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Tweets and Retweets @ COVID-19 and AI: A Virtual Conference – Human-Centered Artificial Intelligence Institute, Stanford University, 4/1/2020, 9AM PST – 3:30PM PST @StanfordHAI  BY @pharma_BI and @AVIVA1950

COVID-19 and AI: A Virtual Conference – Human-Centered Artificial Intelligence Institute, Stanford University, 4/1/2020, 9AM PST – 3:30PM PST @StanfordHAI @pharma_BI @AVIVA1950

Real Time coverage: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2020/04/01/covid-19-and-ai-a-virtual-conference-human-centered-artificial-intelligence-stanford-university-4-1-2020-9am-pst-330pm-pst/

Aviva Lev-Ari
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@StanfordHAI @pharma_BI @AVIVA1950 pharmaceuticalintelligence.com/coronavirus-po Fei-Fei Li AGE Fatality rate and infection rate of the aged Interaction between Acute Infection and Chronic Disease Safety of home – AI sensors at home Sensors data on secure systems clinically data recognized detection

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@StanfordHAI @pharma_BI @AVIVA1950 pharmaceuticalintelligence.com/coronavirus-po Identifying COVID-19 Vaccine Candidates with ML Binbin Chen, MD and Ph.D. Student, Department of Genetics, Stanford University Immunogenic component of vaccine for COVID-19 spike protein bind epitome

Aviva Lev-Ari
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@StanfordHAI @pharma_BI @AVIVA1950 pharmaceuticalintelligence.com/coronavirus-po Repurposing Existing Drugs to Fight COVID-19 Stefano Rensi #NLP Mine the literature for Proteins: Genomes genes proteins Biophysics #docking simulations for energy of 18 molecules as inhibitors  Selection of candidate

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@StanfordHAI @pharma_BI @AVIVA1950 pharmaceuticalintelligence.com/coronavirus-po #ML can be helpful in critical care navigate complexity by automating processes vaccine mutations in the spike protein binding ACE2

Aviva Lev-Ari
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@StanfordHAI @pharma_BI @AVIVA1950 pharmaceuticalintelligence.com/coronavirus-po Mining article on sample size domain ares expert add to the challenges vs CS expertise alone

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@StanfordHAI @pharma_BI @AVIVA1950 pharmaceuticalintelligence.com/coronavirus-po #Virtual #informed #consent of #patient to accelerate ##clinical #trials

Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Xavier Amatriain Lack accessibility to health care systems HC Accessibility and Scalability AI based HC IT System PDA – Personalized Diagnostics Assessment – for self reporting AI Automations + Physicians home testing

Coronavirus Portal
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Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Tina White, Ph.D. Candidate, Department of Mechanical Engineering, Stanford University China death toll >1000 China launched App to monitor quarantine early 1/2020 GPS based new App for contact tracing regulation on data

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Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po John Brownstein Late December 2019 collecting dat a HealthMap – public domain Baidu – has movement information connected with cases Temperature Data published Buoy data base customized to collect MA data on Temperature

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Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Jason Wang commend center in December 2019 All flight entering the country – Level 3 alert country: China Huhan, Hubei Quarantine all arriving from Level 3 alert country National STOKE PILES Activated x5 mask production

Coronavirus Portal
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Aviva Lev-Ari
@AVIVA1950

#AI

pharmaceuticalintelligence.com/coronavirus-po Jason Wang Since 2003 Taiwan is preparing for a Pangemic JAMA paper on the topic is beebn reported  Location of patient Taiwan National Epidemic Center 100 persons 24×7 in the Command Center Taiwan activated

Coronavirus Portal
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Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Michele Barry,TRACE together – Bluetooth tool on distance among people CHINA – contact racing surveillence scanning temp strict social distancing Hong Kong – tracing bracelets for quarantine Street locations of infected

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Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Michele Barry 5Million people travel out of Huhan Singapore – Free testing 1st country Temp testing stay at home, text phone from Authorities, show picture they are in quarantine for 5 days if negative  TRACE together

Coronavirus Portal
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Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Seema Yasmin March 7, 2020 Italy news quarantine of 16 million lockdown large movement of people moving out of lockeddown areas, this movement based on information lead to spread of the viral spread

Coronavirus Portal
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Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Nigam Shah,  Operational Planning – Utilization – Resource planning Clinical – who to test Research Questions – ACE2 receptors

Coronavirus Portal
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Aviva Lev-Ari
@AVIVA1950

Coronavirus Portal
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Aviva Lev-Ari
@AVIVA1950

I am at

TODAY

for our Portal @

Coronavirus Portal
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3

Aviva Lev-Ari
@AVIVA1950

covering in real time Stanford HAI – COVID-19 and AI: A Virtual Conference youtu.be/z4105Exe23Q via

Stanford HAI – COVID-19 and AI: A Virtual Conference
COVID-19 and AI: A Virtual Conference will address a developing public health crisis. Sponsored by the Stanford Institute for Human-Centered Artificial Intel…
youtube.com

Aviva Lev-Ari
@AVIVA1950

I am at

TODAY

for our Portal @

Coronavirus Portal
CORONAVIRUS PORTAL @LPBI   Launched on 3/14/2020 OPEN TO GUEST AUTHORS on Seven Selected Topics & Lead Curator for Contact:   Development of Medical Counter-measures for 2019-nCoV, Co…
pharmaceuticalintelligence.com
3

Aviva Lev-Ari
@AVIVA1950

covering in real time Stanford HAI – COVID-19 and AI: A Virtual Conference youtu.be/z4105Exe23Q via

Stanford HAI – COVID-19 and AI: A Virtual Conference
COVID-19 and AI: A Virtual Conference will address a developing public health crisis. Sponsored by the Stanford Institute for Human-Centered Artificial Intel…
youtube.com

Aviva Lev-Ari
@AVIVA1950

I am at

TODAY

for our Portal @

Coronavirus Portal
CORONAVIRUS PORTAL @LPBI   Launched on 3/14/2020 OPEN TO GUEST AUTHORS on Seven Selected Topics & Lead Curator for Contact:   Development of Medical Counter-measures for 2019-nCoV, Co…
pharmaceuticalintelligence.com
3

Aviva Lev-Ari
@AVIVA1950

covering in real time Stanford HAI – COVID-19 and AI: A Virtual Conference youtu.be/z4105Exe23Q via

Stanford HAI – COVID-19 and AI: A Virtual Conference
COVID-19 and AI: A Virtual Conference will address a developing public health crisis. Sponsored by the Stanford Institute for Human-Centered Artificial Intel…
youtube.com
1

Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Stanford Institute for Human-Centered Artificial Intelligence (HAI) Conference on COVID-19 and AI: A Virtual Conference on April 1, 2020 beginning at 9:00am (PDT). event covered in real time

Coronavirus Portal
CORONAVIRUS PORTAL @LPBI   Launched on 3/14/2020 OPEN TO GUEST AUTHORS on Seven Selected Topics & Lead Curator for Contact:   Development of Medical Counter-measures for 2019-nCoV, Co…
pharmaceuticalintelligence.com

 

Stanford HAI
@StanfordHAI

Vaccines are one of the most powerful tools to curb a pandemic and prevent its recurrence,

says. He discusses how AI tools built upon immunology knowledge and data can increase the chances of finding an effective vaccine. stanford.io/3aBidgh

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Aviva Lev-Ari
@AVIVA1950

I am at

TODAY

for our Portal @

Coronavirus Portal
CORONAVIRUS PORTAL @LPBI   Launched on 3/14/2020 OPEN TO GUEST AUTHORS on Seven Selected Topics & Lead Curator for Contact:   Development of Medical Counter-measures for 2019-nCoV, Co…
pharmaceuticalintelligence.com
2

Aviva Lev-Ari
@AVIVA1950

covering in real time Stanford HAI – COVID-19 and AI: A Virtual Conference youtu.be/z4105Exe23Q via

Stanford HAI – COVID-19 and AI: A Virtual Conference
COVID-19 and AI: A Virtual Conference will address a developing public health crisis. Sponsored by the Stanford Institute for Human-Centered Artificial Intel…
youtube.com
1

Aviva Lev-Ari
@AVIVA1950

Aviva Lev-Ari
@AVIVA1950

I am at

TODAY

for our Portal @

Coronavirus Portal
CORONAVIRUS PORTAL @LPBI   Launched on 3/14/2020 OPEN TO GUEST AUTHORS on Seven Selected Topics & Lead Curator for Contact:   Development of Medical Counter-measures for 2019-nCoV, Co…
pharmaceuticalintelligence.com
2

Aviva Lev-Ari
@AVIVA1950

covering in real time Stanford HAI – COVID-19 and AI: A Virtual Conference youtu.be/z4105Exe23Q via

Stanford HAI – COVID-19 and AI: A Virtual Conference
COVID-19 and AI: A Virtual Conference will address a developing public health crisis. Sponsored by the Stanford Institute for Human-Centered Artificial Intel…
youtube.com
1

Aviva Lev-Ari
@AVIVA1950

pharmaceuticalintelligence.com/coronavirus-po Stanford Institute for Human-Centered Artificial Intelligence (HAI) Conference on COVID-19 and AI: A Virtual Conference on April 1, 2020 beginning at 9:00am (PDT). event covered in real time

Coronavirus Portal
CORONAVIRUS PORTAL @LPBI   Launched on 3/14/2020 OPEN TO GUEST AUTHORS on Seven Selected Topics & Lead Curator for Contact:   Development of Medical Counter-measures for 2019-nCoV, Co…
pharmaceuticalintelligence.com

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Curation of Resources for High Risk People  to COVID-19 Infection :Guidances for Transplant Patients

Curator: Stephen J. Williams, PhD

 

From the American Society of Transplantation

Source: https://www.myast.org/information-transplant-professionals-and-community-members-regarding-2019-novel-coronavirus

INFORMATION FOR TRANSPLANT PROFESSIONALS AND COMMUNITY MEMBERS REGARDING 2019 NOVEL CORONAVIRUS

The recent outbreak of a novel coronavirus (COVID-19) in Wuhan, Hubei Province, China and the finding of infection in many other countries including the United States has led to questions among transplant programs, Organ Procurement Organizations (OPOs) and patients. The Organ Procurement and Transplantation Network (OPTN) strives to provide up-to-date information to answer these questions and to provide guidance as needed. Accordingly, the OPTN Ad Hoc Donor Transmission Advisory Committee (DTAC), American Society of Transplantation (AST) and the American Society of Transplant Surgeons (ASTS), after careful review of information available from the Centers for Disease Control and Prevention (CDC), offers information to transplant programs and OPOs in light of these concerns. Please visit the OPTN  website for more information.

The American Society of Transplantation recently conducted a Town Hall on guidances for transplant patients with regard to the COVID-19 pandemic.  A video recording of the Town Hall is given below

 

 

Description of the Town Hall by the AST: A number of transplant organizations from around the world have partnered to develop this educational webinar for the organ donation and transplantation communities. Our goal is to share experiences to date and respond to your questions about the impact of COVID-19 on organ donation and transplantation.

 

This webinar was recorded on March 23, 2020.

 

Resource Handout: https://www.myast.org/sites/default/f…

AST COVID-19 Page: https://www.myast.org/covid-19-inform…

 

The American Society of Transplantation has other up to date resources on their webpage at https://www.myast.org/covid-19-information#

AST Resources For Transplant Professionals 

Information for Transplant Professionals (Updated 3/31/20)

Medication Access and Drug Shortage Concerns During the COVID-19 Pandemic: Frequently Asked Questions (posted 3/31/20)

AST Resources For Transplant Recipients and Candidates 

Information for Transplant Recipients and Candidates (Updated 3/30/20)

Other Resources like videos and further articles

Frequently Asked Questions can be found here https://www.myast.org/coronavirus-disease-2019-covid-19-frequently-asked-questions-transplant-candidates-and-recipients

Mark Spigler from the American Kidney Fund listed some tips specifically for kidney transplant recipients. In his blog

Coronavirus, COVID-19 and kidney patients: what you need to know he wrote:

Because transplant recipients take immunosuppressive drugs, they are at higher risk of infection from viruses such as cold or flu. To limit the possibility of being exposed to the coronavirus that causes COVID-19, transplant patients should follow the CDC’s tips to avoid catching or spreading germs, and contact their health care provider if they develop cold or flu-like symptoms. By being informed and taking your own personal precautions, you can help reduce your risk of coming in contact with the coronavirus that causes COVID-19. You can find more information and resources for kidney patients by visiting our special coronavirus webpage at KidneyFund.org/coronavirus. We’ll update the page with important information for kidney patients and their caregivers as the coronavirus crisis continues to unfold.

Resources from the National Kidney Foundation

Source: https://www.kidney.org/coronavirus/transplant-coronavirus

Coronavirus and Kidney Transplants (please click on the links below)

For more information concerning various issues on COVID-19 please see our Coronavirus Portal at:

https://pharmaceuticalintelligence.com/coronavirus-portal/

 

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From @Harvardmed Center for Bioethics: The Medical Ethics of the Corona Virus Crisis

Reporter: Stephen J. Williams, Ph.D.

