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  • gsgs
    replied
    > The 2013 Yunnan bat virus genome sequence {"RaTG13"} is now available
    > from GenBank with accession number MN996532 15.


    Last edited by gsgs; February 6, 2020, 04:14 AM.

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  • gsgs
    replied
    >An outbreak of respiratory illness caused by a novel coronavirus (nCoV-2019, NC_045512.2 40)
    >first identified in Wuhan China has resulted in over seven thousand confirmed cases.
    >So far, the nCoV-2019 has been reported to share 96% sequence identity to the RaTG13 genome
    >(EPI_ISL_402131). However, the S1 Receptor Binding Domain (RBD) of the nCoV-2019 genome
    >was noticeably divergent between the two at amino acid residues 350 to 550 – Figure 1A.
    >We aimed to identity coronaviruses related to nCoV-2019 in viral metagenomics datasets
    >available in the public domain. In a recently published dataset describing viral diversity in
    >Malayan pangolins (PRJNA573298 87) we used VirMAP 38 to reconstruct a coronavirus genome
    >(approximately 84% complete from samples SRR10168377 33 and SRR10168378 20) that
    >shared 97% amino acid identity across the same RBD segment – Figure 1B. This result
    i>ndicates a potential recombination event for nCoV-2019.
    >Edit -
    >From the coordinates shown in this preprint 121 (Figure 4), it looks like most of the differences between RaTG13 >and nCoV-2019 are restricted to loop 2 of the receptor binding motif (positions ~450-500).

    -----------------------------------------------------------------------------------
    > t seems unlikely that the receptor binding domain–and especially the receptor binding motif–would be nearly identical to one
    > found in pangolin through random chance.
    > incidentally, pangolins were sold in the market at the center of all of this 119.

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  • bertrand789
    replied
    Le virus de la peste porcine africaine me semble un virus d'une tique qui d?sormais se multiplie sur animaux ? sang chaud. Il pose des probl?mes car il impose des changements zoo techniques pas simple ? mettre en œuvre... On a expliqu? les pourquoi ou comment, de sa survenue ?

    S'il est envisage, que pour le coronavirus de chauve souris, pour par mutation il faudrait 65 ans pour arriver ? celui ?voqu?, je suis surpris qu'en 65 ans, rien n'ai ?t? vu. En tout cas, pour celui qui atteint les porcelets, donc Hku2, on a expliqu? les pourquoi ou comment de sa survenue ?

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  • Pathfinder
    replied
    Originally posted by bertrand789 View Post
    La m?me source a produit aussi ceci : https://www.nature.com/articles/s41586-018-0010-9
    Here's What Makes Coronavirus and African Swine Fever Different

    Jennifer Shike
    January 31, 2020 12:40 PM
    ...
    Saif says the best examples of CoV that infect the gut and cause diarrhea and deaths in pigs are porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus that first emerged in the U.S. in 2013-14. Both are still present in pigs.

    These viruses are members of two different groups of coronaviruses – alpha and delta CoV. Saif explains they are genetically distinct and do not cross-protect against one another. 2019-nCoV is part of a third distinct group of coronaviruses (beta CoV) and is genetically and antigenically distinct from these two swine coronaviruses, she adds.
    ...
    Could 2019-nCoV Impact the Swine Industry?

    There is no evidence from China that 2019-nCoV came from pigs or even that it could infect pigs, Saif says. In addition, there was no previous data that the related SARS CoV infected pigs.
    ...

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  • bertrand789
    replied
    L'un des probl?mes me semble que lors de la fermeture des proc?dures judiciaires ont du ?tre ouvertes. Je crains que certains ?levages ou fournisseurs d'animaux interdits ont alimente x lieux. En revanche, je suis s?r qu'ils cherchent et vu leurs comp?tences, ils vont trouver. Pour faire entrevoir de fa?on imag?e, le dossier march? global, en Chine, c'est comme celui de la vente d'arme au U. S. A. En tout cas entre le dossier peste porcine africaine et celui ci cela doit ?tre lourd... Ils doivent ?tre f?licit?s et non critiques, de mon point de vue... Mais apr?s la phase de crise, il faudra vraiment trai

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  • alert
    replied
    Originally posted by Vibrant62 View Post
    I have a question - how much reassortment / recombination goes on between CoV viruses of different clades. For example if 2019 nCoV meets MERS, is there a risk of reassortment?
    Yeah, I'd think that's one of the real dangers. Because MERS is much more severe, and you might get a resultant virus that spreads as easily as 2019 nCoV but has the severity of MERS.

    I'm also concerned about what happens if someone gets co-infected with 2019 nCoV and one of the four seasonal human coronaviruses, which seems more likely than a MERS co-infection.

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  • Pathfinder
    replied
    Mining coronavirus genomes for clues to the outbreak’s origins

    By Jon CohenJan. 31, 2020 , 6:20 PM
    ...
    “One of the biggest takeaway messages [from the viral sequences] is that there was a single introduction into humans and then human-to-human spread,” says Trevor Bedford, a bioinformatics specialist at the University of Washington and Fred Hutchinson Cancer Research Center.
    ...
    The longer a virus circulates in a human populations, the more time it has to develop mutations that differentiate strains in infected people, and given that the 2019-nCoV sequences analyzed to date differ from each other by seven nucleotides at most, this suggests it jumped into humans very recently. But it remains a mystery which animal spread the virus to humans.
    ...
    According to Xinhua, the state-run news agency, “environmental sampling” of the Wuhan seafood market has found evidence of 2019-nCoV. Of the 585 samples tested, 33 were positive for 2019-nCoV and all were in the huge market’s western portion, which is where wildlife were sold. “The positive tests from the wet market are hugely important,” says Edward Holmes, an evolutionary biologist at the University of Sydney ...
    ...
    Yet there have been no preprints or official scientific reports on the sampling, so it’s not clear which, if any, animals tested positive. “Until you consistently isolate the virus out of a single species, it’s really, really difficult to try and determine what the natural host is,” says Kristian Andersen, an evolutionary biologist at Scripps Research.
    ...
    It’s not just a “curious interest” to figure out what sparked the current outbreak, Daszak says. “If we don't find the origin, it could still be a raging infection at a farm somewhere, and once this outbreak dies, there could be a continued spillover that’s really hard to stop. But the jury is still out on what the real origins of this are.”

