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20-413: Rousettus bat coronavirus HKU9 is bat Betacoronavirus . Betacoronavirus Betacoronavirus (β-CoVs or Beta-CoVs) 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
40-675: A limited number of reference sequences. A paper released in the Journal of Clinical Microbiology evaluated the 16S rRNA gene sequencing results analyzed with GenBank in conjunction with other freely available, quality-controlled, web-based public databases, such as the EzTaxon -e and the BIBI databases. The results showed that analyses performed using GenBank combined with EzTaxon -e (kappa = 0.79) were more discriminative than using GenBank (kappa = 0.66) or other databases alone. GenBank, being
60-853: A public database, may contain sequences wrongly assigned to a particular species, because the initial identification of the organism was wrong. A recent article published in Genome showed that 75% of mitochondrial Cytochrome c oxidase subunit I sequences were wrongly assigned to the fish Nemipterus mesoprion resulting from continued usage of sequences of initially misidentified individuals. The authors provide recommendations how to avoid further distribution of publicly available sequences with incorrect scientific names. Numerous published manuscripts have identified erroneous sequences on GenBank. These are not only incorrect species assignments (which can have different causes) but also include chimeras and accession records with sequencing errors. A recent manuscript on
80-510: 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 the genus in that they have an additional shorter (8 nm) spike-like protein called hemagglutinin esterase (HE) ( P15776 ). It
100-775: Is an open access , annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States ) as part of the International Nucleotide Sequence Database Collaboration (INSDC). GenBank and its collaborators will receive sequences produced in laboratories throughout
120-473: 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 is cleaved into 16 nonstructural proteins (see UniProt annotation of SARS rep , P0C6X7 ). As of May 2013, GenBank has 46 published complete genomes of
140-454: Is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers. Only original sequences can be submitted to GenBank. Direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin. Upon receipt of a sequence submission, the GenBank staff examines the originality of
160-502: 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 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
180-462: 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 the alpha- and betacoronavirus spike protein is cataloged as InterPro : IPR018548 . The spike protein, a type 1 fusion machine , assembles into
200-518: The GenBank project transitioned to the newly created National Center for Biotechnology Information (NCBI) . The GenBank release notes for release 250.0 (June 2022) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months". As of 15 June 2022, GenBank release 250.0 has over 239 million loci , 1,39 trillion nucleotide bases, from 239 million reported sequences. The GenBank database includes additional data sets that are constructed mechanically from
220-702: The Theoretical Biology and Biophysics Group at Los Alamos National Laboratory (LANL) and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank. Funding was provided by the National Institutes of Health , the National Science Foundation , the Department of Energy , and the Department of Defense . LANL collaborated on GenBank with
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#1732801234888240-561: The data and assigns an accession number to the sequence and performs quality assurance checks. The submissions are then released to the public database, where the entries are retrievable by Entrez or downloadable by FTP . Bulk submissions of Expressed Sequence Tag (EST), Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group also processes complete microbial genome sequences. Walter Goad of
260-588: The firm Bolt, Beranek, and Newman , and by the end of 1983 more than 2,000 sequences were stored in it. In the mid-1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL. As one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI /Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992,
280-911: 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 GenBank The GenBank sequence database
300-482: The main sequence data collection, and therefore are excluded from this count. Public databases which may be searched using the National Center for Biotechnology Information Basic Local Alignment Search Tool (NCBI BLAST), lack peer-reviewed sequences of type strains and sequences of non-type strains. On the other hand, while commercial databases potentially contain high-quality filtered sequence data, there are
320-447: 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 is the first betacoronavirus belonging to lineage C that is known to infect humans. The name "betacoronavirus"
340-410: 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 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
360-475: 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
380-498: The world from more than 500,000 formally described species . The database started in 1982 by Walter Goad and Los Alamos National Laboratory . GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months. Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences. GenBank
400-470: 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 the African camel population. Contributing to this diversity are several recombination events that had taken place in the past between closely related betacoronaviruses of
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