From Harvard Medical School Center for Bioethics

source: https://bioethics.hms.harvard.edu/news/medical-ethics-corona-virus-crisis

The Medical Ethics of the Corona Virus Crisis

Executive Director Christine Mitchell discusses the importance of institutions talking through the implications of their decisions with the New Yorker.

Center Executive Director Christine Mitchell spoke with the New Yorker’s Isaac Chotiner about the decisions that may need to be made on limiting movement and, potentially, rationing supplies and hospital space.

“So, in the debate about allocating resources in a pandemic, we have to work with our colleagues around what kind of space is going to be made available—which means that other people and other services have to be dislocated—what kind of supplies we’re going to have, whether we’re going to reuse them, how we will reallocate staff, whether we can have staff who are not specialists take care of patients because we have way more patients than the number of specialized staff,” says Mitchell.

Read the full Q&A in the New Yorker.

 

Note: The following is taken from the Interview in the New Yorker.

As the novel coronaviruscovid-19, spreads across the globe, governments have been taking increasingly severe measures to limit the virus’s infection rate. China, where it originated, has instituted quarantines in areas with a large number of cases, and Italy—which is now facing perhaps the most serious threat outside of China—is entirely under quarantine. In the United States, the National Guard has been deployed to manage a “containment area” in New Rochelle, New York, where one of the country’s largest clusters has emerged. As the number of cases rises, we will soon face decisions on limiting movement and, potentially, rationing supplies and hospital space. These issues will be decided at the highest level by politicians, but they are often influenced by medical ethicists, who advise governments and other institutions about the way to handle medical emergencies.

One of those ethicists, with whom I recently spoke by phone, is Christine Mitchell, the executive director at the Center for Bioethics at Harvard Medical School. Mitchell, who has master’s degrees in nursing and philosophical and religious ethics, has been a clinical ethicist for thirty years. She founded the ethics program at Boston Children’s Hospital, and has served on national and international medical-ethics commissions. During our conversation, which has been edited for length and clarity, we discussed what ethicists tend to focus on during a health crisis, how existing health-care access affects crisis response, and the importance of institutions talking through the ethical implications of their decisions.

What coronavirus-related issue has most occupied your mental space over the past weeks?

One of the things I think about but that we don’t often have an opportunity to talk about, when we are mostly focussing on what clinicians are doing and trying to prepare for, is the more general ways this affects our society. People get sick out there in the real world, and then they come to our hospitals, but, when they are sick, a whole bunch of them don’t have health insurance, or are afraid to come to a hospital, or they don’t have coverage for sick time or taking a day off when their child is sick, so they send their child to school. So these all have very significant influences on our ability to manage population health and community transmission that aren’t things that nurses and physicians and people who work in acute-care hospitals and clinics can really affect. They are elements of the way our society is structured and has failed to meet the needs of our general population, and they influence our ability to manage a crisis like this.

Is there anything specifically about a pandemic or something like coronavirus that makes these issues especially acute?

If a person doesn’t have health insurance and doesn’t come to be tested or treated, and if they don’t have sick-time coverage and can’t leave work, so they teach at a school, or they work at a restaurant, or do events that have large numbers of people, these are all ways in which the spread of a virus like this has to be managed—and yet can’t be managed effectively because of our social-welfare policies, not just our health-care resources.

Just to take a step back, and I want to get back to coronavirus stuff, but what got you interested in medical ethics?

What got me interested were the actual kinds of problems that came up when I was taking care of patients, starting as early as when I was in nursing school and was taking care of a patient who, as a teen-ager, had a terminal kind of cancer that his parents didn’t want him to know about, and which the health-care team had decided to defer to the parents. And yet I was spending every day taking care of him, and he was really puzzled about why he was so sick and whether he was going to get better, and so forth. And so of course I was faced with this question of, What do I do if he asks me? Which, of course, he did.

And this question about what you should tell an adolescent and whether the deference should be to his parents’ judgment about what’s best for him, which we would ordinarily respect, and the moral demands of the relationship that you have with a patient, was one of the cases that reminded me that there’s a lot more to being a nurse or a health-care provider than just knowing how to give cancer chemotherapy and change a bed, or change a dressing, or whatever. That a lot of it is in the relationship you have with a patient and the kinds of ethical choices they and their families are facing. They need your information, but also your help as they think things through. That’s the kind of thing that got me interested in it. There are a whole host of those kinds of cases, but they’re more individual cases.

As I began to work in a hospital as an ethicist, I began to worry about the broader organizational issues, like emergency preparedness. Some years ago, here in Boston, I had a joint appointment running the ethics program at Children’s Hospital and doing clinical ethics at Harvard Medical School. We pulled together a group, with the Department of Public Health and the emergency-preparedness clinicians in the Harvard-affiliated hospitals, to look at what the response within the state of Massachusetts should be to big, major disasters or rolling pandemics, and worked on some guidelines together.

When you looked at the response of our government, in a place like Washington State or in New York City, what things, from a medical-ethics perspective, are you noticing that are either good or maybe not so good?

To be candid and, probably, to use language that’s too sharp for publication, I’m appalled. We didn’t get ourselves ready. We’ve had outbreaks—sars in 2003, H1N1 in 2009, Ebola in 2013, Zika in 2016. We’ve known, and the general population in some ways has known. They even have movies like “Contagion” that did a great job of sharing publicly what this is like, although it is fictional, and that we were going to have these kinds of infectious diseases in a global community that we have to be prepared to handle. And we didn’t get ourselves as ready, in most cases, as we should have. There have been all these cuts to the C.D.C. budget, and the person who was the Ebola czar no longer exists in the new Administration.

And it’s not just this Administration. But the thing about this Administration that perhaps worries me the most is a fundamental lack of respect for science and the facts. Managing the crisis from a public-relations perspective and an economic, Dow Jones perspective are important, but they shouldn’t be fudging the facts. And that’s the piece that makes me feel most concerned—and not just as an ethicist. And then, of course, I want to see public education and information that’s forthright and helps people get the treatment that they need. But the disrespect for the public, and not providing honest information, is . . . yeah, that’s pretty disconcerting.

