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48-400: 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 the reservoir for the subgenus Embecovirus , while bats are the reservoir for
96-519: A benefit to pathogenic bacteria by allowing repair of DNA damage, particularly damages that occur in the inflammatory, oxidizing environment associated with infection of a host. When two or more viruses, each containing lethal genomic damages, infect the same host cell, the virus genomes can often pair with each other and undergo HRR to produce viable progeny. This process, referred to as multiplicity reactivation, has been studied in lambda and T4 bacteriophages , as well as in several pathogenic viruses. In
144-449: A chromosome if they know the frequency of the crossovers. Geneticists can also use this method to infer the presence of certain genes. Genes that typically stay together during recombination are said to be linked . One gene in a linked pair can sometimes be used as a marker to deduce the presence of the other gene. This is typically used to detect the presence of a disease-causing gene. The recombination frequency between two loci observed
192-481: A form of recombination. Recombination also occurs in the reoviridae (dsRNA)(e.g. reovirus), orthomyxoviridae ((-)ssRNA)(e.g. influenza virus ) and coronaviridae ((+)ssRNA) (e.g. SARS ). Recombination in RNA viruses appears to be an adaptation for coping with genome damage. Switching between template strands during genome replication, referred to as copy-choice recombination, was originally proposed to explain
240-535: A novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) int er chromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes (random orientation of pairs of homologous chromosomes in meiosis I); & (2) int ra chromosomal recombination, occurring through crossing over. During meiosis in eukaryotes , genetic recombination involves
288-486: 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 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
336-542: A variety of exogenous agents (e.g. UV light , X-rays , chemical cross-linking agents) can be repaired by homologous recombinational repair (HRR). These findings suggest that DNA damages arising from natural processes , such as exposure to reactive oxygen species that are byproducts of normal metabolism, are also repaired by HRR. In humans, deficiencies in the gene products necessary for HRR during meiosis likely cause infertility In humans, deficiencies in gene products necessary for HRR, such as BRCA1 and BRCA2 , increase
384-574: Is a common mechanism used in DNA repair . Gene conversion – the process during which homologous sequences are made identical also falls under genetic recombination. Genetic recombination and recombinational DNA repair also occurs in bacteria and archaea , which use asexual reproduction . Recombination can be artificially induced in laboratory ( in vitro ) settings, producing recombinant DNA for purposes including vaccine development. V(D)J recombination in organisms with an adaptive immune system
432-596: Is a small probability of recombination at any location along a chromosome, the frequency of recombination between two locations depends on the distance separating them. Therefore, for genes sufficiently distant on the same chromosome, the amount of crossover is high enough to destroy the correlation between alleles. Tracking the movement of genes resulting from crossovers has proven quite useful to geneticists. Because two genes that are close together are less likely to become separated than genes that are farther apart, geneticists can deduce roughly how far apart two genes are on
480-411: Is a type of site-specific genetic recombination that helps immune cells rapidly diversify to recognize and adapt to new pathogens . During meiosis, synapsis (the pairing of homologous chromosomes) ordinarily precedes genetic recombination. Genetic recombination is catalyzed by many different enzymes . Recombinases are key enzymes that catalyse the strand transfer step during recombination. RecA ,
528-461: Is altered. Gene conversion has often been studied in fungal crosses where the 4 products of individual meioses can be conveniently observed. Gene conversion events can be distinguished as deviations in an individual meiosis from the normal 2:2 segregation pattern (e.g. a 3:1 pattern). Recombination can occur between DNA sequences that contain no sequence homology . This can cause chromosomal translocations , sometimes leading to cancer. B cells of
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#1732772207291576-555: Is called recombinant DNA . A prime example of such a use of genetic recombination is gene targeting , which can be used to add, delete or otherwise change an organism's genes. This technique is important to biomedical researchers as it allows them to study the effects of specific genes. Techniques based on genetic recombination are also applied in protein engineering to develop new proteins of biological interest. Examples include Restriction enzyme mediated integration , Gibson assembly and Golden Gate Cloning . DNA damages caused by
