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Thread: Useful coronavirus info

  1. #141
    Ok, I wasted a fair chunk of my morning on this:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521053/

    So, three closely related betacoronavirus, one in cattle, one in dogs and one in us. So far so what?

    But what about this:

    https://virological.org/t/remarkable...2-in-china/399

    However, bizarrely, no one seems to have followed this up.


    Now at this point I feely admit move I'm going to move well, well beyond my competence.

    However the amino acid sequence for the Sars Cov-2 nucleocapsid protein is:

    MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQG LPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRI RGGDGKMK DLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPA NNAAIVLQ LPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARM AGNGGDAA LALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAY NVTQAFGR RGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTP SGTWLTYT GAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQ RQKKQQTV
    TLLPAADLDDFSKQLQQSMSSADSTQA#

    source: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512



    The sequence for the HCoV-OC43 nucleocapsid protein is:

    MSFTPGKQSSSRASSGNRSGNGILKWADQSDQFRNVQTRGRRAQ
    PKQTATSQQPSGGNVVPYYSWFSGITQFQKGKEFEFVEGQGVPIAPGVPA TEAKGYWY RHNRRSFKTADGNQRQLLPRWYFYYLGTGPHAKDQYGTDIDGVYWVASNQ ADVNTPAD IVDRDPSSDEAIPTRFPPGTVLPQGYYIEGSGRSAPNSRSTSRTSSRASS AGSRSRAN SGNRTPTSGVTPDMADQIASLVLAKLGKDATKPQQVTKHTAKEVRQKILN KPRQKRSP NKQCTVQQCFGKRGPNQNFGGGEMLKLGTSDPQFPILAELAPTAGAFFFG SRLELAKV QNLSGNPDEPQKDVYELRYNGAIRFDSTLSGFETIMKVLNENLNAYQQQD GMMNMSPK PQRQRGHKNGQGENDNISVAVPKSRVQQNKSRELTAEDISLLKKMDEPYT EDTSEI

    source https://www.ncbi.nlm.nih.gov/nuccore/NC_006213


    Running that through a string comparison tool:

    https://www.tools4noobs.com/online_tools/string_similarity/

    gives a 49.6% match with SARS COV-2.


    I've used this really simple string comparison tool, because I understand it.
    however, there's a tool designed for the job in hand which could do a better job:

    https://web.expasy.org/cgi-bin/sim/sim.pl?prot

    but I don't really understand it or the variables available, so I'll stick with the crayons.


    The sequence for the CRCoV (dogs) nucleocapsid protein is:

    MSFTPGKQSSSRASSGNRSGNGILKWADQSDQSRNVQTRGRRAQ PKQTATSQQPSGGNVVPYYSWFSGITQFQKGRDFEFAEGQGVPIAPGVPA TEAKGYWY RHNRRSFKTADGNQRQLLPRWYFYYLGTGPHAKDQYGTDIDGFFWVASNQ ADVNTPAD IPDRDPSSDEAIPTRFPPGTVLPQGYYIEGSGRSAPNSRSTSRASSRASS AGSRSRAN SGNRTPTSGVTPDMADQIASLVLAKLGKDATKPQQVTKQTAKEIRQKILN KPRQKRSP NKQCTVQQCFGKRGPNQNFGGGEMLKLGTSDPQFPILAELAPTAGAFFFG SRLELAKV QNLSGNLDEPQKDVYELRYNGAIRFDSTLSGFETIMKVLNENLNAYQQQD GMMNMSPK PQRQRGQKNGQGENDNISVAAPKSRVQQNKSRELTAEDISLLKKMDEPYT EDTSE

    Running that through the string comparison tool, that gives a 55.03% match with SARS COV-2.

    Source https://www.ncbi.nlm.nih.gov/nuccore/JX860640

    and BCOV (cattle)


    MSFTPGKQSSSRASSGNRSGNGILKWADQSDQSRNVQTRGRRAQ PKQTATSQQPSGGNVVPYYSWFSGITQFQKGKEFEFAEGQGVPIAPGVPA TEAKGYWY RHNRRSFKTADGNQRQLLPRWYFYYLGTGPHAKDQYGTDIDGVYWVASNQ ADVNTPAD ILDRDPSSDEAIPTRFPPGTVLPQGYYIEGSGRSAPNSRSTSRASSRASS AGSRSRAN SGNRTPTSGVTPDMADQIASLVLAKLGKDAAKPQQVTKQTAKEIRQKILN KPRQKRSP NKQCTVQQCFGKRGPNQNFGGGEMLKLGTSDPQFPILAELAPTAGAFFFG SRLELAK
    QNLSGNLDEPQKDVYELRYNGAIRFDSTLSGFETIMKVLNENLNAYQQQD GTMNMSPK PQRQRGQKNGQGENDNISVAAPKSRVQQNKIRELTAEDISLLKKMDEPFT EDTSEI


    Source:

    https://www.ncbi.nlm.nih.gov/nuccore/NC_003045



    Running that through the string comparison tool, that gives a 56.51% match with SARS COV-2.