SOURCE

https://www.newyorker.com/news/q-and-a/the-medical-ethics-of-the-coronavirus-crisis

See more on this and #COVID19 on this Online Open Access Journal at our Coronavirus Portal at

https://pharmaceuticalintelligence.com/coronavirus-portal/

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Glycobiology vs Proteomics: Glycobiologists Prespective in the effort to explain the origin, etiology and potential therapeutics for the Coronavirus Pandemic (COVID-19)

 Curator: Ofer Markman, PhD

 The sugars involved in a viral disease are unique in many ways when compared with the DNA/RNA or the proteins involved: they are almost totally dependent on the infected cells and thus are not affected by the viral mutation rate or by the virus at all. Nevertheless they are affected by the cells, their type and their sugar production mechanisms and in some respect to the production rate by which the virus is replicated in the infected cells. Mutations may have nevertheless major effect not on the structures of the glycans but rather on the existence of the glycosylation site, and thus the glycan at all, but not on its structures.

This may make the gycomolecule a good target for diagnostics as stability in the molecule may mean longer life shelve of diagnostics kits.

Unique sugars are already predicted/found in the virus from certain Chinese origin, in this case an o-linked glycan/s not previously detected.

  • The proximal origin of SARS-CoV-2

Kristian G. AndersenAndrew RambautW. Ian Lipkin, Edward C. Holmes & Robert F. Garry

Nature Medicine (2020)Cite this article

https://www.nature.com/articles/s41591-020-0820-9

  • The covid-19 coronavirus epidemic has a natural origin, scientists say

https://globalhealthnewswire.com/2020/03/17/the-covid-19-coronavirus-epidemic-has-a-natural-origin-scientists-say/

  • Emerging WuHan (COVID-19) coronavirus: glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26

Naveen Vankadari & Jacqueline A. Wilce

https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1739565

Nevertheless, if the virus can infect multiple cells once current cells are not going to be available for any reason those viruses may present other glycans.

Once one starts to treat the infected person via modulation of protein production or by other means the change in the dynamic of protein production vs. protein glycosylation may cause changes in protein glycosyation, including their structures, this is well known to biotechnologists producing glycoproteins in labs and production.

This may either be a problem in understanding the state of disease or an advantage as it may help following response to the treatment and help as a co-treatment diagnostics.

Early Studies include the following:

  • Carbohydrate-based Diagnostics: A New Approach to COVID-19 Testing?

Mar 19, 2020 | Original story from Iceni Diagnostics

https://www.technologynetworks.com/diagnostics/news/carbohydrate-based-diagnostics-a-new-approach-to-covid-19-testing-332313

Glycans may play a role in treatment as well. TAMIFLU a case in point. Tamiflu is directed to the flu enzyme Neuraminidaze that is part of the viral structures. This approach was also explored to develop treatments.

  • Pneumagen Ltd Leverages its Novel Glycan Approach to Target Coronavirus (COVID-19) Infections

March 17, 2020 PR-M03-20-NI-024

https://www.pharmasalmanac.com/articles/pneumagen-ltd-leverages-its-novel-glycan-approach-to-target-coronavirus-covid-19-infections

Glycans do not only effect their own involvement in treatment/diagnostics they also are effecting protein based diagnostics for this see statement by Dr. Michael Mercier of UAH

  • We’re dealing with COVID-19, but what’s a virus in the first place?

23-Mar-2020 8:45 AM EDT, by University of Alabama Huntsville

https://www.newswise.com/articles/we-re-dealing-with-covid-19-but-what-s-a-virus-in-the-first-place

 

Other related articles on this topic published on this topic in this Open Access Online Scientific Journal include the following: 

 

The Relevance of Glycans in the Viral Pathology of COVID-19

Reporter: Ofer Markman, PhD

https://pharmaceuticalintelligence.com/2020/03/23/glycans-in-the-viral-pathology-of-covid-19/

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Reporter: Gail S. Thornton, M.A.

The following article is reprinted from the Anchorage Daily News.

https://www.adn.com/alaska-news/2020/03/18/one-of-alaskas-first-confirmed-coronavirus-patients-tells-his-story/

One of Alaska’s first confirmed coronavirus patients tells his story

March 19, 2020

A Ketchikan man who contracted the illness caused by the new coronavirus is speaking out about his experience.

In a social media post and an interview with the Ketchikan Daily News, he described his symptoms, how he was tested and his experience communicating with Alaska public health officials.

As of Wednesday morning, Glenn Brown, the attorney for the Ketchikan Gateway Borough, is one of nine people statewide who have confirmed cases of the virus. Officials have not said any of the people with confirmed cases have been hospitalized.

Brown said in a Facebook post that he was feeling better and was notified by public health officials that he’d tested positive for COVID-19 on Tuesday afternoon.

“I became sick Saturday morning with fever, headache, general achiness and chills,” Brown wrote.

Brown said he has “no idea” how he contracted the illness.

“I interacted with no one in recent weeks who was exhibiting obvious symptoms,” he wrote.

According to a statement Tuesday from the Ketchikan Emergency Operations Center saying one of its employees tested positive for the virus, the employee had a history of travel to the Lower 48. The Ketchikan Emergency Operations Center on Wednesday confirmed Brown is the employee.

The Ketchikan Daily News reported that Brown had recently traveled to Oregon and Juneau before returning to Ketchikan on March 9.

After public health officials told Brown his diagnosis, he said that he went through more than an hour of questions with them, he told the Ketchikan Daily News.

“I used everything from cellphone records to work calendars to debit card bills, to recall everybody that I may have had contact with,” Brown told the Ketchikan Daily News. “I wanted to provide that information to public health, (so) that they could alert those people and really hope to kind of arrest this thing.”

Brown told the paper that public health officials focused on two days before he developed symptoms of the illness. Brown had been “working closely with borough staff and upper management” in those days as part of his job, the paper reported.

“I apologize for causing undue concern for anyone, especially my co-workers at the Borough,” Brown said in the Facebook post.

Ketchikan Gateway Borough employees in direct contact with Brown were instructed to self-quarantine for two weeks, according to the Ketchikan Emergency Operations Center statement.

The statement also said that the borough had hired a service to disinfect the now-closed White Cliff Building, which houses the Ketchikan Borough offices.

According to the Ketchikan Daily News, the last time Brown was at the borough’s White Cliff Building was Friday.

The paper reported that as of Tuesday night, there were no plans to test people who had been in direct contact with Brown.

A public information officer for Ketchikan’s Emergency Operations Center told the Ketchikan Daily News that she understood that to be tested, people would need to have “several” symptoms of the virus.

“I would also ask that you join me and all of Ketchikan to actively minimize community transmission so that we can protect our seniors or other medically vulnerable folks in Ketchikan,” Brown wrote. “I pray that we all make it through this largely unharmed, and together.”

The first person in Alaska to test positive for COVID-19 was an air cargo pilot who arrived at Ted Stevens Anchorage International Airport on March 11, officials announced last week. He went through the airport’s North Terminal, which is separate from the domestic terminal.

