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SARS-CoV-2 Gamma Variant
The Gamma variant (P.1) was one of the variants of SARS-CoV-2, the virus that causes COVID-19. This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid substitutions, ten of which in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T. It was first detected by the National Institute of Infectious Diseases (NIID) of Japan, on 6 January 2021 in four people who had arrived in Tokyo having visited Amazonas, Brazil, four days earlier. It was subsequently declared to be in circulation in Brazil. Under the simplified naming scheme proposed by the World Health Organization, P.1 was labeled Gamma variant, and was considered a variant of concern until March 2022, when it was largely displaced by the delta and omicron variants. Gamma caused widespread infection in early 2021 in the city of Manaus, the capital of Amazonas, although the city had already experienced widespread infection in May 2020, with a study i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Public Health England
Public Health England (PHE) was an executive agency of the Department of Health and Social Care in England which began operating on 1 April 2013 to protect and improve health and wellbeing and reduce health inequalities. Its formation came as a result of the reorganisation of the National Health Service (England), National Health Service (NHS) in England outlined in the Health and Social Care Act 2012. It took on the role of the Health Protection Agency, the National Treatment Agency for Substance Misuse and a number of other health bodies. It was an executive agency of the Department of Health and Social Care, and a distinct delivery organisation with operational autonomy. On 29 March 2021, the Government of the United Kingdom, UK Government announced that PHE would be disbanded and that its public health functions would be transferred, in proposals to reform public health structures. From 1 October 2021, PHE's health protection functions were formally transferred into the UK H ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Manaus
Manaus () is the List of capitals of subdivisions of Brazil, capital and largest city of the States of Brazil, Brazilian state of Amazonas (Brazilian state), Amazonas. It is the List of largest cities in Brazil, seventh-largest city in Brazil, with an estimated 2022 population of 2,063,689 distributed over a land area of about . Located at the east centre of the state, the city is the centre of the Greater Manaus, Manaus metropolitan area and the largest metropolitan area in the North Region, Brazil, North Region of Brazil by urban landmass. It is situated near Meeting of Waters, the confluence of the Rio Negro (Amazon), Negro and Amazon River, Amazon rivers. It is one of the two cities in the Amazon rainforest with a population of over 1 million people, alongside Belém. The city was founded in 1669 as the Fort of São José do Rio Negro. It was elevated to a town in 1832 with the name of "Manaus", an altered spelling of the indigenous Manaós peoples, and legally transformed in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
The New York Times
''The New York Times'' (''NYT'') is an American daily newspaper based in New York City. ''The New York Times'' covers domestic, national, and international news, and publishes opinion pieces, investigative reports, and reviews. As one of the longest-running newspapers in the United States, the ''Times'' serves as one of the country's Newspaper of record, newspapers of record. , ''The New York Times'' had 9.13 million total and 8.83 million online subscribers, both by significant margins the List of newspapers in the United States, highest numbers for any newspaper in the United States; the total also included 296,330 print subscribers, making the ''Times'' the second-largest newspaper by print circulation in the United States, following ''The Wall Street Journal'', also based in New York City. ''The New York Times'' is published by the New York Times Company; since 1896, the company has been chaired by the Ochs-Sulzberger family, whose current chairman and the paper's publ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Reading Frame
In molecular biology, reading frames are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames will be "open" (the "reading", however, refers to the RNA produced by transcription of the DNA and its subsequent interaction with the ribosome in translation). Such an open reading frame (ORF) may contain a start codon (usually AUG in terms of RNA) and by definition cannot extend beyond a stop codon (usually UAA, UAG or UGA in RNA). That start codon (not necessarily the first) indicates where translation may start. The transcription termination site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete protein would be made during translation. In eukaryotic genes with multiple exons, introns are removed and exons are then joined together after transcription to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Synonymous Substitution
A synonymous substitution (often called a ''silent'' substitution though they are not always silent) is the evolutionary substitution of one base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence is not modified. This is possible because the genetic code is " degenerate", meaning that some amino acids are coded for by more than one three-base-pair codon; since some of the codons for a given amino acid differ by just one base pair from others coding for the same amino acid, a mutation that replaces the "normal" base by one of the alternatives will result in incorporation of the same amino acid into the growing polypeptide chain when the gene is translated. Synonymous substitutions and mutations affecting noncoding DNA are often considered silent mutations; however, it is not always the case that the mutation is silent. Since there are 22 codes for 64 codons, roughly we should expect a random substitution to be synonymous with pro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coronavirus Nucleocapsid Protein
