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Spike (S) glycoprotein (sometimes also called spike protein, [2] formerly known as E2 [3]) is the largest of the four major structural proteins found in coronaviruses. [4] The spike protein assembles into trimers that form large structures, called spikes or peplomers, [3] that project from the surface of the virion.
The coronavirus RNA genome has a 5′ methylated cap and a 3′ polyadenylated tail, which allows it to act like a messenger RNA and be directly translated by the host cell's ribosomes. The host ribosomes translate the initial overlapping open reading frames ORF1a and ORF1b of the virus genome into two large overlapping polyproteins, pp1a and ...
Throughout the COVID-19 pandemic, the genome of SARS-CoV-2 viruses has been sequenced many times, resulting in identification of thousands of distinct variants. In a World Health Organization analysis from July 2020, ORF1ab was the most frequently mutated gene, followed by the S gene encoding the spike protein .
For this reason the spike protein has been the focus of development for COVID-19 vaccines in response to the COVID-19 pandemic caused by the virus SARS-CoV-2. [11] [12] A subgenus of the betacoronaviruses, known as embecoviruses (not including SARS-like coronaviruses), have an additional shorter surface protein known as hemagglutinin esterase. [13]
Viruses that possess HEs include influenza C virus, toroviruses, and coronaviruses of the subgenus Embecovirus (which does not include SARS-like coronaviruses). HEs is a dimer transmembrane protein consisting of two monomers, each monomer is made of three domains. The three domains are: membrane fusion, esterase, and receptor binding domains.
SARS-CoV-2 is the seventh known coronavirus to infect people, after 229E, NL63, OC43, HKU1, MERS-CoV, and the original SARS-CoV. [105] Like the SARS-related coronavirus implicated in the 2003 SARS outbreak, SARS‑CoV‑2 is a member of the subgenus Sarbecovirus (beta-CoV lineage B). [106] [107] Coronaviruses undergo frequent recombination. [108]
M is a glycoprotein whose glycosylation varies according to coronavirus subgroup; N-linked glycosylation is typically found in the alpha and gamma groups while O-linked glycosylation is typically found in the beta group. [8] [9] There are some exceptions; for example, in SARS-CoV, a betacoronavirus, the M protein has one N-glycosylation site.
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