Alaska’s chief medical officer, Dr. Anne Zink, said last week the man had self-isolated and was “stable.”

On Monday, officials said two older men in Fairbanks were diagnosed with the illness. Both had recently traveled to the Lower 48, Zink said, but were not traveling together.

In addition to the Anchorage case, the case in Ketchikan and the two in Fairbanks, officials on Tuesday announced that two more people had become sick with the virus — one in Fairbanks and one in Anchorage — bringing the total number of confirmed cases as of Wednesday morning to six.

Zink said that both of those cases were also travel-related. None of the three people who tested positive for COVID-19 on Tuesday were hospitalized, Zink said.

Fairbanks Memorial Hospital released a statement Tuesday saying a woman with a history of recent travel had tested positive for COVID-19.

“She self-isolated prior to testing,” the statement said. “This patient has been notified and is in stable condition and does not require hospitalization.”

A University of Alaska Fairbanks employee was one of the people who had recently tested positive for the virus in Alaska, university officials said Tuesday.

An internal email advised anyone who had used the O’Neill Building, which houses the College of Fisheries and Ocean Sciences, to stay home and monitor themselves for two weeks.

State and local officials have taken a series of steps to stem the spread of COVID-19 in Alaska, including closing schools, calling on hospitals to halt elective surgeries and shutting down dine-in service at all restaurants, bars, breweries, cafes and similar businesses.

About this Author

Morgan Krakow

Morgan Krakow is a general assignment reporter for the Anchorage Daily News. She is a 2019 graduate of the University of Oregon and spent the past summer as a reporting intern on the general assignment desk of The Washington Post. Contact her at mkrakow@adn.com.

###

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Responses to the #COVID-19 outbreak from Oncologists, Cancer Societies and the NCI: Important information for cancer patients

Curator: Stephen J. Williams, Ph.D.

UPDATED 3/20/2020

Among the people who are identified at risk of coronovirus 2019 infection and complications of the virus include cancer patients undergoing chemotherapy, who in general, can be immunosuppressed, especially while patients are undergoing their treatment.  This has created anxiety among many cancer patients as well as their care givers and prompted many oncologist professional groups, cancer societies, and cancer centers to formulate some sort of guidelines for both the cancer patients and the oncology professional with respect to limiting the risk of infection to coronavirus (COVID19). 

 

This information will be periodically updated and we are working to get a Live Twitter Feed to bring oncologist and cancer patient advocacy groups together so up to date information can be communicated rapidly.  Please see this page regularly for updates as new information is curated.

IN ADDITION, I will curate a listing of drugs with adverse events of immunosuppression for people who might wonder if the medications they are taking are raising their risk of infections.

Please also see @pharma_BI for updates as well.

Please also see our Coronavirus Portal at https://pharmaceuticalintelligence.com/coronavirus-portal/

For ease of reading information for patients are BOLDED and in RED

ASCO’s Response to COVID-19

From the Cancer Letter: The following is a guest editorial by American Society of Clinical Oncology (ASCO) Executive Vice President and Chief Medical Officer Richard L. Schilsky MD, FACP, FSCT, FASCO. This story is part of The Cancer Letter’s ongoing coverage of COVID-19’s impact on oncology. A full list of our coverage, as well as the latest meeting cancellations, is available here.

 

The worldwide spread of the coronavirus (COVID-19) presents unprecedented challenges to the cancer care delivery system.

Our patients are already dealing with a life-threatening illness and are particularly vulnerable to this viral infection, which can be even more deadly for them. Further, as restrictions in daily movement and social distancing take hold, vulnerable patients may be disconnected from friends, family or other support they need as they manage their cancer.

As providers, we rely on evidence and experience when treating patients but now we face uncertainty. There are limited data to guide us in the specific management of cancer patients confronting COVID-19 and, at present, we have no population-level guidance regarding acceptable or appropriate adjustments of treatment and practice operations that both ensure the best outcome for our patients and protect the safety of our colleagues and staff.

As normal life is dramatically changed, we are all feeling anxious about the extreme economic challenges we face, but these issues are perhaps even more difficult for our patients, many of whom are now facing interruption

As we confront this extraordinary situation, the health and safety of members, staff, and individuals with cancer—in fact, the entire cancer community—is ASCO’s highest priority.

ASCO has been actively monitoring and responding to the pandemic to ensure that accurate information is readily available to clinicians and their patients. Recognizing that this is a rapidly evolving situation and that limited oncology-specific, evidence-based information is available, we are committed to sharing what is known and acknowledging what is unknown so that the most informed decisions can be made.

To help guide oncology professionals as they deal with the impact of coronavirus on both their patients and staff, ASCO has collated questions from its members, posted responses at asco.org and assembled a compendium of additional resources we hope will be helpful as the virus spreads and the disease unfolds. We continue to receive additional questions regarding clinical care and we are updating our FAQs on a regular basis.

We hope this information is helpful even when it merely confirms that there are no certain answers to many questions. Our answers are based on the best available information we identify in the literature, guidance from public health authorities, and input received from oncology and infectious disease experts.

For patients, we have posted a blog by Dr. Merry Jennifer Markham, chair of ASCO’s Cancer Communications Committee. This can be found on Cancer.Net, ASCO’s patient information website, and it provides practical guidance to help patients reduce their risk of exposure, better understand COVID-19 symptoms, and locate additional information.

This blog is available both in English and Spanish. Additional blog posts addressing patient questions will be posted as new questions are received and new information becomes available.

Find below a Tweet from Dr.Markham which includes links to her article on COVID-19 for cancer patients

https://twitter.com/DrMarkham/status/1237797251038220289?s=20

NCCN’s Response to COVID-19 and COVID-19 Resources

JNCCN: How to Manage Cancer Care during COVID-19 Pandemic

Experts from the Seattle Cancer Care Alliance (SCCA)—a Member Institution of the National Comprehensive Cancer Network® (NCCN®)—are sharing insights and advice on how to continue providing optimal cancer care during the novel coronavirus (COVID-19) pandemic. SCCA includes the Fred Hutchinson Cancer Research Center and the University of Washington, which are located in the epicenter of the COVID-19 outbreak in the United States. The peer-reviewed article sharing best practices is available for free online-ahead-of-print via open access at JNCCN.org.

Coronavirus disease 2019 (COVID-19) Resources for the Cancer Care Community

NCCN recognizes the rapidly changing medical information relating to COVID-19 in the oncology ecosystem, but understands that a forum for sharing best practices and specific institutional responses may be helpful to others.  Therefore, we are expeditiously providing documents and recommendations developed by NCCN Member Institutions or Guideline Panels as resources for oncology care providers. These resources have not been developed or reviewed by the standard NCCN processes, and are provided for information purposes only. We will post more resources as they become available so check back for additional updates.