624-507: Is derived from Ancient Greek ἄλφα ( álpha , "the first 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 . The virion is enveloped and spherical measuring 120–160 nm in diameter and a core shell of about 65 nm. Glycoproteins and trimers form large surface projections which create
672-446: 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 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
720-406: Is the crossing-over value . It is the frequency of crossing over between two linked gene loci ( markers ), and depends on the distance between the genetic loci observed. For any fixed set of genetic and environmental conditions, recombination in a particular region of a linkage structure ( chromosome ) tends to be constant, and the same is then true for the crossing-over value which is used in
768-601: Is well documented in male Drosophila melanogaster . The "Haldane-Huxley rule" states that achiasmy usually occurs in the heterogametic sex . Heterochiasmy occurs when recombination rates differ between the sexes of a species. In humans, each oocyte has on average 41.6 ± 11.3 recombinations, 1.63-fold higher than sperms. This sexual dimorphic pattern in recombination rate has been observed in many species. In mammals, females most often have higher rates of recombination. Numerous RNA viruses are capable of genetic recombination when at least two viral genomes are present in
816-873: The Diamond Princess cruise, two mutations, 29736G > T and 29751G > T (G13 and G28) were located in Coronavirus 3′ stem-loop II-like motif (s2m) of SARS-CoV-2. Although s2m is considered an RNA motif highly conserved in 3' untranslated region among many coronavirus species, this result also suggests that s2m of SARS-CoV-2 is RNA recombination /mutation hotspot. SARS-CoV-2's entire receptor binding motif appeared, based on preliminary observations, to have been introduced through recombination from coronaviruses of pangolins . However, more comprehensive analyses later refuted this suggestion and showed that SARS-CoV-2 likely evolved solely within bats and with little or no recombination. Nowak and Ohtsuki noted that
864-468: 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" is derived from Ancient Greek βῆτα ( bē̂ta , "the second letter of the Greek alphabet "), and κορώνη (korṓnē, “garland, wreath”), meaning crown, which describes
912-560: The genomes of an asexual population tend to accumulate more deleterious mutations over time than beneficial or reversing mutations. Chromosomal crossover involves recombination between the paired chromosomes inherited from each of one's parents, generally occurring during meiosis . During prophase I (pachytene stage) the four available chromatids are in tight formation with one another. While in this formation, homologous sites on two chromatids can closely pair with one another, and may exchange genetic information. Because there
960-420: The immune system perform genetic recombination, called immunoglobulin class switching . It is a biological mechanism that changes an antibody from one class to another, for example, from an isotype called IgM to an isotype called IgG . In genetic engineering , recombination can also refer to artificial and deliberate recombination of disparate pieces of DNA, often from different organisms, creating what
1008-512: The poliovirus RNA-dependent RNA polymerase (RdRp) is able to carry out recombination. Recombination appears to occur by a copy choice mechanism in which the RdRp switches (+)ssRNA templates during negative strand synthesis. Recombination by RdRp strand switching also occurs in the (+)ssRNA plant carmoviruses and tombusviruses . Recombination appears to be a major driving force in determining genetic variability within coronaviruses, as well as
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#17327722072911056-533: The 5'-end of the genome encode the major non-structural proteins expressed as a fusion protein by ribosomal frameshift . These include regions with protease , helicase and RNA polymerase motifs. There are seven other genes downstream which encode structural proteins. These are expressed from a 3'-coterminal nested set of subgenomic mRNAs . Both types of Alphacoronavirus 1 , feline coronavirus (FCoV) and canine coronavirus (CCoV), are known to exist in two serotypes. Serotype II targets Aminopeptidase N , while
1104-512: The ability of coronavirus species to jump from one host to another and, infrequently, for the emergence of novel species, although the mechanism of recombination in is unclear. In early 2020, many genomic sequences of Australian SARS‐CoV‐2 isolates have deletions or mutations (29742G>A or 29742G>U; "G19A" or "G19U") in the s2m, suggesting that RNA recombination may have occurred in this RNA element. 29742G("G19"), 29744G("G21"), and 29751G("G28") were predicted as recombination hotspots. During
