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<SX viewer='molstar'  load='' size='323' side='right' caption='Cryo-EM structure of a single spike that consists of 3 chains, colored green, brown and purple (PDB-ID [[6vsb]]).' scene='83/839266/Automatic_colors_occlusion/1'>
[[Image:Ezgif.com-video-to-gif 240px 65pc speed.gif|left|240px|thumb|<span style="font-size:100%">SARS-CoV-2 virus. The <span style="color:blue">spikes</span>, that adorn the <span style="color:red">'''virus surface'''</span>, impart a '''''corona''''' like appearance [http://www.drugtargetreview.com/news/57287/3d-visualisation-of-covid-19-surface-released-for-researchers (Fusion Animation)].</span>]]
<span style="font-size:100%">
A novel coronavirus SARS-CoV-2, detected in Wuhan, China in 2019, was found to cause severe respiratory illness named '''''COVID-19'''''<ref>[http://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it Naming the coronavirus disease (COVID-19) and the virus that causes it]</ref>.

Here is  <snapshot name='83/839292/Surface/1'>surface representation</snapshot>
Here is  <snapshot name='83/839266/Automatic_colors_occlusion/1'>cartoon represenation</snapshot>

A [http://youtu.be/hwVl_-lnoys '''''video'''''] (by [http://elarasystems.com Elara Systems)] shows how the virus [http://youtu.be/hwVl_-lnoys '''interacts with its human (host) cell'''], via its spikes (whose 3D structure was determined in the McLellan Lab<ref name="McLellan">PMID:32075877</ref>), thus permitting the viral genome to enter its host & begin infection.

Details of the '''3D structure & function''' of the key proteins & RNA inside the virus can be seen in the NY Times [http://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html '''''Bad News Wrapped in Protein: Inside the Coronavirus Genome'''''].
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== Potential treatments for COVID-19 ==
* [http://www.dropbox.com/s/tb5nvaq7f6o38kt/COVID-19%204.12.20.pdf?dl=0 '''COVID-19: What are our therapeutic options?'''] - Slides courtesy of [http://www.utsouthwestern.edu/labs/jain-mamta/  '''Prof. Mamta K. Jain, MD, MPH'''], [http://www.utsouthwestern.edu/ UT Southwestern Medical Center].

* '''Oxygen administration''' could be more important than pressurised air when treating the illness induced by SARS-CoV-2. Homology modeling & molecular docking suggests that SARS-CoV-2 reduces hemoglobin's capacity to carry oxygen, resulting in the respiratory syndrome <ref>COVID-19 Disease ORF8 and Surface Glycoprotein Inhibit Heme Metabolism by Binding to Porphyrin [http://chemrxiv.org/articles/COVID-19_Disease_ORF8_and_Surface_Glycoprotein_Inhibit_Heme_Metabolism_by_Binding_to_Porphyrin/11938173/6]</ref>.

* [http://economictimes.indiatimes.com/news/international/world-news/oxford-university-begins-enrolling-over-500-volunteers-for-coronavirus-vaccine-trial/articleshow/74864754.cms?utm_source=contentofinterest&utm_medium=text&utm_campaign=cppst Oxford Univ begins enrolling over 500 volunteers for a '''coronavirus vaccine trial'''], additional information at [http://www.jenner.ac.uk '''The Jenner Inst'''].

* An int'l group of scientists (UK, Israel & USA) are trying to combat COVID-19 via a massive crystal-based fragment screen. They determined 3D structures of [http://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem/Downloads.html over '''90 fragments''' with '''66 in the active site'''].  Details  are available [http://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html at the '''Diamond Light Source''']. Contributions are welcome in many different forms [http://covid.postera.ai/covid '''PostEra''']. 

* 31-Mar-2020 ''NY Times''  [http://www.nytimes.com/2020/03/31/health/cdc-masks-coronavirus.html C.D.C. Weighs Advising Everyone to Wear a Mask].

* 27-Mar-2020 ''Science'' - Not wearing masks to protect against coronavirus is a '''big mistake''', Dr. George Gao, Director General of the Chinese CDC says in [http://www.sciencemag.org/news/2020/03/not-wearing-masks-protect-against-coronavirus-big-mistake-top-chinese-scientist-says ''Science''].  

