19 Corvids (Canada Jay) - Corona Virus Structure

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Title: 19 Corvids (Canada Jay) - Corona Virus Structure
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My Notes
--------
May 6, 2020

In this workbook, I model the structure of the corona virus that causes Covid-19, and compare it with the structure of other corona visuses and viruses in general.

I good way to think about the structure is in terms of the life-cycle.
The whole virus enters a cell, breaks into parts, which cause various things to happen within the cell, which cause production of new parts, which assemble into a new virus that exits the cell. Repeat ...
See [ref 12], for example.

May 7
Start a Xholon model

References
----------
(1) https://gist.github.com/kenwebb/83a84a36531417b7fcad8e078deb9daa
    19 Corvids (Raven) - XML can be Virus-like

(2) https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2
    This article is about the virus strain that causes COVID-19.
    For the strain that causes SARS, see Severe acute respiratory syndrome coronavirus.
    For the species to which both strains belong, see Severe acute respiratory syndrome-related coronavirus.

(3) https://en.wikipedia.org/wiki/Positive-sense_single-stranded_RNA_virus

(4) https://en.wikipedia.org/wiki/Coronavirus

(5) https://en.wikipedia.org/wiki/Virus
    A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. 
    When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or virions
    Viral populations do not grow through cell division, because they are acellular. Instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell.
    Their life cycle differs greatly between species, but there are six basic stages in their life cycle:
    1. Attachment
    2. Penetration
    3. Uncoating
    4. Replication
    5. Assembly
    6. Release

(6) https://en.wikipedia.org/wiki/Viral_replication
    Viruses multiply only in living cells. The host cell must provide the energy and synthetic machinery and the low molecular-weight precursors for the synthesis of viral proteins and nucleic acids.

(7) https://en.wikipedia.org/wiki/Coronavirus_disease_2019
    Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

(8) https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome-related_coronavirus 
    This article is about a species of coronavirus comprising multiple strains.
    For the strain that causes SARS, see Severe acute respiratory syndrome coronavirus.
    For the strain that causes COVID-19, see Severe acute respiratory syndrome coronavirus 2.
    
    There are hundreds of other strains of SARS-CoV, all of which are only known to infect non-human species:
    
    Genome
    The SARS-related coronavirus is an enveloped, positive-sense, single-stranded RNA virus.
    
    Morphology
    The morphology of the SARS-related coronavirus is characteristic of the coronavirus family as a whole. The viruses are large pleomorphic spherical particles with bulbous surface projections that form a corona around the particles in electron micrographs. The size of the virus particles is in the 80–90 nm range. The envelope of the virus in electron micrographs appears as a distinct pair of electron dense shells.

    The viral envelope consists of a lipid bilayer where the membrane (M), envelope (E) and spike (S) proteins are anchored. The spike proteins provide the virus with its bulbous surface projections. The spike protein's interaction with its complement host cell receptor is central in determining the tissue tropism, infectivity, and species range of the virus.

    Inside the envelope, there is the nucleocapsid, which is formed from multiple copies of the nucleocapsid (N) protein, which are bound to the positive-sense single-stranded (~30 kb) RNA genome in a continuous beads-on-a-string type conformation. The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host.
    
    Life cycle
    SARS-related coronavirus follows the replication strategy typical of all coronaviruses.
    KSW the subsequent sub-sections describe the life cycle
    KSW see also the related diagram

(9) https://commons.wikimedia.org/wiki/File:Coronavirus_virion_structure.svg
    153kb

(10) https://viralzone.expasy.org/
(11) https://viralzone.expasy.org/9056
    lots of technical data
(12) https://viralzone.expasy.org/9096
    Coronavirus life-cycle
    shows how many of the parts are created and then assembled

(13) https://coronavirus.jhu.edu/

(14) https://coronavirus.jhu.edu/covid-19-basics/understanding-covid-19
    COVID-19 BASICS
    Understanding the COVID-19 Pandemic
    Insights from Johns Hopkins University Experts

(15) https://www.sib.swiss/about-sib/news/10660-sib-resources-supporting-sars-cov-2-research
    SIB resources supporting SARS-CoV-2 research.
    Swiss Institute of Bioinformatics

()

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