the surface of the host cell and causes infection. The divergence in this domain indicates that, unlike SARS-CoV-2,
800-407: The brood parasitism of the cuckoo . Parasites follow a wide variety of evolutionary strategies, placing their hosts in an equally wide range of relationships. Parasitism implies host–parasite coevolution , including the maintenance of gene polymorphisms in the host, where there is a trade-off between the advantage of resistance to a parasite and a cost such as disease caused by the gene. It
840-494: The lab leak theory for the COVID-19 pandemic . The sequence of RaTG13 was reconstructed from metagenomic sampling (a common practice in environmental virology), and as such, could potentially be an in-silico chimera . RaTG13 has not been confirmed to exist in nature, to have been cultured or isolated in any laboratory, or to be a viable human pathogen. A live virus "RaTG13" has never been detected in any laboratory sample from
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#1732801386913880-464: The myxosporean parasite reproduces sexually inside the sludge worm . And where the host harbors the different parasite's phases at different sites within its body, the host is both intermediate and definitive: for example trichinosis , a disease caused by roundworms , where the host has immature juveniles in its muscles and reproductive adults in its digestive tract. Micropredation is an evolutionarily stable strategy within parasitism, in which
920-705: The African camel population. Contributing to this diversity are several recombination events that had taken place in the past between closely related betacoronaviruses of the subgenus Embecovirus . Also the betacoronavirus, Human SARS-CoV , appears to have had a complex history of recombination between ancestral coronaviruses that were hosted in several different animal groups. Alpha- and betacoronaviruses mainly infect bats, but they also infect other species like humans , camels , and rodents . Betacoronaviruses that have caused epidemics in humans generally induce fever and respiratory symptoms. They include: Within
960-1720: The RaTG13 virus might not use angiotensin-converting enzyme 2 (ACE2) as its entry site into the cell. Further, the S protein of RaTG13 virus lacks the furin cleavage motif RRAR↓S. The binding affinity between RATG13 and hACE2 is lower than that between SARS-CoV-2 RBD and hACE2. 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 Betacoronavirus Betacoronavirus (β-CoVs or Beta-CoVs)
1000-553: The WIV or elsewhere. Based on its sequence, RaTG13 is a positive-strand RNA virus with an outer membrane. Its genome is approximately 29,800 nucleotides. The genome encodes a replicase (ORF1a/1b) and four structural proteins; including a spike protein (S), membrane protein (M), envelope protein (E) and nucleocapsid protein (N); and five viral accessory proteins , including ORF3a (NS3), ORF6 (NS6), ORF7a (NS7a), ORF7b (NS7b) and ORF8 (NS8). RaTG13 bears strong resemblance to
1040-530: The alpha- and betacoronavirus spike protein is cataloged as InterPro : IPR018548 . The spike protein, a type 1 fusion machine , assembles into a trimer ( PDB : 3jcl , 6acg ); its core structure resembles that of paramyxovirus F (fusion) proteins. The receptor usage is not very conserved; for example, among Sarbecovirus , only a sub-lineage containing SARS share the ACE2 receptor. The viruses of subgenera Embecovirus differ from all others in
1080-564: The betacoronavirus genus containing four such lineages: A, B, C, D. In older literature, this genus is also known as "group 2 coronaviruses". The genus is in the subfamily Orthocoronavirinae in the family Coronaviridae , of the order Nidovirales . The betacoronaviruses of the greatest clinical importance concerning humans are OC43 and HKU1 (which can cause the common cold ) of lineage A, SARS-CoV-1 and SARS-CoV-2 (the causes of SARS and COVID-19 respectively) of lineage B, and MERS-CoV (the cause of MERS ) of lineage C. MERS-CoV
1120-449: The cleaner. Remoras (also called suckerfish) can swim freely but have evolved suckers that enable them to adhere to smooth surfaces, gaining a free ride ( phoresis ), and they spend most of their lives clinging to a host animal such as a whale, turtle or shark. However, the relationship may be mutualistic, as remoras, though not generally considered to be cleaner fish , often consume parasitic copepods : for example, these are found in
1160-543: The fungus from the soil. Over 95% of plant families have been shown to have mycorrhizal associations. Another such relationship is between leguminous plants and certain nitrogen-fixing bacteria called rhizobia that form nodules on the roots of the plant. The host supplies the bacteria with the energy needed for nitrogen fixation and the bacteria provide much of the nitrogen needed by the host. Such crops as beans , peas , chickpeas and alfalfa are able to fix nitrogen in this way, and mixing clover with grasses increases