* 23-Mar-2020 A USA, French & UK study '''identified 69 drugs to test against the coronavirus'''<ref> Gordon, et al. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing: bioRxiv (online)  2020 [http://doi.org/10.1101/2020.03.22.002386 http://doi.org/10.1101/2020.03.22.002386]</ref>. As reported in the [http://www.nytimes.com/2020/03/22/science/coronavirus-drugs-chloroquine.html?action=click&module=Top%20Stories&pgtype=Homepage ''NY Times''].

* 20-Mar-2020 - Analysis by Abby Olena  in ''The Scientist'' on [http://www.the-scientist.com/news-opinion/remdesivir-works-great-against-coronaviruses-in-the-lab-67298?utm_campaign=TS_OTC_2020&utm_source=hs_email&utm_medium=email&utm_content=85306117&_hsenc=p2ANqtz--t49MmUS_nL_8CL8wosEbymFBDq_4smPhI1pSJmSKWA0bURCpjoMb1eYxIVv30SDzsuiNd9PRGTPC30x-gelTGjK-9r9wPWaMjEZIqjaz5Y0tgW5w&_hsmi=85306117 '''Remdesivir Works Against Coronaviruses in the Lab''']

== Videos helping to explain COVID-19 ==
<html5media height="225" width="400">http://www.youtube.com/watch?v=HhNo_IOPOtU</html5media><br>
The Czech Republic took the uncommon step of making '''wearing of masks mandatory''' in public spaces, prompting a [http://www.sciencemag.org/news/2020/03/would-everyone-wearing-face-masks-help-us-slow-pandemic '''grassroots effort to make masks'''], with '''wonderful''' results<br>.
<br>
<html5media height="160" width="400">http://w.soundcloud.com/player/?url=http%3A//api.soundcloud.com/tracks/775538998&color=%23ff5500&auto_play=false&hide_related=false&show_comments=true&show_user=true&show_reposts=false&show_teaser=true</html5media><br>
Scientists have turned the coronavirus spike protein structure into '''music(!!)''', as reported in [http://www.sciencemag.org/news/2020/04/scientists-have-turned-structure-coronavirus-music?fbclid=IwAR0-kIT3mVjRHe18Y7wf3KrqaBIvIk9JGG9KuJsbA0zN6gsov0Np0p_jO9A# ''Science''] by [http://soundcloud.com/user-275864738/viral-counterpoint-of-the-coronavirus-spike-protein-2019-ncov Soundcloud].<br>
<br>
<html5media height="225" width="400">http://www.youtube.com/watch?v=hm7BmIJrLZE</html5media><br>
Japan researchers show how '''Coronavirus spreads through micro droplets'''. These tiny droplets containing the virus can stay in the air for extended periods.<br>
<br>
<html5media height="225" width="400">http://www.youtube.com/watch?v=qzARpgx8cvE</html5media><br>
Speaking face-to-face is exchanging saliva, so '''stop speaking face-to-face and stay healthy''' by [http://stoptheviruscovid19.github.io '''stoptheviruscovid'''].<br>
<br>
<html5media height="225" width="400">http://www.youtube.com/watch?v=Kas0tIxDvrg</html5media><br>
Modeling an epidemic (6-Mar-2020) '''''We're not ready for the next epidemic''''' by [http://3b1b.co/covid-thanks '''3blue1brown'''].<br>
<br>
<html5media  height="225" width="400">http://www.youtube.com/watch?v=s2EVlqql_f8</html5media><br>
'''Fighting Coronavirus with Soap''' by [http://pdb101.rcsb.org/ '''PDB-101'''].<br> 
<br>
<html5media  height="225" width="400">http://www.youtube.com/watch?v=I0TmBsHaGmI</html5media><br>
'''Animation''' of '''3D structure/function of Coronavirus-CoV-2 proteins''' by [http://www.biolution.net '''biolution GmBH'''].<br>
<br>
<html5media height="225" width="400">http://www.youtube.com/watch?v=I-Yd-_XIWJg</html5media><br>
'''COVID-19 outbreak shown via 3D animation (11-Feb 11-2020)''' by [http://www.scientificanimations.com '''Sci Animations'''].<br>
<br>
<html5media height="225" width="400">http://www.youtube.com/watch?v=6Af6b_wyiwI</html5media><br>
'''Bill Gates Ted Talk (3-Apr-2015) ''We're not ready for the next epidemic''''' by [http://www.ted.com/talks '''Ted Talks'''].
<br>
<html5media height="225" width="400">http://www.youtube.com/watch?v=uSDC5L7qYUc</html5media><br>
'''George W. Bush''' urged us to '''prepare for future pandemics in 2005''', at the NIH.<br>
<br>
<html5media height="225" width="400">http://www.youtube.com/watch?v=B00tJnbktVo&feature=youtu.be&t=210</html5media><br>
'''Jürgen Bosch Presentation (31-Mar-2020) ''Coronavirus: How it Ticks and What we are Doing to Stop it''''' by [http://www.linkedin.com/in/jubosch '''Jürgen Bosch'''].