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  • bertrand789
    replied
    des lieux ou des porcs et des humains cohabitent en Chine cela me semble exister d'une part , d'autre part on ne sait rien de ce qui se passe sur les porcs sauvages chinois , donc les sangliers ...

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  • Vibrant62
    replied
    I have a question - how much reassortment / recombination goes on between CoV viruses of different clades. For example if 2019 nCoV meets MERS, is there a risk of reassortment?

    Leave a comment:


  • bertrand789
    replied
    La m?me source a produit aussi ceci : https://www.nature.com/articles/s41586-018-0010-9

    Leave a comment:


  • gsgs
    replied
    http://virological.org/t/ncov-2019-s...ic-dataset/362

    So far, the nCoV-2019 has been reported to share 96% sequence identity to the RaTG13
    genome (EPI_ISL_402131). However, the S1 Receptor Binding Domain (RBD) of the nCoV-2019
    genome was noticeably divergent between the two at amino acid residues 350 to 550 – Figure 1A.
    We aimed to identity coronaviruses related to nCoV-2019 in viral metagenomics datasets available
    in the public domain. In a recently published dataset describing viral diversity in
    Malayan pangolins (PRJNA573298 10) we used VirMAP 11 to reconstruct a coronavirus genome
    (approximately 84% complete from samples SRR10168377 2 and SRR10168378 1) that
    shared 97% amino acid identity across the same RBD segment – Figure 1B. This result
    indicates a potential recombination event for nCoV-2019.

    [these are amino-acids, but what about nucleotides ?
    I remember the amino-acid conservation in inner segments of flu-A in mallards]

    pangolin=Schuppentier , https://en.wikipedia.org/wiki/Pangolin

    Leave a comment:


  • gsgs
    replied
    https://flutrackers.com/forum/forum/...ations-cloning

    [after WIV1 in 2012]
    The sampling of this bat cave in Yunnan continued for another 5 years. From these samples,
    the research team isolated 3 live viruses in succession, and obtained the full-length genomic
    sequences of a total of 15 bat SARS-like coronaviruses. Surprisingly, the 15 strains contained
    all the genome components of the SARS virus.
    Hu Ben, an assistant researcher at the Wuhan Institute of Virology, Chinese Academy of Sciences:
    Shi Zhengli
    ...
    fuchsia line
    the highest similarity between SARS-like coronaviruses found in bat caves and their respective
    genes is above 97%,
    After 13 years of virus tracing, the origin of the SARS virus was finally found.

    [ one of those Yunnan cave viruses must have been RaTG13 , 96% similar to 2019-nCoV ]

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  • gsgs
    replied
    how are these pictures called ? Also 3dim ? I didn't first understand it
    and did the same in multi-pics, one per chart..
    It looks as if the mutation rate is just different in different areas
    I figured out that RatG13 is at GISAID
    can we email or pm seems that i can't pm or send visitor message
    You might apply some function to account for the mutationrates per region
    Isn't it likely that China has many more bat-sequences with
    multiple strains but only academics publish because it's good for their career
    I complete my genbank downloads ... still reorginising data with my old flu-tools

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  • JJackson
    replied
    This is a useful visualisation tool https://nextstrain.org/ncov

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  • JJackson
    replied
    This is interesting https://www.bilibili.com/read/cv4457676/ it is in Chinese but this worked for me https://translate.google.com/transla...2Fcv4457676%2F

    This is the first I have seen on lab tests with live nCoV virus.
    They look at two questions
    1] Is the ACE2 receptor, used by SARS, also used here. They used HeLa cells modified to display various ACE2 receptors from humans, bats, civets, pigs and mice - the virus grew in all but mice so mice are probably out as a lab animal unless a there is a linage with modified ACE2s.
    2] They also looked at serum treatments and both human and horse anti-sera worked well and could be a useful therapeutic at least as a stop gap measure.
    This graphic nicely illustrates just how far RaTG13 has wondered from the pack (it is rooted against nCoV2019) and helpfully provides a nucleotide and AA scale across the top. ZC45 seems to share a high homology across ORF1a but reverts to the pack for the Spike protein. I assume that ORF just stands for Open Reading frame but it seems odd that it is not given a designation based on a protein produced as they account for 2/3 of the genome.

    Click image for larger version  Name:	nCoV tree.JPG Views:	0 Size:	51.1 KB ID:	825460
    I can not find the paper I found RaTG13 was from 2013 but it definitely gave that as the date and stated the host as horse shoe bat. For RaTG13 to hold such a high % homology for so long makes me wonder if there is another host species in which this RBD configuration needs to be conserved and nCoV came from this source and RaTG13 is a reintroduction to bats and ZC45 is a recombination event. As is often the case in wild animal sampling there are just too few relevant sequences to be sure we have any real understanding of the viral genetic dynamics much of what we do have is due to post SARS investigation and fairly dated given the speed of viral evolution.
    Last edited by JJackson; April 29, 2020, 05:58 PM.

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