1200-912: The genus Betacoronavirus (Group 2 CoV), four subgenera or lineages (A, B, C, and D) have traditionally been recognized. The four lineages have also been named using Greek letters or numerically. A fifth subgenus, Hibecovirus , was added more recently. Member subgenera and species include: Betacoronavirus 1 China Rattus coronavirus HKU24 Human coronavirus HKU1 Murine coronavirus Myodes coronavirus 2JL14 Severe acute respiratory syndrome–related coronavirus (SARSr-CoV or SARS-CoV) Hedgehog coronavirus 1 Middle East respiratory syndrome-related coronavirus (MERS-CoV) Pipistrellus bat coronavirus HKU5 Tylonycteris bat coronavirus HKU4 Eidolon bat coronavirus C704 Rousettus bat coronavirus GCCDC1 Rousettus bat coronavirus HKU9 Bat Hp-betacoronavirus Zhejiang2013 Host cell In biology and medicine ,
1240-447: The genus in that they have an additional shorter (8 nm) spike-like protein called hemagglutinin esterase (HE) ( P15776 ). It is believed to have been acquired from influenza C virus . Coronaviruses have a large genome size that ranges from 26 to 32 kilobases. The overall structure of β-CoV genome is similar to that of other CoVs, with an ORF1ab replicase polyprotein ( rep , pp1ab ) preceding other elements. This polyprotein
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1280-401: The mollusc shell; the crab may not ever need to replace its abode again and is well-camouflaged by the overgrowth of sponge. An important hosting relationship is mycorrhiza , a symbiotic association between a fungus and the roots of a vascular host plant. The fungus receives carbohydrates, the products of photosynthesis, while the plant receives phosphates and nitrogenous compounds acquired by
1320-496: The other. For example, termites are hosts to the protozoa that live in their gut and which digest cellulose , and the human gut flora is essential for efficient digestion . Many corals and other marine invertebrates house zooxanthellae , single-celled algae, in their tissues. The host provides a protected environment in a well-lit position for the algae, while benefiting itself from the nutrients produced by photosynthesis which supplement its diet. Lamellibrachia luymesi ,
1360-428: The sea and on land, making use of smaller animals to clean them of parasites. Cleaners include fish, shrimps and birds; hosts or clients include a much wider range of fish, marine reptiles including turtles and iguanas, octopus, whales, and terrestrial mammals. The host appears to benefit from the interaction, but biologists have disputed whether this is a truly mutualistic relationship or something closer to parasitism by
1400-618: The spring of 2012, three miners cleaning bat feces in an abandoned copper mine near the town of Tongguan in Mojiang Hani Autonomous County developed fatal pneumonia . Out of concerns that the miner's cases could represent a novel disease, serum samples collected from the miners were sent to the Wuhan Institute of Virology and tested by Shi Zhengli and her group for Ebola virus , Nipah virus , and bat SARSr-CoV Rp3. The samples tested negative. To uncover
1440-532: The stomach contents of 70% of the common remora . Many molluscs , barnacles and polychaete worms attach themselves to the carapace of the Atlantic horseshoe crab ; for some this is a convenient arrangement, but for others it is an obligate form of commensalism and they live nowhere else. The first host to be noticed in ancient times was human: human parasites such as hookworm are recorded from ancient Egypt from 3000 BC onwards, while in ancient Greece ,
1480-455: The strategies involved verging on predation . Generally, the host is kept alive until the parasitoid is fully grown and ready to pass on to its next life stage. A guest's relationship with its host may be intermittent or temporary, perhaps associated with multiple hosts, making the relationship equivalent to the herbivory of a wild-living animal. Another possibility is that the host–guest relationship may have no permanent physical contact, as in
1520-534: The tender young foliage with high concentrations of damaging chemicals on which polyphagous species cannot feed, having to make do with older leaves. There is a trade off between offspring quality and quantity; the specialist maximises the chances of its young thriving by paying great attention to the choice of host, while the generalist produces larger numbers of eggs in sub-optimal conditions. Some insect micropredators migrate regularly from one host to another. The hawthorn-carrot aphid overwinters on its primary host,
1560-528: The virus from several different hosts (such as human and bird). This co-infection provides an opportunity for mixing of the viral genes between existing strains, thereby producing a new viral strain. An influenza vaccine produced against an existing viral strain might not be effective against this new strain, which then requires a new influenza vaccine to be prepared for the protection of the human population. Some hosts participate in fully mutualistic interactions with both organisms being completely dependent on
1600-443: The yield of pastures. Neurotransmitter tyramine produced by commensal Providencia bacteria, which colonize the gut of the nematode Caenorhabditis elegans , bypasses the requirement for its host to biosynthesise tyramine. This product is then probably converted to octopamine by the host enzyme tyramine β-hydroxylase and manipulates a host sensory decision. Hosts of many species are involved in cleaning symbiosis , both in
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