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54-419: Severe acute respiratory syndrome coronavirus 1 ( SARS-CoV-1 ), previously known as severe acute respiratory syndrome coronavirus ( SARS-CoV ), is a strain of coronavirus that causes severe acute respiratory syndrome ( SARS ), the respiratory illness responsible for the 2002–2004 SARS outbreak . It is an enveloped , positive-sense , single-stranded RNA virus that infects the epithelial cells within

108-699: A zoonotic origin of the virus: more than 33% of the first detected cases of SARS in Guangdong corresponded to animal or food handlers. Seroprevalence studies reinforced this zoonotic link (a high proportion of asymptomatic animal handlers at markets in Guangdong Province had antibodies against SARS-CoV). On April 12, 2003, scientists working at the Michael Smith Genome Sciences Centre in Vancouver finished mapping

162-651: A G, and 5-methyl-cytosine (created from cytosine by DNA methylation ) is read as a C. With current technology, it is difficult to sequence small amounts of DNA, as the signal is too weak to measure. This is overcome by polymerase chain reaction (PCR) amplification. Once a nucleic acid sequence has been obtained from an organism, it is stored in silico in digital format. Digital genetic sequences may be stored in sequence databases , be analyzed (see Sequence analysis below), be digitally altered and be used as templates for creating new actual DNA using artificial gene synthesis . Digital genetic sequences may be analyzed using

216-413: A chassis for the expression of simple proteins. These strains, such as BL21, are genetically modified to minimize protease activity, hence enabling potential for high efficiency industrial scale protein production . Strains of yeasts are the most common subjects of eukaryotic genetic modification, especially with respect to industrial fermentation . The term has no official ranking status in botany;

270-593: A living thing encodes the necessary information for that living thing to survive and reproduce. Therefore, determining the sequence is useful in fundamental research into why and how organisms live, as well as in applied subjects. Because of the importance of DNA to living things, knowledge of a DNA sequence may be useful in practically any biological research . For example, in medicine it can be used to identify, diagnose and potentially develop treatments for genetic diseases . Similarly, research into pathogens may lead to treatments for contagious diseases. Biotechnology

324-456: A rice plant, all the descendants of the genetically modified rice plant are a strain with unique genetic information that is passed on to later generations; the strain designation, which is normally a number or a formal name, covers all the plants that descend from the originally modified plant. The rice plants in the strain can be bred to other rice strains or cultivars , and if desirable plants are produced, these are further bred to stabilize

378-478: A rough measure of how conserved a particular region or sequence motif is among lineages. The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence, suggest that this region has structural or functional importance. Although DNA and RNA nucleotide bases are more similar to each other than are amino acids,

432-408: Is a burgeoning discipline, with the potential for many useful products and services. RNA is not sequenced directly. Instead, it is copied to a DNA by reverse transcriptase , and this DNA is then sequenced. Current sequencing methods rely on the discriminatory ability of DNA polymerases, and therefore can only distinguish four bases. An inosine (created from adenosine during RNA editing ) is read as

486-458: Is a decrease in the number of lymphocytes circulating in the blood. In the SARS outbreak of 2003, about 9% of patients with confirmed SARS-CoV-1 infection died. The mortality rate was much higher for those over 60 years old, with mortality rates approaching 50% for this subset of patients. In March 2003, WHO established a global network of leading laboratories to collaborate in the identification of

540-400: Is a specific genetic code by which each possible combination of three bases corresponds to a specific amino acid. The central dogma of molecular biology outlines the mechanism by which proteins are constructed using information contained in nucleic acids. DNA is transcribed into mRNA molecules, which travel to the ribosome where the mRNA is used as a template for the construction of

594-415: Is believed to contain around 20,000–25,000 genes. In addition to studying chromosomes to the level of individual genes, genetic testing in a broader sense includes biochemical tests for the possible presence of genetic diseases , or mutant forms of genes associated with increased risk of developing genetic disorders. Genetic testing identifies changes in chromosomes, genes, or proteins. Usually, testing

