In January, virologists in China isolated a new virus. In March the Coronaviridae Study Group of the International Committee on Taxonomy of Viruses named the virus SARS-CoV-2. Most people call it the coronavirus. The virus causes a disease called Covid-19. The vocabulary can be very confusing. The goal of this article is to shed some light on the various terms.

Let’s start with taxonomy, a scheme of classification of things, especially living things. A Swedish naturalist named Carolus Linnaeus is considered the “Father of Taxonomy”. In the 1700s, Linnaeus developed a method we still use today to name and organize species. The table below shows one version of the Linnaean Classification of Humans.

Kingdom

Animalia

Phylum

Chordata

Subphylum

Vertebrata

Class

Mammalia

Subclass

Theria

Infraclass

Eutheria

Order

Primates

Suborder

Anthropoidea

Superfamily

Hominoidea

Family

Hominidae

Genus

Homo

Species

Sapiens

The level of detail can make your head hurt. We humans are often referred to simply as Homo Sapiens. There is much more detail beyond the table if you want to drill down. When it comes to viruses, the taxonomy makes the human taxonomy look really simple. See the following table from Nature.com to get a glimpse of it. The complete 8,000-word article is here.

To put the complexity in perspective, consider SARS-CoV-2, the cause of the pandemic, is one of 6,828 virus species which have been named. Researchers say they know of hundreds of thousands more species. Some believe there may be trillions waiting to be found. This is the virosphere.

The good news is there are a number of profound research projects underway to deal with the world of viruses. This is incredibly important because viruses are not going away. Some experts are saying a new and different virus will appear next year or even later this year. Hopefully, we will be ready. The wake up call this time was so loud and clear, I believe we will be prepared.

One new approach under development is the use of synbio, as described in last week’s e-brief. A vaccine made from synthetic ingredients can potentially offer some significant advantages. The big one is scalability. Synbio vaccines could be produced efficiently for millions or even billions of doses. Synbio vaccines are developed using computer models, not flasks and test tubes. With billions of calculations, a nanoparticle can be designed which has the exact properties desired. The really big breakthrough with synbio is the attachment of multiple different viral molecules to the nanoparticle and thereby create a universal coronavirus vaccine. One vaccine for all corona viruses. That will be the breakthrough.

Another positive development in the silver lining of the coronavirus cloud is tech companies large and small are jumping in the boat to help. For example, IBM is collaborating with the White House Office of Science and Technology Policy and the Department of Energy to launch the COVID-19 High Performance Computing Consortium. The Consortium will provide supercomputing power to researchers developing predictive models to analyze the coronavirus progression and identify potential treatments. Researchers from around the world can submit proposals, and the Consortium will select the projects which could have the most immediate impact. Other partners in the consortium include NASA, MIT, and the Argonne National Laboratory.

Another significant Covid-19 effort is taking place at Oak Ridge National Laboratory in Oak Ridge, Tennessee. As of November 2019, Oak Ridge had the fastest supercomputer in the world. It is capable of performing one thousand million million (1015) operations per second.

Scientists at Oak Ridge have deployed the massive supercomputer to look for compounds which can bind to the “spike protein” of the virus. It is the spike protein which the virus uses to infect host cells. The right compound could render the spike protein ineffective, and the virus would be stopped from spreading. Using digital models, the supercomputer can simulate how particles in the viral protein would react to different drug compounds. The researchers started with a list of 77 compounds and narrowed it down to the top seven most promising candidates which could become effective treatments for covid-19. The research is at the early stage but I believe we can be hopeful.

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The coronavirus numbers are growing as expected, and will be growing much more. There are many websites with coronavirus information. I did some digging around to find the ones which presented the data I wanted to see. I am sharing below the sites I have found most useful to see how the data is trending. Fyi.

Global
States 
Connecticut
Florida 
New York
Pennsylvania

The numbers are going to rise significantly from what already looks high. We should not be surprised or alarmed. More tests are going to happen and more cases will be found. If you are interested in the impact of the numbers, I suggest reading “The Sober Math Everyone Must Understand about the Pandemic” by Jason Warner. The essence of his article is if we take action on social distancing now, we can bend the curve and save a lot of lives and avoid a crisis for our healthcare system. If we do not do a good job of social distancing, like what millennials were doing on Florida beaches, then we face catastrophe. Jason’s article steps through the numbers, and it is not pretty.