    Just for fun, the sequence for the SARS COV nucleocapsid protein is:

    MSDNGPQSNQRSAPRITFGGPTDSTDNNQNGGRNGARPKQRRPQ
    GLPNNTASWFTALTQHGKEELRFPRGQGVPINTNSGPDDQIGYYRRATRR VRGGDGKM
    KELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDHIGTRNP NNNAATVL
    QLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRGNSRNSTPGSSRGNSPAR MASGGGET
    ALALLLLDRLNQLESKVSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKQ YNVTQAFG
    RRGPEQTQGNFGDQDLIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVT PSGTWLTY
    HGAIKLDDKDPQFKDNVILLNKHIDAYKTFPPTEPKKDKKKKTDEAQPLP QRQKKQPT
    VTLLPAADMDDFSRQLQNSMSGASADSTQA
    NKQCTVQQCFGKRGPNQNFGGGEMLKLGTSDPQFPILAELAPTAGAFFFG SRLELAKV
    QNLSGNPDEPQKDVYELRYNGAIRFDSTLSGFETIMKVLNENLNAYQQQD GMMNMSPK
    PQRQRGHKNGQGENDNISVAVPKSRVQQNKSRELTAEDISLLKKMDEPYT EDTSEI

    is a 76.66% match


    However, what gets me excited isn't this, it's this: we now know that there are some animal coronaviruses
    that cause a T Cell immune response that targets the shell protein, rather than the spike protein of
    SARS COV 2. The paper that describes these doesn't specify, but these look like excellent candidates.
    However, we also have a slightly mysterious, and at first blush, not hugely high quality, paper that suggests that
    prior infection with HCoV-OC43 provides protection against SARS COV-2.

    That makes the fact that the coding for the shell of HCoV-OC43 and CRCoV is a 97.84 match look like quite an unexpected
    result. (BCOV is 96.38)

    So we've got at least two viruses that share almost identical coding, one in dogs, one in humans and both have a little empirical
    evidence that they might just provide a degree of immune response against coronavirus. That's pretty cool.

    To be quite clear, this is a whole pile of correlations stacked together. However, it's an interesting pattern which I have dug
    out of the data largely for my own amusement.

    However, I do think it's a bit exciting as it's quite a pattern. Let's see how things develop...

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  3. #142
    Another Member crownpuller's Avatar
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    For our protection and to help contain the further spread of the virus; social distancing measures have been put in place to guide us.
    One of these measures is clearly marked spacing for queues.

    The following are from my standing in line for Costa...

    This is the lady who was next in line behind me:

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    She was 'glued' to her smart phone and repeatedly side-stepped closer to me; to the point where I had to tell her to back off !

    This is the couple who were in front of me:

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    The guy exiting had to ask them to move; then they immediately returned to blocking the doorway after he had passed !

    I despair. Is it really that difficult ?!
    Some people have opinions - The rest of us have taste.

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  7. #144
    Another Member crownpuller's Avatar
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    ^^^ Trumped.
    It beggars belief.
    Some people have opinions - The rest of us have taste.

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  9. #145
    I heard reports of these prolonged symptoms, I think here's a good case recount: https://www.bbc.com/news/stories-53948028

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  11. #146
    Moderator gnuyork's Avatar
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    Quote Originally Posted by crownpuller View Post

    I despair. Is it really that difficult ?!
    Apparently it really is.

    Experiencing the same here, as well as the "masks for show" people, meaning wearing it around their chin or just covering their mouth only. One guy had a mask just covering his nose, but his mouth was exposed.

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  13. #148

  14. #149
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    Quote Originally Posted by Matt View Post
    Ok, I wasted a fair chunk of my morning on this:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521053/

    ..
    Is this why the pharma companies were able to fast-trak a vaccine in record time?
    .
    .
    .

    Retired from Fire/Rescue January 2019 with 30 years on the job

  15. #150
    I think it's worth posting here -- 'Stanford Scientists Reverse Engineer Moderna Vaccine, Post Code on Github': https://www.vice.com/en/article/7k9g...code-on-github

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