1152-418: The appearance of solar corona. This genus, like other coronaviruses, has a spike protein with a type I fusion machine (S2) and a receptor-binding domain (S1). It assembles into a trimer. Unlike beta- and gammacoronaviruses, this protein is not cleaved into two halves. The genome is positive-sense , single-stranded RNA with a length of 27 to 29 kilobases and a 3'- polyA tail. Two large, overlapping ORFs at
1200-522: 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 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
1248-403: The arms of the chromosomes flanking the recombination event remain in the parental configuration. Thus, explanations for the adaptive function of meiosis that focus exclusively on crossing-over are inadequate to explain the majority of recombination events. Achiasmy is the phenomenon where autosomal recombination is completely absent in one sex of a species. Achiasmatic chromosomal segregation
1296-701: The bacterial RecA protein is RadA. Bacteria regularly undergo genetic recombination in three main ways: Sometimes a strand of DNA is transferred into the target cell but fails to be copied as the target divides. This is called an abortive transfer . In eukaryotes , recombination during meiosis is facilitated by chromosomal crossover . The crossover process leads to offspring having different combinations of genes from those of their parents, and can occasionally produce new chimeric alleles . The shuffling of genes brought about by genetic recombination produces increased genetic variation . It also allows sexually reproducing organisms to avoid Muller's ratchet , in which
1344-400: The case of pathogenic viruses, multiplicity reactivation may be an adaptive benefit to the virus since it allows the repair of DNA damages caused by exposure to the oxidizing environment produced during host infection. See also reassortment . A molecular model for the mechanism of meiotic recombination presented by Anderson and Sekelsky is outlined in the first figure in this article. Two of
1392-508: The chief recombinase found in Escherichia coli , is responsible for the repair of DNA double strand breaks (DSBs). In yeast and other eukaryotic organisms there are two recombinases required for repairing DSBs. The RAD51 protein is required for mitotic and meiotic recombination, whereas the DNA repair protein, DMC1 , is specific to meiotic recombination. In the archaea, the ortholog of
1440-557: The family Coronaviridae . Both the Alpha - and Betacoronavirus lineages descend from the bat viral gene pool . Alphacoronaviruses were previously known as " phylogroup 1 coronaviruses". The Alphacoronavirus genus is very diverse, particularly in bats. Most bat originating strains haven't been successfully isolated and cultured in laboratory. Alphacoronaviruses infecting other mammal species have been much better studied, see List of Coronavirus live isolates . The name alphacoronavirus
1488-624: The first months of the COVID-19 pandemic, such a recombination event was suggested to have been a critical step in the evolution of SARS-CoV-2's ability to infect humans. Linkage disequilibrium analysis confirmed that RNA recombination with the 11083G > T mutation also contributed to the increase of mutations among the viral progeny. The findings indicate that the 11083G > T mutation of SARS-CoV-2 spread during Diamond Princess shipboard quarantine and arose through de novo RNA recombination under positive selection pressure. In three patients on
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1536-399: The first of the four genera ( Alpha -, Beta- , Gamma- , and Delta- ) of coronaviruses . They are positive-sense , single-stranded RNA viruses that infect mammals , including humans . They have spherical virions with club-shaped surface projections formed by trimers of the spike protein , and a viral envelope . Alphacoronaviruses are in the subfamily Orthocoronavirinae of
1584-546: The four chromatids present early in meiosis (prophase I) are paired with each other and able to interact. Recombination, in this model, is initiated by a double-strand break (or gap) shown in the DNA molecule (chromatid) at the top of the figure. Other types of DNA damage may also initiate recombination. For instance, an inter-strand cross-link (caused by exposure to a cross-linking agent such as mitomycin C) can be repaired by HRR. Two types of recombinant product are produced. Indicated on
1632-945: 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 Alphacoronavirus See text Alphacoronaviruses (Alpha-CoV) are members of
1680-420: The origin of life ( abiogenesis ) is also the origin of biological evolution . They pointed out that all known life on earth is based on biopolymers and proposed that any theory for the origin of life must involve biological polymers that act as information carriers and catalysts. Lehman argued that recombination was an evolutionary development as ancient as the origins of life. Smail et al. proposed that in