I posted an op-ed piece in a technical newsletter called TNW. The title of the op-ed is “Mobile voting is far from perfect, but it’s better than what we have now”. The current situation of voting challenges is proof perfect. You can read the op-ed it here. The Congress could do remote voting very easily and safely. One Senator said the Senate should get with it in the 21st century. The vote on the rescue package was 96-0. The four missing Senators were at home. Senators are so technically unaware they could agree on a way to allow the four Senators to vote remotely. The speaker of the house said, “We can not vote from home”. As I have said so many times, we can put a robot on Mars, but we can’t figure out how to vote remotely.


The next author event is scheduled for May 15th at Founders Hall in Ridgefield, CT. Time will tell if it will need to be rescheduled.

Date

Time

Location

June 11, 2020

7:00 PM

Ridgefield Library
472 Main Street, Ridgefield, CT 06877

May 15, 2020

1:00 PM

Founders Hall
193 Danbury Rd, Ridgefield, CT 06877

March 19, 2020 (to be rescheduled)

11:30 AM

AdventHealth Palm Coast Community Forum
60 Memorial Medical Pkwy
Palm Coast, FL 32164

February 14, 2020

8:30 AM

Senior Provider Information Network
2 Corporate Dr.
Palm Coast, FL

February 6, 2020

1:00 PM

Hammock Dunes Club
Palm Coast, FL
Private event: Request invite
Mail to [email protected]

November 14, 2019

1:00 PM

New Fairfield Senior Center
33 CT-37
New Fairfield, CT

October 9, 2019

5:30 PM

Crowne Plaza Hotel
18 Old Ridgebury Rd
Danbury, CT

August 29, 2019

5:30 PM

The Boiler Room
Hawley Silk Mill
8 Silk Mill Drive
Hawley, PA

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Microscopic virus close up with 3D rendering

The numbers continue to grow and, as Dr. Fauci says, it is going to get worse before it gets better. If we all do a good job in social distancing, the curve will bend sooner rather than later. The government is pulling out all stops for therapeutic solutions, as Dr. Kuhn described on Thursday. As I wrote last week, there is a silver lining to the dark cloud hovering over all of us. One of the numerous positive things going on is the development of a vaccine for Covid-19.

Significant progress is being made by Moderna Therapeutics, CureVac, and Inovio Pharmaceuticals, who are going as fast as possible to begin human testing. Nevertheless, the approach they are taking uses biological DNA and RNA as the core ingredient. As advanced as the current development process is, vaccines as we know them have a number of shortcomings. The most visible shortcoming is they take years to develop and manufacture. Potentially more significant is they become obsolete if and when the virus evolves, which it will. There are already multiple strains, and there will be more. Finally, the immune response the vaccines produce may not be strong enough to be effective.

A totally new approach is under development using synbio. The Bill and Melinda Gates Foundation has put $60 million into coronavirus research including for the synbio effort. If you read Daniel Suarez science fiction novels (among my favorite authors) you have already heard of synbio. It takes a major role in his book, Change Agent, which takes place in 2045, and is about Interpol’s Genetic Crime Division which grapples with a new type of crime: illicit genetic editing. It is quite a thriller.

Synbio stands for synthetic biology. Synbio is mostly about the design and construction of new biological parts, devices, and systems, and the re-design of existing, natural biological systems. More specific to the issue of the day, synbio may replace the DNA and RNA ingredients mother nature has provided for the development of vaccines with synthetic ingredients.

A vaccine made from synthetic ingredients can potentially offer some significant advantages. The big one is scalability. Synbio vaccines could be produced efficiently for millions or even billions of doses. Another advantage is synthetic ingredients do not need to be refrigerated. This would be a huge benefit for places like sub-Saharan Africa.

Synbio vaccines are developed using computer models, not flasks and test tubes. With billions of calculations, a nanoparticle can be designed which has the exact properties desired. The really big breakthrough with synbio is the attachment of viral molecules to the nanoparticle. Neil King at the University of Washington and his synbio colleagues knew there would be another coronavirus epidemic, like the SARS and MERS outbreaks before the current Covid-19 outbreak. King said, “…there will be another one after this,” perhaps from yet another member of this virus family. We need a universal coronavirus vaccine.” One vaccine for all corona viruses. That will be the breakthrough.