Documents

Links

National Cancer Institute Response to COVID-19

More information at https://www.cancer.gov/contact/emergency-preparedness/coronavirus

What people with cancer should know: https://www.cancer.gov/coronavirus

Get the latest public health information from CDC: https://www.coronavirus.gov

Get the latest research information from NIH: https://www.nih.gov/coronavirus

 

Coronavirus: What People with Cancer Should Know

ON THIS PAGE

Both the resources at cancer.gov (NCI) as well as the resources from ASCO are updated as new information is evaluated and more guidelines are formulated by members of the oncologist and cancer care community and are excellent resources for those living with cancer, and also those who either care for cancer patients or their family and relatives.

Related Resources for Patients (please click on links)

 

 

 

Some resources and information for cancer patients from Twitter

Twitter feeds which may be useful sources of discussion and for cancer patients include:

 

@OncLive OncLive.com includes healthcare information for patients and includes videos and newsletters

 

 

@DrMarkham Dr. Markham is Chief of Heme-Onc & gyn med onc @UF | AD Med Affairs @UFHealthCancer and has collected very good information for patients concerning #Covid19 

 

 

@DrMaurieMarkman Dr. Maurie Markman is President of Medicine and Science (Cancer Centers of America, Philadelphia) @CancerCenter #TreatThePerson #Oncology #Genomics #PrecisionMedicine and hosts a great online live Tweet feed discussing current topics in cancer treatment and care for patients called #TreatThePerson Chat

UPDATED 3/20/2020 INFORMATION FROM NCI DESIGNATED CANCER CENTERS FOR PATIENTS/PROVIDERS

The following is a listing with links of NCI Designated Comprehensive Cancer Centers and some select designated Cancer Centers* which have information on infectious risk guidance for cancer patients as well as their physicians and caregivers.   There are 51 NCI Comprehensive Cancer Centers and as more cancer centers formulate guidance this list will be updated. 

 

Cancer Center State Link to COVID19 guidance
City of Hope CA Advice for cancer patients, survivors and caregivers
Jonsson Cancer Center at UCLA CA Cancer and COVID19
UCSF Hellen Diller Family Comprehensive Cancer CA COVID-19 Links for Patients and Providers
Lee Moffit FL Protecting against Coronavirus 19
University of Kansas Cancer Center* KS COVID19 Info for patients
Barbara & Karmanos Cancer Institute (Wayne State) MI COVID19 Resources
Rogel Cancer Center (Univ of Michigan) MI COVID19 Patient Specific Guidelines
Alvin J. Siteman Cancer Center (MO) Coronavirus
Fred & Pamela Buffet CC* NE Resources for Patients and Providers
Rutgers Cancer Institute of NJ NJ What patients should know about COVID19
Memorial Sloan Kettering NY What COVID19 means for cancer patients
Herbert Irving CC (Columbia University) NY Coronavirus Resource Center
MD Anderson Cancer  TX Planning for Patients, Providers
Hunstman Cancer Center UT COVID19 What you need to know
Fred Hutchinson WA COVID19 What patients need to know

 

 

Please also see related information on Coronavirus 2019 and Cancer and Immunotherapy at the following links on the Open Access Online Journal:

Volume Two: Cancer Therapies: Metabolic, Genomics, Interventional, Immunotherapy and Nanotechnology in Therapy Delivery 

at

https://pharmaceuticalintelligence.com/biomed-e-books/series-c-e-books-on-cancer-oncology/volume-two-immunotherapy-in-cancer-radiation-oncology/

AND

Coronavirus Portal

 

 

 

 

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Predicting the Protein Structure of Coronavirus: Inhibition of Nsp15 can slow viral replication and Cryo-EM – Spike protein structure (experimentally verified) vs AI-predicted protein structures (not experimentally verified) of DeepMind (Parent: Google) aka AlphaFold

 

Curators: Stephen J. Williams, PhD and Aviva Lev-Ari, PhD, RN

This illustration, created at the Centers for Disease Control and Prevention (CDC), reveals ultrastructural morphology exhibited by coronaviruses. Note the spikes that adorn the outer surface of the virus, which impart the look of a corona surrounding the virion, when viewed electron microscopically. A novel coronavirus virus was identified as the cause of an outbreak of respiratory illness first detected in Wuhan, China in 2019.

Image and Caption Credit: Alissa Eckert, MS; Dan Higgins, MAM available at https://phil.cdc.gov/Details.aspx?pid=23311

 

UPDATED on 3/11/2020

Coronaviruses

According to the World Health Organization, coronaviruses make up a large family of viruses named for the crown-like spikes found on their surface (Figure 1). They carry their genetic material in single strands of RNA and cause respiratory problems and fever. Like HIV, coronaviruses can be transmitted between animals and humans.  Coronaviruses have been responsible for the Severe Acute Respiratory Syndrome (SARS) pandemic in the early 2000s and the Middle East Respiratory Syndrome (MERS) outbreak in South Korea in 2015. While the most recent coronavirus, COVID-19, has caused international concern, accessible and inexpensive sequencing is helping us understand COVID-19 and respond to the outbreak quickly.

Figure 1. Coronaviruses with the characteristic spikes as seen under a microscope.

First studies that explore genetic susceptibility to COVID-19 are now being published. The first results indicate that COVID-19 infects cells using the ACE2 cell-surface receptor. Genetic variants in the ACE2 receptor gene are thus likely to influence how effectively COVID-19 can enter the cells in our bodies. Researchers hope to discover genetic variants that confer resistance to a COVID-19 infection, similar to how some variants in the CCR5 receptor gene make people immune to HIV. At Nebula Genomics, we are monitoring the latest COVID-19 research and will add any relevant discoveries to the Nebula Research Library in a timely manner.

The Role of Genomics in Responding to COVID-19

Scientists in China sequenced COVID-19’s genome just a few weeks after the first case was reported in Wuhan. This stands in contrast to SARS, which was discovered in late 2002 but was not sequenced until April of 2003. It is through inexpensive genome-sequencing that many scientists across the globe are learning and sharing information about COVID-19, allowing us to track the evolution of COVID-19 in real-time. Ultimately, sequencing can help remove the fear of the unknown and allow scientists and health professionals to prepare to combat the spread of COVID-19.