1728-470: 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 the order Nidovirales . The betacoronaviruses of the greatest clinical importance concerning humans are OC43 and HKU1 (which can cause
1776-617: The pairing of homologous chromosomes . This may be followed by information transfer between the chromosomes. The information transfer may occur without physical exchange (a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed) (see SDSA – Synthesis Dependent Strand Annealing pathway in Figure); or by the breaking and rejoining of DNA strands, which forms new molecules of DNA (see DHJ pathway in Figure). Recombination may also occur during mitosis in eukaryotes where it ordinarily involves
1824-626: The positive correlation of recombination events over short distances in organisms with a DNA genome (see first Figure, SDSA pathway). Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans. Especially in coronaviruses, recombination may also occur even among distantly related evolutionary groups (subgenera), due to their characteristic transcription mechanism, that involves subgenomic mRNAs that are formed by template switching. When replicating its (+)ssRNA genome ,
1872-413: The production of genetic maps . In gene conversion, a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed. Gene conversion occurs at high frequency at the actual site of the recombination event during meiosis . It is a process by which a DNA sequence is copied from one DNA helix (which remains unchanged) to another DNA helix, whose sequence
1920-508: The receptor for Serotype I is unknown. The difference is due to a different spike protein. There is a common ancestor for FCoV and CCoV. This ancestor gradually evolved into FCoV I and CCoV I. An S protein from an unknown virus was recombined into the ancestor and gave rise to CCoV II. CCoV II once again recombined with FCoV to create FCoV II. CCoV II gradually evolved into TGEV. A spike deletion in TGEV creates PRCV. All these viruses are sorted into
1968-427: The right side is a "crossover" (CO) type, where the flanking regions of the chromosomes are exchanged, and on the left side, a "non-crossover" (NCO) type where the flanking regions are not exchanged. The CO type of recombination involves the intermediate formation of two "Holliday junctions" indicated in the lower right of the figure by two X-shaped structures in each of which there is an exchange of single strands between
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2016-426: The risk of cancer (see DNA repair-deficiency disorder ). In bacteria, transformation is a process of gene transfer that ordinarily occurs between individual cells of the same bacterial species. Transformation involves integration of donor DNA into the recipient chromosome by recombination. This process appears to be an adaptation for repairing DNA damages in the recipient chromosome by HRR. Transformation may provide
2064-430: The same host cell. Recombination is largely responsible for RNA virus diversity and immune evasion. RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among picornaviridae ( (+)ssRNA ) (e.g. poliovirus ). In the retroviridae ((+)ssRNA)(e.g. HIV ), damage in the RNA genome appears to be avoided during reverse transcription by strand switching,
2112-785: 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 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
2160-424: 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 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
2208-430: The subgenus Tegacovirus . The following subgenera and species are recognized: Genetic recombination Genetic recombination (also known as genetic reshuffling ) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes , genetic recombination during meiosis can lead to
2256-585: The two participating chromatids. This pathway is labeled in the figure as the DHJ (double-Holliday junction) pathway. The NCO recombinants (illustrated on the left in the figure) are produced by a process referred to as "synthesis dependent strand annealing" (SDSA). Recombination events of the NCO/SDSA type appear to be more common than the CO/DHJ type. The NCO/SDSA pathway contributes little to genetic variation, since
2304-509: The two sister chromosomes formed after chromosomal replication. In this case, new combinations of alleles are not produced since the sister chromosomes are usually identical. In meiosis and mitosis, recombination occurs between similar molecules of DNA ( homologous sequences ). In meiosis, non-sister homologous chromosomes pair with each other so that recombination characteristically occurs between non-sister homologues. In both meiotic and mitotic cells, recombination between homologous chromosomes
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