Sharon Begley wrote a beautiful article in STAT which explains the synbio efforts underway in much more detail. See To develop a coronavirus vaccine, synthetic biologists try to outdo nature. STAT has great articles about life sciences and the fast-moving business of making medicines.

The coronavirus numbers are growing, and will be growing much more. There are gazillions of websites with coronavirus information. I did some digging around to find the ones which presented the data I wanted to see. I am sharing below the sites I have found most useful to see how the data is trending. Fyi.

Global
States 
Connecticut
Florida 
New York
Pennsylvania

The numbers are going to rise significantly from what already looks high. We should not be surprised or alarmed. More tests are going to happen and more cases will be found. If you are interested in the impact of the numbers, I suggest reading “The Sober Math Everyone Must Understand about the Pandemic” by Jason Warner. The essence of his article is if we take action on social distancing now, we can bend the curve and save a lot of lives and crisis for our healthcare system. If we do not do a good job of social distancing, like what millennials have been doing on Florida beaches, then we face catastrophe. Jason’s article steps through the numbers, and it is not pretty.


I posted an op-ed piece in a technical newsletter called TNW. The title of the op-ed is “Mobile voting is far from perfect, but it’s better than what we have now”. The current situation of voting challenges is proof perfect. You can read the op-ed it here. The Congress could do remote voting very easily and safely. One Senator said the Senate should get with it in the 21st century. The speaker of the house said, “We can not vote from home”.


The next author event is scheduled for May 15th at Founders Hall in Ridgefield, CT. Time will tell if it will need to be rescheduled.

Date

Time

Location

June 11, 2020

7:00 PM

Ridgefield Library
472 Main Street, Ridgefield, CT 06877

May 15, 2020

1:00 PM

Founders Hall
193 Danbury Rd, Ridgefield, CT 06877

March 19, 2020 (to be rescheduled)

11:30 AM

AdventHealth Palm Coast Community Forum
60 Memorial Medical Pkwy
Palm Coast, FL 32164

February 14, 2020

8:30 AM

Senior Provider Information Network
2 Corporate Dr.
Palm Coast, FL

February 6, 2020

1:00 PM

Hammock Dunes Club
Palm Coast, FL
Private event: Request invite
Mail to [email protected]

November 14, 2019

1:00 PM

New Fairfield Senior Center
33 CT-37
New Fairfield, CT

October 9, 2019

5:30 PM

Crowne Plaza Hotel
18 Old Ridgebury Rd
Danbury, CT

August 29, 2019

5:30 PM

The Boiler Room
Hawley Silk Mill
8 Silk Mill Drive
Hawley, PA

Tagged with: ,

Novel Coronavirus. Microscope virus close up. 3d rendering.

One thing all the Coronavirus experts agree on is the virus will continue to spread for some time. One important question related to this is how contagious is the virus? The key measure is transmissibility, how rapidly the disease spreads. Transmissibility is indicated by its reproductive number, abbreviated as Ro and pronounced R-nought or r-zero. Ro represents the average number of people to which a single infected person transmits the virus. On January 23, the World Health Organization estimated Ro for covid-19 to be between 1.4 and 2.5. Other studies have estimated Ro between 2.4 and 4.0. An outbreak with a Ro less than 1 will gradually disappear. A Ro of 4.0 would produce an extremely bad situation. For comparison, the Ro for the common flu is 1.3 and for SARS it was 2.0.

If we do nothing, then Ro will be high and the number of cases and deaths will be very high. As predicted by some, if we do nothing, the spread could go exponential and lead to millions of cases. If we take aggressive actions, however, the Ro will be lower and the growth rates of the disease will be flattened.

The spread of the disease to date should be a wake up call for every person and organization. Supplies are being hoarded which should already have been on hand. Action plans are rolling out, but they should have been ready from Day 1. The government is prepared for hurricanes but not totally prepared for a pandemic. The good news is the Federal, State, and Local governments are learning a lot from the situation and the emergency plans to reduce bureaucracy should have a very positive impact. Public private partnerships in retail and lab testing are set to solve the critical problem of testing. The wake up call may lead to a silver lining in the coronavirus cloud. Following are some components of the silver lining.