The nucleocapsid (N) protein is a protein that packages the positive-sense RNA genome of coronaviruses to form ribonucleoprotein structures enclosed within the viral capsid. The N protein is the most highly expressed of the four major coronavirus structural proteins. In addition to its interactions with RNA, N forms protein-protein interactions with the coronavirus membrane protein (M) during the process of viral assembly. N also has additional functions in manipulating the cell cycle of the host cell. The N protein is highly immunogenic and antibodies to N are found in patients recovered from SARS and COVID-19. History COVID-19 was first identified in January 2020. A patient in the state of Washington was given a diagnosis of coronavirus infection on 20 January. A group of scientists based at the Centers for Disease Control and Prevention in Atlanta, Georgia isolated the virus from nasopharyngeal and oropharyngeal swabs and were able to characterize the genomic seq ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ORF8
ORF8 is a gene that encodes a viral accessory protein, Betacoronavirus NS8 protein, in coronaviruses of the subgenus ''Sarbecovirus''. It is one of the least well conserved and most variable parts of the genome. In some viruses, a deletion splits the region into two smaller open reading frames, called ORF8a and ORF8b - a feature present in many SARS-CoV viral isolates from later in the SARS epidemic, as well as in some bat coronaviruses. For this reason the full-length gene and its protein are sometimes called ORF8ab. The full-length gene, exemplified in SARS-CoV-2, encodes a protein with an immunoglobulin domain of unknown function, possibly involving interactions with the host immune system. It is similar in structure to the ORF7a protein, suggesting it may have originated through gene duplication. Structure ORF8 in SARS-CoV-2 encodes a protein of 121 amino acid residues with an N-terminal signal sequence. ORF8 forms a dimer that is covalently linked by disulfide bon ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coronavirus Spike Protein
Spike (S) glycoprotein (sometimes also called spike protein, formerly known as E2) is the largest of the four major structural proteins found in coronaviruses. The spike protein assembles into trimers that form large structures, called spikes or peplomers, that project from the surface of the virion. The distinctive appearance of these spikes when visualized using negative stain transmission electron microscopy, "recalling the solar corona", gives the virus family its main name. The function of the spike glycoprotein is to mediate viral entry into the host cell by first interacting with molecules on the exterior cell surface and then fusing the viral and cellular membranes. Spike glycoprotein is a class I fusion protein that contains two regions, known as S1 and S2, responsible for these two functions. The S1 region contains the receptor-binding domain that binds to receptors on the cell surface. Coronaviruses use a very diverse range of receptors; HCoV-NL63, SARS-CoV ( ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ORF1ab
ORF1ab (also ORF1a/b) refers collectively to two open reading frames (ORFs), ORF1a and ORF1b, that are conserved in the genomes of nidoviruses, a group of viruses that includes coronaviruses. The genes express large polyproteins that undergo proteolysis to form several nonstructural proteins with various functions in the viral life cycle, including proteases and the components of the replicase-transcriptase complex (RTC). Together the two ORFs are sometimes referred to as the replicase gene. They are related by a programmed ribosomal frameshift that allows the ribosome to continue translating past the stop codon at the end of ORF1a, in a -1 reading frame. The resulting polyproteins are known as pp1a and pp1ab. Expression ORF1a is the first open reading frame at the 5' end of the genome. Together ORF1ab occupies about two thirds of the genome, with the remaining third at the 3' end encoding the structural proteins and accessory proteins. It is translated from a 5' capped ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GISAID
GISAID (), the Global Initiative on Sharing All Influenza Data, previously the Global Initiative on Sharing Avian Influenza Data, is a global science initiative established in 2008 to provide access to genomic data of influenza viruses. The database was expanded to include the coronavirus responsible for the COVID-19 pandemic, as well as other pathogens. The database has been described as "the world's largest repository of COVID-19 sequences". GISAID facilitates genomic epidemiology and real-time surveillance to monitor the emergence of new COVID-19 viral strains across the planet. Since its establishment as an alternative to sharing avian influenza data via conventional public-domain archives, GISAID has facilitated the exchange of outbreak genome data during the Influenza A virus subtype H1N1, H1N1 2009 swine flu pandemic, pandemic in 2009, the Influenza A virus subtype H7N9, H7N9 epidemic in 2013, the Coronavirus disease 2019, COVID-19 COVID-19 pandemic, pandemic and the 2022� ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Assignment Of Named Global Outbreak Lineages
The Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) is a software tool developed by Dr. Áine O'Toole and members of the Andrew Rambaut laboratory, with an associated web application developed by the Centre for Genomic Pathogen Surveillance in South Cambridgeshire. Its purpose is to implement a dynamic nomenclature (known as the Pango nomenclature) to classify Lineage (genetic), genetic lineages for SARS-CoV-2, the virus that causes COVID-19. A user with a full genome sequence of a sample of SARS-CoV-2 can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage (Pango lineage). Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage. Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage. This latter feature draws on publicly available ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SARS-CoV-2 Zeta Variant
Zeta variant, also known as lineage P.2, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in the state of Rio de Janeiro; it harbors the E484K mutation, but not the N501Y and K417T mutations. It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus. Under the simplified naming scheme proposed by the World Health Organization, P.2 was labeled "Zeta variant", and was considered a variant of interest (VOI), but not a variant of concern. A second wave was preceded in November 2020 by an increase in the prevalence of the Zeta variant among genetic sequences from São Paulo state, deposited into the GISAID database. As of July 2021, Zeta is no longer considered a variant of interest by the WHO. __TOC__ Mutations The Zeta genome has 3 amino acid mutations: E484K, D614G, and V1176F, all of which are found in the virus's spike protein code. According to the Centers for Disease Control and Prevention ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
