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Novel coronavirus

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Novel coronavirus ( nCoV ) is a provisional name given to coronaviruses of medical significance before a permanent name is decided upon. Although coronaviruses are endemic in humans and infections normally mild, such as the common cold (caused by human coronaviruses in ~15% of cases), cross-species transmission has produced some unusually virulent strains which can cause viral pneumonia and in serious cases even acute respiratory distress syndrome and death .

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20-453: The following viruses could initially be referred to as "novel coronavirus", before being formally named: All four viruses are part of the Betacoronavirus genus within the coronavirus family. The word "novel" indicates a "new pathogen of a previously known type" ( i.e. known family ) of virus. Use of the word conforms to best practices for naming new infectious diseases published by

40-534: Is a database of protein families , protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models ) which describe protein families, domains or sites. Models are built from

60-401: 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

80-466: 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

100-552: Is in the public domain , since its content can be used "by any individual and for any purpose". InterPro aims to release data to the public every 8 weeks, typically within a day of the UniProtKB release of the same proteins. InterPro provides an API for programmatic access to all InterPro entries and their related entries in Json format. There are six main endpoints for the API corresponding to

120-456: 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

140-451: 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

160-723: Is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the InterPro database. Signatures which represent equivalent domains, sites or families are put into the same entry and entries can also be related to one another. Additional information such as a description, consistent names and Gene Ontology (GO) terms are associated with each entry, where possible. InterPro contains three main entities: proteins, signatures (also referred to as "methods" or "models") and entries. The proteins in UniProtKB are also

180-609: The University of Alabama at Birmingham found a more than ten-fold increase in use of expressions such as "Chinese virus" or "Wu flu virus" on Twitter compared to before the outbreak. The researchers voiced concerns whether such terminology could hinder public health efforts or be stigmatizing. No such effects were observed in the wake of the MERS outbreaks being referred to as "Camel flu virus" or "Middle East virus". Betacoronavirus See text Betacoronavirus (β-CoVs or Beta-CoVs)

200-666: The World Health Organization (WHO) in 2015. Historically, pathogens have sometimes been named after locations, individuals, or specific species. However, this practice is now explicitly discouraged by the WHO. The official permanent names for viruses and for diseases are determined by the ICTV and the WHO's ICD , respectively. At the beginning of the COVID-19 pandemic in Hubei a 2020 study from

220-700: 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

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240-526: 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

260-461: The amino acid sequences of known families or domains and they are subsequently used to search unknown sequences (such as those arising from novel genome sequencing) in order to classify them. Each of the member databases of InterPro contributes towards a different niche, from very high-level, structure-based classifications ( SUPERFAMILY and CATH-Gene3D) through to quite specific sub-family classifications ( PRINTS and PANTHER ). InterPro's intention

280-564: 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

300-406: The central protein entities in InterPro. Information regarding which signatures significantly match these proteins are calculated as the sequences are released by UniProtKB and these results are made available to the public (see below). The matches of signatures to proteins are what determine how signatures are integrated together into InterPro entries: comparative overlap of matched protein sets and

320-423: The different InterPro data types: entry, protein, structure, taxonomy, proteome and set. InterProScan is a software package that allows users to scan sequences against member database signatures. Users can use this signature scanning software to functionally characterize novel nucleotide or protein sequences. InterProScan is frequently used in genome projects in order to obtain a "first-pass" characterisation of

340-889: 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 InterPro InterPro

360-447: 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

380-415: The location of the signatures' matches on the sequences are used as indicators of relatedness. Only signatures deemed to be of sufficient quality are integrated into InterPro. As of version 81.0 (released 21 August 2020) InterPro entries annotated 73.9% of residues found in UniProtKB with another 9.2% annotated by signatures that are pending integration. InterPro also includes data for splice variants and

400-502: The proteins contained in the UniParc and UniMES databases. The signatures from InterPro come from 13 "member databases", which are listed below. InterPro consists of seven types of data provided by different members of the consortium: InterPro entries can be further broken down into five types: The database is available for text- and sequence-based searches via a webserver, and for download via anonymous FTP. Like other EBI databases, it

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