Next-generation DNA sequencing technology has enabled us to understand COVID-19 is ~30,000 bases long. Moreover, researchers in China determined that COVID-19 is also almost identical to a coronavirus found in bats and is very similar to SARS. These insights have been critical in aiding in the development of diagnostics and vaccines. For example, the Centers for Disease Control and Prevention developed a diagnostic test to detect COVID-19 RNA from nose or mouth swabs.

Moreover, a number of different government agencies and pharmaceutical companies are in the process of developing COVID-19 vaccines to stop the COVID-19 from infecting more people. To protect humans from infection inactivated virus particles or parts of the virus (e.g. viral proteins) can be injected into humans. The immune system will recognize the inactivated virus as foreign, priming the body to build immunity against possible future infection. Of note, Moderna Inc., the National Institute of Allergy and Infectious Diseases, and Coalition for Epidemic Preparedness Innovations identified a COVID-19 vaccine candidate in a record 42 days. This vaccine will be tested in human clinical trials starting in April.

For more information about COVID-19, please refer to the World Health Organization website.

SOURCE

https://blog.nebula.org/role-of-genomics-coronavirus-covid-19/?utm_source=Nebula%20Genomics&utm_medium=email&utm_campaign=COVID-19

Aviva Lev-Ari
13.3K Tweets

Aviva Lev-Ari
@AVIVA1950

My BIO lnkd.in/eEyn69r MediaPharma ex-SRI ex-MITRE ex-McGraw-Hill Followed by

Aviva Lev-Ari
@AVIVA1950

Predicting the #ProteinStructure of #Coronavirus: #Inhibition of #Nsp15 #Cryo-EM – #spike #protein structure (#experimentally verified) vs #AI-predicted protein structures (not verified) of

(

) #AlphaFold

Quote Tweet
Eric Topol
@EricTopol
·
The problem w/ visionaries is that we don’t recognize them in a timely manner (too late) Ralph Baric @UNCpublichealth and Vineet Menachery deserve recognition for being 5 yrs ahead of #COVID19 nature.com/articles/nm.39 @NatureMedicine pnas.org/content/113/11 @PNASNews via @hoondy

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Senior, A.W., Evans, R., Jumper, J. et al. Improved protein structure prediction using potentials from deep learningNature 577, 706–710 (2020)https://doi.org/10.1038/s41586-019-1923-7

Abstract

Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence1. This problem is of fundamental importance as the structure of a protein largely determines its function2; however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures3. Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force4 that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction5 (CASP13)—a blind assessment of the state of the field—AlphaFold created high-accuracy structures (with template modelling (TM) scores6 of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined7. https://doi.org/10.1038/s41586-019-1923-7

[ALA added bold face]

COVID-19 outbreak

The scientific community has galvanised in response to the recent COVID-19 outbreak, building on decades of basic research characterising this virus family. Labs at the forefront of the outbreak response shared genomes of the virus in open access databases, which enabled researchers to rapidly develop tests for this novel pathogen. Other labs have shared experimentally-determined and computationally-predicted structures of some of the viral proteins, and still others have shared epidemiological data. We hope to contribute to the scientific effort using the latest version of our AlphaFold system by releasing structure predictions of several under-studied proteins associated with SARS-CoV-2, the virus that causes COVID-19. We emphasise that these structure predictions have not been experimentally verified, but hope they may contribute to the scientific community’s interrogation of how the virus functions, and serve as a hypothesis generation platform for future experimental work in developing therapeutics. We’re indebted to the work of many other labs: this work wouldn’t be possible without the efforts of researchers across the globe who have responded to the COVID-19 outbreak with incredible agility.

Knowing a protein’s structure provides an important resource for understanding how it functions, but experiments to determine the structure can take months or longer, and some prove to be intractable. For this reason, researchers have been developing computational methods to predict protein structure from the amino acid sequence.  In cases where the structure of a similar protein has already been experimentally determined, algorithms based on “template modelling” are able to provide accurate predictions of the protein structure. AlphaFold, our recently published deep learning system, focuses on predicting protein structure accurately when no structures of similar proteins are available, called “free modelling”.  We’ve continued to improve these methods since that publication and want to provide the most useful predictions, so we’re sharing predicted structures for some of the proteins in SARS-CoV-2 generated using our newly-developed methods.

It’s important to note that our structure prediction system is still in development and we can’t be certain of the accuracy of the structures we are providing, although we are confident that the system is more accurate than our earlier CASP13 system. We confirmed that our system provided an accurate prediction for the experimentally determined SARS-CoV-2 spike protein structure shared in the Protein Data Bank, and this gave us confidence that our model predictions on other proteins may be useful. We recently shared our results with several colleagues at the Francis Crick Institute in the UK, including structural biologists and virologists, who encouraged us to release our structures to the general scientific community now. Our models include per-residue confidence scores to help indicate which parts of the structure are more likely to be correct. We have only provided predictions for proteins which lack suitable templates or are otherwise difficult for template modeling.  While these understudied proteins are not the main focus of current therapeutic efforts, they may add to researchers’ understanding of SARS-CoV-2.

Normally we’d wait to publish this work until it had been peer-reviewed for an academic journal. However, given the potential seriousness and time-sensitivity of the situation, we’re releasing the predicted structures as we have them now, under an open license so that anyone can make use of them.

Interested researchers can download the structures here, and can read more technical details about these predictions in a document included with the data. The protein structure predictions we’re releasing are for SARS-CoV-2 membrane protein, protein 3a, Nsp2, Nsp4, Nsp6, and Papain-like proteinase (C terminal domain). To emphasise, these are predicted structures which have not been experimentally verified. Work on the system continues for us, and we hope to share more about it in due course.

Citation:  John Jumper, Kathryn Tunyasuvunakool, Pushmeet Kohli, Demis Hassabis, and the AlphaFold Team, “Computational predictions of protein structures associated with COVID-19”, DeepMind website, 5 March 2020, https://deepmind.com/research/open-source/computational-predictions-of-protein-structures-associated-with-COVID-19

SARS-COV-2 MEMBRANE PROTEIN: A RENDERING OF ONE OF OUR PROTEIN STRUCTURE PREDICTIONS

SOURCES

Computational predictions of protein structures associated with COVID-19

https://deepmind.com/research/open-source/computational-predictions-of-protein-structures-associated-with-COVID-19

AlphaFold: Using AI for scientific discovery 

https://deepmind.com/blog/article/AlphaFold-Using-AI-for-scientific-discovery

 

DeepMind has shared its results with researchers at the Francis Crick Institute, a biomedical research lab in the UK, as well as offering it for download from its website.