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648-437: Is considered genetically identical after 20 generations of sibling-mating. Many rodent strains have been developed for a variety of disease models, and they are also often used to test drug toxicity. The common fruit fly ( Drosophila melanogaster ) was among the first organisms used for genetic analysis , has a simple genome , and is very well understood. It has remained a popular model organism for many other reasons, like

702-406: Is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end . For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers , specifying the sequence

756-410: Is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure . The sequence represents genetic information . Biological deoxyribonucleic acid represents the information which directs the functions of an organism . Nucleic acids also have a secondary structure and tertiary structure . Primary structure

810-421: Is most common species for prokaryotic strain engineering. Scientists have succeeded in establishing viable minimal genomes from which new strains can be developed. These minimal strains provide a near guarantee that experiments on genes outside the minimal framework will not be effected by non-essential pathways. Optimized strains of E. coli are typically used for this application. E. coli are also often used as

864-437: Is qualitatively related to the sequences' evolutionary distance from one another. Roughly speaking, high sequence identity suggests that the sequences in question have a comparatively young most recent common ancestor , while low identity suggests that the divergence is more ancient. This approximation, which reflects the " molecular clock " hypothesis that a roughly constant rate of evolutionary change can be used to extrapolate

918-510: Is shared with scientists worldwide via the GSC website (see below). Donald Low of Mount Sinai Hospital in Toronto described the discovery as having been made with "unprecedented speed". The sequence of the SARS coronavirus has since been confirmed by other independent groups. Molecular epidemiological research demonstrated the virus isolated in 2002–2003 in south China and the virus isolated in

972-448: Is sometimes mistakenly referred to as "primary sequence". However there is no parallel concept of secondary or tertiary sequence. Nucleic acids consist of a chain of linked units called nucleotides. Each nucleotide consists of three subunits: a phosphate group and a sugar ( ribose in the case of RNA , deoxyribose in DNA ) make up the backbone of the nucleic acid strand, and attached to

1026-461: Is unknown whether the virus was originally introduced to the market by civets, humans, or another animal. In 2005, two studies identified a number of SARS-like coronaviruses in Chinese bats . Although the bat SARS virus did not replicate in cell culture, in 2008, American researchers altered the genetic structure of bat SARS virus with the human receptor binding domain both in the bat virus and in

1080-548: Is used to find changes that are associated with inherited disorders. The results of a genetic test can confirm or rule out a suspected genetic condition or help determine a person's chance of developing or passing on a genetic disorder. Several hundred genetic tests are currently in use, and more are being developed. In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA , RNA , or protein to identify regions of similarity that may be due to functional, structural , or evolutionary relationships between

1134-613: The Chinese Center for Disease Control and Prevention of the University of Hong Kong and the Guangzhou Center for Disease Control and Prevention established a genetic link between the SARS coronavirus appearing in civets and humans, confirming claims that the virus might have transmitted from the animal species to humans. Infected palm civets at the market were traced to farms where no infected animals were found. It

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1188-495: The H5N1 influenza virus. While funding for such research has aroused controversy at times due to safety concerns, leading to a temporary pause, it has subsequently proceeded. In biotechnology, microbial strains have been constructed to establish metabolic pathways suitable for treating a variety of applications. Historically, a major effort of metabolic research has been devoted to the field of biofuel production. Escherichia coli

1242-724: The genetic sequence of a coronavirus believed to be linked to SARS. The team was led by Marco Marra and Caroline Astell and worked in collaboration with the British Columbia Centre for Disease Control and the National Microbiology Laboratory in Winnipeg , Manitoba , using samples from infected patients in Toronto . The map, hailed by the WHO as an important step forward in fighting SARS,

1296-426: The 10 nucleotide sequence. Thus there is a 30% difference. In biological systems, nucleic acids contain information which is used by a living cell to construct specific proteins . The sequence of nucleobases on a nucleic acid strand is translated by cell machinery into a sequence of amino acids making up a protein strand. Each group of three bases, called a codon , corresponds to a single amino acid, and there