  1. The development time for vaccines must continue to get shorter. The good news on this is they can sequence the genome of the virus in hours. Sequencing the first human genome cost about $1 billion and took 13 years to complete. In the case of the coronavirus, the detection of the virus was confirmed in France on Friday, January 24. Later that day, the Institut Pasteur received samples of three suspected cases they detected with the novel coronavirus and began preparation for the sequencing. The process started on Monday and was completed early Tuesday evening. Remarkable. The next step is the process for creating, testing, and manufacturing a vaccine. The process to get from recipe to tested and available vaccine needs a major upgrade and modernization.
  2. A major information technology (IT) upgrade is needed between state and federal public health organizations. Now that millions of test kits are being distributed, the public will be asking what were the results. As it stands, the answer from the government will have to be, “We don’t know”. This is a problem I wrote about in Health Attitude in 2015. State governments have been reluctant to share data with the Federal government. It is partly cultural and partly because there is no efficient way to do the sharing. The bureaucracy involved is immense. The Feds have spent hundreds of millions on incentives to get states to share their data but it is not happening as it could. The benefits of sharing will be huge. Once millions of consumers, labs, and providers add data to an anonymized national database, a multitude of data will become available for the greater good. Researchers can study the anonymized data and gain insights about the health of the population at a community level, nationally, or globally. This will be extremely helpful for establishing travel bans and imposing quarantines on a more pinpointed basis rather than a cancel everything everywhere approach. Hopefully, better data sharing will be in place before the next pandemic.
  3. A big question which needs an answer is what is the best therapeutic for treating covid-19? Various drugs are being tried. This is new. Historically, if you have a certain disease, you are prescribed a certain drug. For example, if you have breast cancer, then take XYZ drug. Oncologists have learned a combination of drugs may work better than the normally prescribed drug. Either approach in a sense implies one size fits all. In fact, every cancer is different and very personal. This is where AI and machine learning (ML) come in. Globally, more than 350,000 chemical compounds (including mixtures of chemicals) have been registered for production and use. Might one of them work to cure covid-19? I would say it is likely. How do they find the chemicals which can work? ML can be applied to all hundreds of thousands of possible cures based on the genomic sequence of the patient and of the novel coronavirus. You might think of it as a digital clinical trial done in hours, not months. I am confident this type of approach will evolve. 
  4. Like you, I have been receiving emails from a lot of organizations ranging from global travel companies to our local dry cleaner. They are all very similar. One I received caught my eye. They said, “Currently, our entire staff is equipped to work remotely and to support our clients and one another via phone and email. We will send updates to you as appropriate, and information regarding our status and availability will be posted on our website”. This is an organization which was prepared. Many were not. Many companies and schools and conferences are saying they are going remote: e-learning, e-meetings, e-conferences. Saying you are e-whatever doesn’t make it happen. Do all the employees and customers have access to reliable high-speed bandwidth? Probably not. Are they all trained on how the e-engagement works? Probably not. Effective e-whatever takes a lot of planning, testing, and training. The good news is bandwidth is generally much better than it was a decade ago. The wakeup call will result in organizations asking key questions. How well do we function as an e-organization? Before we go back to “normal” do we really need everybody to go back to the way it was? Can we streamline our organization and our services by fine tuning our e-capabilities?
  5. The pandemic is exposing the weaknesses of our paper-based government, including how we vote. Social separation is being urged but to vote, thousands had to stand in line for hours. Those that voted remotely did so by licking an envelope and stamp. Online and mobile voting can work with security, privacy, accuracy, and verifiability if we put our mind to it. Digital discourse can strengthen our democracy. The discourse doesn’t have to be in crowded rooms. Hopefully, the wake up call will get policymakers thinking about the many things we do by touching paper touched by others. Real estate closings, bank loans, paying for things with cash, and the list goes on.

The pandemic has provided a wake up call. If we do nothing, hide like a hermit, and hope it goes away, things will get worse. If we take aggressive actions as described at coronavirus.gov, we can flatten the curves and start thinking about covid-21 and how we can prepare now.

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