“Normally we’d wait to publish this work until it had been peer-reviewed for an academic journal. However, given the potential seriousness and time-sensitivity of the situation, we’re releasing the predicted structures as we have them now, under an open license so that anyone can make use of them,” it said. [ALA added bold face]

There are 93,090 cases of COVID-19, and 3,198 deaths, spread across 76 countries, according to the latest report from the World Health Organization at time of writing. ®

SOURCE

https://www.theregister.co.uk/2020/03/06/deepmind_covid19_outbreak/

 

  • MHC content – The spike protein is thought to be the key to binding to cells via the angiotensin II receptor, the major mechanism the immune system uses to distinguish self from non-self

Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies

Syed Faraz Ahmed 1,† , Ahmed A. Quadeer 1, *,† and Matthew R. McKay 1,2, *

1 Department of Electronic and Computer Engineering, The Hong Kong University of Science and

Technology, Hong Kong, China; sfahmed@connect.ust.hk

2 Department of Chemical and Biological Engineering, The Hong Kong University of Science and

Technology, Hong Kong, China

* Correspondence: eeaaquadeer@ust.hk.com (A.A.Q.); m.mckay@ust.hk (M.R.M.)

These authors contributed equally to this work.

Received: 9 February 2020; Accepted: 24 February 2020; Published: 25 February 2020

Abstract:

The beginning of 2020 has seen the emergence of COVID-19 outbreak caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There is an imminent need to better understand this new virus and to develop ways to control its spread. In this study, we sought to gain insights for vaccine design against SARS-CoV-2 by considering the high genetic similarity between SARS-CoV-2 and SARS-CoV, which caused the outbreak in 2003, and leveraging existing immunological studies of SARS-CoV. By screening the experimentally determined SARS-CoV-derived B cell and T cell epitopes in the immunogenic structural proteins of SARS-CoV, we identified a set of B cell and T cell epitopes derived from the spike (S) and nucleocapsid (N) proteins that map identically to SARS-CoV-2 proteins. As no mutation has been observed in these identified epitopes among the 120 available SARS-CoV-2 sequences (as of 21 February 2020), immune targeting of these epitopes may potentially offer protection against this novel virus. For the T cell epitopes, we performed a population coverage analysis of the associated MHC alleles and proposed a set of epitopes that is estimated to provide broad coverage globally, as well as in China. Our findings provide a screened set of epitopes that can help guide experimental efforts towards the development of vaccines against SARS-CoV-2.

Keywords: Coronavirus; 2019-nCoV; 2019 novel coronavirus; SARS-CoV-2; COVID-19; SARS-CoV; MERS-CoV; T cell epitopes; B cell epitopes; vaccine [ALA added bold face]

SOURCE

https://www.mdpi.com/1999-4915/12/3/254/pdf

 

Selected Online COMMENTS to

https://forums.theregister.co.uk/forum/all/2020/03/06/deepmind_covid19_outbreak/

MuscleguySilver badge

Re: Protein structure prediction has been done for ages…

Not quite, Natural Selection does not measure methods, it measures outputs, usually at the organism level.

Sure correct folding is necessary for much protein function and we have prions and chaperone proteins to get it wrong and right.

The only way NS measures methods and mechanisms is if they are very energetically wasteful. But there are some very wasteful ones out there. Beta-Catenin at the end of point of Wnt signalling comes particularly to mind.

Chemist

Re: Does not matter at all

“Determining the structure of the virus proteins might also help in developing a molecule that disrupts the operation of just those proteins, and not anything else in the human body.”

Well it might, but predicting whether a ‘drug’ will NOT interact with any other of the 20000+ protein in complex organisms is well beyond current science. If we could do that we could predict/avoid toxicity and other non-mechanism related side-effects & mostly we can’t.

rob miller

Title

There are 480 structures on PDBe resulting from a search on ‘coronavirus,’ the top hits from MERS and SARS. PR stunt or not, they did win the most recent CASP ‘competition’, so arguably it’s probably our best shot right now – and I am certainly not satisfied that they have been sufficiently open in explaining their algorithms though I have not checked in the last few months. No one is betting anyone’s health on this, and it is not like making one wrong turn in a series of car directions. Latest prediction algorithms incorporate contact map predictions, so it’s not like a wrong dihedral angle sends the chain off in the wrong direction. A decent model would give something to run docking algorithms against with a series of already approved drugs, then we take that shortlist into the lab. A confirmed hit could be an instantly available treatment, no two year wait as currently estimated. [ALA added bold face]

jelabarre59Silver badge

Re: these structure predictions have not been experimentally verified

Naaaah. Can’t possibly be a stupid marketing stunt.

Well yes, a good possibility. But it can also be trying to build on the open-source model of putting it out there for others to build and improve upon. Essentially opening that “peer review” to a larger audience quicker. [ALA added bold face]

We shall see.

Anonymous Coward

Anonymous CowardWhat bothers me, besides the obvious PR stunt, is that they say this prediction is licensed. How can a prediction from software be protected by, I presume, patents? And if this can be protected without even verifying which predictions actually work, what’s to stop someone spitting out millions of random, untested predictions just in case they can claim ownership later when one of them is proven to work? [ALA added bold face]

 

 

SOURCES

 

  • AI-predicted protein structures could unlock vaccine for Wuhan coronavirus… if correct… after clinical trials It’s not quite DeepMind’s ‘Come with me if you want to live’ moment, but it’s close, maybe

Experimentally derived by a group of scientists at the University of Texas at Austin and the National Institute of Allergy and Infectious Diseases, an agency under the US National Institute of Health. They both feature a “Spike protein structure.”

  • Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

See all authors and affiliations

Science  19 Feb 2020:
eabb2507
DOI: 10.1126/science.abb2507

 

  • Israeli scientists: We have developed a coronavirus vaccine

https://www.fromthegrapevine.com/health/coronavirus-vaccine-israel-migal-research-institute-david-zigdon

Other related articles published in this Open Access Online Scientific Journal include the following:

 

  • Group of Researchers @ University of California, Riverside, the University of Chicago, the U.S. Department of Energy’s Argonne National Laboratory, and Northwestern University solve COVID-19 Structure and Map Potential Therapeutics

Reporters: Stephen J Williams, PhD and Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2020/03/06/group-of-researchers-solve-covid-19-structure-and-map-potential-therapeutic/

 

  • Is It Time for the Virtual Scientific Conference?: Coronavirus, Travel Restrictions, Conferences Cancelled Curator:

Stephen J. Williams, PhD

https://pharmaceuticalintelligence.com/2020/03/06/is-it-time-for-the-virtual-scientific-conference-coronavirus-travel-restrictions-conferences-cancelled/

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