1350-518: The International Union of Pure and Applied Chemistry ( IUPAC ) are as follows: For example, W means that either an adenine or a thymine could occur in that position without impairing the sequence's functionality. These symbols are also valid for RNA, except with U (uracil) replacing T (thymine). Apart from adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U), DNA and RNA also contain bases that have been modified after

1404-484: The Netherlands, demonstrated that the SARS coronavirus fulfilled Koch's postulates , thereby confirming it as the causative agent. In the experiments, macaques infected with the virus developed the same symptoms as human SARS patients. A virus very similar to SARS was discovered in late 2019. This virus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causative pathogen of COVID-19 ,

1458-1466: The Yunnan cave of WIV16 or in other yet-to-be-identified bat caves is considered highly likely. A phylogenetic tree based on whole-genome sequences of SARS-CoV-1 and related coronaviruses is: 16BO133 , 86.3% to SARS-CoV-1, Rhinolophus ferrumequinum , North Jeolla , South Korea JTMC15 , 86.4% to SARS-CoV-1, Rhinolophus ferrumequinum , Tonghua , Jilin Bat SARS CoV Rf1, 87.8% to SARS-CoV-1, Rhinolophus ferrumequinum , Yichang , Hubei BtCoV HKU3, 87.9% to SARS-CoV-1, Rhinolophus sinicus , Hong Kong and Guangdong LYRa11 , 90.9% to SARS-CoV-1, Rhinolophus affinis , Baoshan , Yunnan Bat SARS-CoV/Rp3, 92.6% to SARS-CoV-1, Rhinolophus pearsoni , Nanning , Guangxi Bat SL-CoV YNLF_31C, 93.5% to SARS-CoV-1, Rhinolophus ferrumequinum , Lufeng , Yunnan Bat SL-CoV YNLF_34C, 93.5% to SARS-CoV-1, Rhinolophus ferrumequinum , Lufeng , Yunnan SHC014-CoV , 95.4% to SARS-CoV-1, Rhinolophus sinicus , Kunming , Yunnan WIV1 , 95.6% to SARS-CoV-1, Rhinolophus sinicus , Kunming , Yunnan WIV16 , 96.0% to SARS-CoV-1, Rhinolophus sinicus Kunming , Yunnan Civet SARS-CoV , 99.8% to SARS-CoV-1, Paguma larvata , market in Guangdong, China SARS-CoV-1 SARS-CoV-2 , 79% to SARS-CoV-1 SARS-CoV-1 follows

1512-504: The amine-group with a carbonyl-group). Hypoxanthine is produced from adenine , and xanthine is produced from guanine . Similarly, deamination of cytosine results in uracil . Given the two 10-nucleotide sequences, line them up and compare the differences between them. Calculate the percent difference by taking the number of differences between the DNA bases divided by the total number of nucleotides. In this case there are three differences in

1566-424: The causative agent of SARS. Early on, labs in the network narrowed the search to members of the paramyxovirus and coronavirus families. Early findings shared by the labs pointed to coronaviruses with increasing consistency. On 21 March, scientists from the University of Hong Kong announced the isolation of a new virus that was strongly suspected to be the causative agent of SARS. Epidemiological evidence suggested

1620-408: The conservation of base pairs can indicate a similar functional or structural role. Computational phylogenetics makes extensive use of sequence alignments in the construction and interpretation of phylogenetic trees , which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The degree to which sequences in a query set differ

1674-481: The desirable traits; the stabilized plants that can be propagated and "come true" (remain identical to the parent plant) are given a cultivar name and released into production to be used by farmers. A laboratory mouse or rat strain is a group of animals that is genetically uniform. Strains are used in laboratory experiments. Mouse strains can be inbred , mutated , or genetically modified , while rat strains are usually inbred . A given inbred rodent population

