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Jul 19, 2020, 01:17 PM
#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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Aug 10, 2020, 08:51 AM
#142
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Aug 10, 2020, 09:52 AM
#143
Yus.
(As stolen from TZUK).
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Aug 10, 2020, 10:21 AM
#144
^^^ Trumped.
It beggars belief.
Some people have opinions - The rest of us have taste.
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Sep 1, 2020, 01:43 AM
#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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Sep 1, 2020, 01:59 PM
#146
Originally Posted by
crownpuller
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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Sep 20, 2020, 12:43 PM
#147
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Dec 13, 2020, 10:52 AM
#148
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Dec 13, 2020, 01:57 PM
#149
Member
Originally Posted by
Matt
Is this why the pharma companies were able to fast-trak a vaccine in record time?
.
.
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Retired from Fire/Rescue January 2019 with 30 years on the job
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Mar 30, 2021, 12:42 AM
#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