== Useful sites on COVID-19 ==
* [http://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.13784 Coronavirus SARS-CoV-2: '''Filtering fact from fiction''' in the infodemic] Q&A with virologist [http://www.imls.uzh.ch/en/research/Greber.html Prof. Urs Greber] by Daniela Ruffell in ''FEBS Lett''<ref>PMID:32246722</ref>.

* [http://deepmind.com/research/open-source/computational-predictions-of-protein-structures-associated-with-COVID-19 Computational predictions of 3D structures of COVID-19 proteins] based on the [http://deepmind.com/blog/article/AlphaFold-Using-AI-for-scientific-discovery AI AlphaFold system]. Coordinates of the 3D structures can be [http://storage.googleapis.com/deepmind-com-v3-datasets/alphafold-covid19/structures_4_3_2020.zip '''download'''] as a '''zip''' file.

* Up to date statistics on [http://www.worldometers.info/coronavirus/coronavirus-cases/ Coronavirus cases world-wide at worldometer]

* A summary of key findings about [http://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html COVID-19] can be found at [http://www.cdc.gov/ the '''CDC'''].

* '''Coronavirus Evolved Naturally''', and ‘Is '''Not''' a Laboratory Construct,’  in a study in Nature Med by Anderson and colleagues <ref>Andersen, et al. The proximal origin of SARS-CoV-2: Nature Med (in press) 2020 [http://dx.doi.org/10.1038/s41591-020-0820-9 http://dx.doi.org/10.1038/s41591-020-0820-9]]</ref>.

* '''Scientists are endeavoring to find antivirals specific to the virus'''. Several drugs such as chloroquine, arbidol, remdesivir & favipiravir are undergoing trials to test their efficacy & safety in the treatment of COVID-19 in China, with some promising results.<ref>PMID:32147628</ref>.

* A computer game, developed at the [http://www.ipd.uw.edu Inst for Protein Design] (Univ Washington), is being used to try to find new lead compounds that might become drugs to treat COVID-19.
<html5media height="225" width="400" >http://www.youtube.com/watch?v=gGvlNo3nMfw</html5media>

== SARS-CoV-2 virus proteins ==
The genome of the SARS-CoV-2 virus codes for 28 proteins:
Out of those, 19 have already been characterized structurally.

* [[SARS-CoV-2 Coronavirus Main Protease| Main protease]]: it is a cysteine protease that is essential for the viral life cycle.


== 3D structural studies on SARS-CoV-2 virus==

* A team of UK & Israeli scientists determined the 3D structures of [http://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem/Downloads.html '''over 90 fragments, 66 of which are in the active site'']. All the experimental details and results are available [http://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html '''online at the Diamond Light Source'''].

* A team of Chinese scientists determined, by Cryo-EM, the''' coronavirus spike receptor-binding domain complexed with its receptor ACE2 PDB-ID''' [http://www.rcsb.org/structure/6LZG 6LZG]. (To be published).

* A team of US and Chinese scientists determined the crystal structure of '''2019-nCoV spike receptor-binding domain bound with ACE2''' [http://www.rcsb.org/structure/6M0J 6M0J] (To be published).

* A team of US scientists determined, by Cryo-EM, the '''structure of the SARS-CoV-2 spike glycoprotein (open & closed states)''' <ref>PMID:32155444</ref>, PDB-ID [http://www.rcsb.org/structure/6VXX 6VXX] & [http://www.rcsb.org/structure/6VYB 6VYB]

* Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022 [http://www.rcsb.org/structure/6W41 6W41] (To be published).

* Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2 [http://www.rcsb.org/structure/6W61 6W61] (To be published).

* Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in complex with AMP [http://www.rcsb.org/structure/6W6Y 6W6Y] (To be published).

* Structure of NSP10 - NSP16 Complex from SARS-CoV-2 [http://www.rcsb.org/structure/6W75 6W75] (To be published).

* Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain [http://www.rcsb.org/structure/6M3M 6M3M] (To be published).

* Crystal structure of Nsp9 RNA binding protein of SARS CoV-2 [http://www.rcsb.org/structure/6W4B 6W4B] (To be published).

* Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2 [http://www.rcsb.org/structure/6W4H 6W4H]  (To be published).

* Cryo-EM structure of the 2019-nCoV RBD/ACE2-B0AT1 complex<ref>PMID:32132184</ref> [http://www.rcsb.org/structure/6M17 6M17].  

* Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2 [http://www.rcsb.org/structure/6VYO 6VYO] (To be published).

* Crystal structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate [http://www.rcsb.org/structure/6W01 6W01] (To be published).

* Crystal structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose [http://www.rcsb.org/structure/6W02 6W02] (To be published).

* Crystal structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2 [http://www.rcsb.org/structure/6VW1 6VW1] (To be published).

* Crystal structure of NSP15 Endoribonuclease from SARS CoV-2 [http://www.rcsb.org/structure/6VWW 6VWW] (To be published).

* Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 [http://www.rcsb.org/structure/6VXS 6VXS] (To be published).

* Crystal structure of the 2019-nCoV HR2 Domain [http://www.rcsb.org/structure/6LVN 6LVN] (To be published).

* Crystal structure of post fusion core of 2019-nCoV S2 subunit [http://www.rcsb.org/structure/6LXT 6LXT] (To be published).

* Crystal structure of '''SARS-CoV-2 main protease''' provides a basis for design of improved α-ketoamide inhibitors, from the Hilgenfeld lab<ref>PMID:32198291</ref>, Apo Struture: PDB-ID [http://www.rcsb.org/structure/6y2e 6Y2E], and complexes with inhibitors: PDB-ID [http://www.rcsb.org/structure/6y2f  6Y2F] and [http://www.rcsb.org/structure/6y2g  6Y2G].

* 3D Structure of '''RNA-dependent RNA polymerase from COVID-19''', a '''major antiviral drug target''' from the Rao lab in Beijing<ref> Gao, et al. Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target: bioRxiv (online) 2020 [http://doi.org/10.1101/2020.03.16.993386 http://doi.org/10.1101/2020.03.16.993386]</ref>.

* Crystal structure of the '''Mpro from COVID-19''' and '''discovery of inhibitors''' in a study by scientists from Shanghai & Beijing <ref> Jin, et al. Structure of Mpro from COVID-19 virus and discovery of its inhibitors: bioRxiv (online) 2020 [http://doi.org/10.1101/2020.02.26.964882 http://doi.org/10.1101/2020.02.26.964882]</ref>, PDB-ID [[2h2z]].

* Crystal structure of '''Nsp15 endoribonuclease NendoU from SARS-CoV-2''' in a study by scientists from USA<ref> Kim, et al. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2: bioRxiv (online) 2020 [http://doi.org/10.1101/2020.03.02.968388 http://doi.org/10.1101/2020.03.02.968388]</ref>, PDB-ID [[6w01]].

* A study by Zhou & colleagues on the structural basis for the '''recognition of the SARS-CoV-2 (COVID-19) by full-length human ACE2''' gives insights to the molecular basis for coronavirus recognition and infection<ref>PMID:32132184</ref>.

* '''The CoV spike (S) glycoprotein is a key target for vaccines, therapeutic antibodies, and diagnostics'''. A study by McLellan and colleagues in "Science" on the Cryo-EM structure of the COVID-19 spike protein. This structure should greatly aid in the rapid development and evaluation of medical countermeasures  to address the ongoing public health crisis<ref name="McLellan" />, PDB-ID [[6vsb]].

* [http://github.com/thorn-lab/coronavirus_structural_task_force Public resource for the structures from beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2]




</SX>
== References ==
<references/>
[[Category: Coronavirus]]
[[Category: Covid-19]]