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1728-457: The ease of its breeding and maintenance, and the speed and volume of its reproduction. Various specific strains have been developed, including a flightless version with stunted wings (also used in the pet trade as live food for small reptiles and amphibians). Genetic sequence A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession

1782-399: The elapsed time since two genes first diverged (that is, the coalescence time), assumes that the effects of mutation and selection are constant across sequence lineages. Therefore, it does not account for possible differences among organisms or species in the rates of DNA repair or the possible functional conservation of specific regions in a sequence. (In the case of nucleotide sequences,

1836-572: The local market in Guangdong , China, found a strain of SARS coronavirus could be isolated from masked palm civets ( Paguma sp.), but the animals did not always show clinical signs. The preliminary conclusion was the SARS virus crossed the species barrier from palm civet to humans, and more than 10,000 masked palm civets were killed in Guangdong Province. The virus was also later found in raccoon dogs ( Nyctereuteus sp.), ferret badgers ( Melogale spp.), and domestic cats. In 2004, scientists from

1890-554: The lungs. The virus enters the host cell by binding to angiotensin-converting enzyme 2 . It infects humans , bats , and palm civets . The SARS-CoV-1 outbreak was largely brought under control by simple public health measures. Testing people with symptoms (fever and respiratory problems), isolating and quarantining suspected cases, and restricting travel all had an effect. SARS-CoV-1 was most transmissible when patients were sick, so its spread could be effectively suppressed by isolating patients with symptoms. On April 16, 2003, following

1944-400: The mice which demonstrated how zoonosis might occur in evolution. Phylogenetic analysis of these viruses indicated a high probability that SARS coronavirus originated in bats and spread to humans either directly or through animals held in Chinese markets. The bats did not show any visible signs of disease, but are the likely natural reservoirs of SARS-like coronaviruses. Bats are likely to be

1998-467: The molecular clock hypothesis in its most basic form also discounts the difference in acceptance rates between silent mutations that do not alter the meaning of a given codon and other mutations that result in a different amino acid being incorporated into the protein.) More statistically accurate methods allow the evolutionary rate on each branch of the phylogenetic tree to vary, thus producing better estimates of coalescence times for genes. Frequently

2052-510: The natural reservoir, that is, the host that harbored the pathogen but that does not show ill effects and serves as a source of infection. No direct progenitor of SARS-CoV was found in bat populations, but WIV16 was found in a cave in Xiyang Yi Ethnic Township , Yunnan, China between 2013 and 2016, and has a 96% genetically similar virus strain. The hypothesis that SARS-CoV-1 emerged through recombinations of bat SARSr-CoVs in

2106-408: The nucleic acid chain has been formed. In DNA, the most common modified base is 5-methylcytidine (m5C). In RNA, there are many modified bases, including pseudouridine (Ψ), dihydrouridine (D), inosine (I), ribothymidine (rT) and 7-methylguanosine (m7G). Hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination (replacement of

2160-885: The outbreak of SARS in Asia and secondary cases elsewhere in the world, the World Health Organization (WHO) issued a press release stating that the coronavirus identified by a number of laboratories was the official cause of SARS. The Centers for Disease Control and Prevention (CDC) in the United States and the National Microbiology Laboratory (NML) in Canada identified the SARS-CoV-1 genome in April 2003. Scientists at Erasmus University in Rotterdam ,

2214-666: The primary structure encodes motifs that are of functional importance. Some examples of sequence motifs are: the C/D and H/ACA boxes of snoRNAs , Sm binding site found in spliceosomal RNAs such as U1 , U2 , U4 , U5 , U6 , U12 and U3 , the Shine-Dalgarno sequence , the Kozak consensus sequence and the RNA polymerase III terminator . In bioinformatics , a sequence entropy, also known as sequence complexity or information profile,

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2268-458: The propagation of which started the COVID-19 pandemic . Severe acute respiratory syndrome (SARS) is the disease caused by SARS-CoV-1. It causes an often severe illness and is marked initially by systemic symptoms of muscle pain , headache , and fever , followed in 2–14 days by the onset of respiratory symptoms, mainly cough, dyspnea , and pneumonia . Another common finding in SARS patients

2322-408: The protein strand. Since nucleic acids can bind to molecules with complementary sequences, there is a distinction between " sense " sequences which code for proteins, and the complementary "antisense" sequence, which is by itself nonfunctional, but can bind to the sense strand. DNA sequencing is the process of determining the nucleotide sequence of a given DNA fragment. The sequence of the DNA of

2376-451: The replication strategy typical of the coronavirus subfamily. The primary human receptor of the virus is angiotensin-converting enzyme 2 (ACE2) and hemaglutinin (HE), first identified in 2003. Human SARS-CoV-1 appears to have had a complex history of recombination between ancestral coronaviruses that were hosted in several different animal groups. In order for recombination to happen at least two SARS-CoV-1 genomes must be present in

2430-478: The reverse order. For example, the complementary sequence to TTAC is GTAA. If one strand of the double-stranded DNA is considered the sense strand, then the other strand, considered the antisense strand, will have the complementary sequence to the sense strand. While A, T, C, and G represent a particular nucleotide at a position, there are also letters that represent ambiguity which are used when more than one kind of nucleotide could occur at that position. The rules of

2484-447: The same area in late 2003 and early 2004 are different, indicating separate species-crossing events. The phylogeny of the outbreak strains shows that the southwestern provinces including Yunnan, Guizhou and Guangxi compare to the human SARS-CoV-1 better than those of the other provinces, but the viruses' evolution is a product of the host interaction and particularity. In late May 2003, studies from samples of wild animals sold as food in

2538-404: The same cell in nature. These phenomena are known respectively as antigenic drift and antigenic shift . Microbial strains can also be differentiated by their genetic makeup using metagenomic methods to maximize resolution within species. This has become a valuable tool to analyze the microbiome . Scientists have modified strains of viruses in order to study their behavior, as in the case of

2592-399: The same host cell. Recombination may occur during genome replication when the RNA polymerase switches from one template to another (copy choice recombination). SARS-CoV-1 is one of seven known coronaviruses to infect humans. The other six are: Strain (biology) It has been said that "there is no universally accepted definition for the terms 'strain', ' variant ', and 'isolate' in

2646-421: The sequences. If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as insertion or deletion mutations ( indels ) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as

2700-408: The sugar is one of a set of nucleobases . The nucleobases are important in base pairing of strands to form higher-level secondary and tertiary structures such as the famed double helix . The possible letters are A , C , G , and T , representing the four nucleotide bases of a DNA strand – adenine , cytosine , guanine , thymine – covalently linked to a phosphodiester backbone. In

2754-427: The term refers to the collective descendants produced from a common ancestor that share a uniform morphological or physiological character. A strain is a designated group of offspring that are either descended from a modified plant (produced by conventional breeding or by biotechnological means), or which result from genetic mutation. As an example, some rice strains are made by inserting new genetic material into

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2808-424: The tools of bioinformatics to attempt to determine its function. The DNA in an organism's genome can be analyzed to diagnose vulnerabilities to inherited diseases , and can also be used to determine a child's paternity (genetic father) or a person's ancestry . Normally, every person carries two variations of every gene , one inherited from their mother, the other inherited from their father. The human genome

2862-433: The typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the 5' to 3' direction. With regards to transcription , a sequence is on the coding strand if it has the same order as the transcribed RNA. One sequence can be complementary to another sequence, meaning that they have the base on each position in the complementary (i.e., A to T, C to G) and in

2916-490: The virology community, and most virologists simply copy the usage of terms from others". A strain is a genetic variant or subtype of a microorganism (e.g., a virus , bacterium or fungus ). For example, a "flu strain" is a certain biological form of the influenza or "flu" virus. These flu strains are characterized by their differing isoforms of surface proteins. New viral strains can be created due to mutation or swapping of genetic components when two or more viruses infect

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