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Case Update, March 29th, 2021; Dr. Shane Crotty on Vaccines and Variants

This is a COVID new case update.  I’ll also discuss new cases world wide, and discuss a new video from immunologist Shane Crotty with lots of important information on vaccines and variants.

In the US, we’re starting to see an increase in new case numbers in several states, Michigan and New York in particular.  This may be because of the relaxing of requirements by many municipalities, but may also be because of some of the new variants arriving in the US.  More on the new variants below. 

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, March 29th, 2021
Endcoronavirus US States, March 29th, 2021

New case numbers have stabilized in California and San Diego County with around 2000 new cases a day in California and 300 in San Diego. We have yet to see a clear uptick in cases in those 2 regions, but we may see this soon.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers have been calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered. Recently, however, this would produce an active case number that is too low to make sense in comparison to San Diego. This graph estimates 17 to days to recover in January, but gradually moves to 22 days for mid-March. I’ve lost confidence that I can make an Active Case plot that is accurate, so this will probably be the last time I post this for California. Let me know if you think it’s still useful.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are reported by San Diego County. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.

Internationally, the US and UK are doing better than average at the moment, but many countries scattered all over the world, with concentrations in Eastern Europe and South America, are seeing new surges in cases. The US and UK are both vaccinating heavily right now, with vaccine rollouts moving slowly in continental Europe, so vaccination may play heavily in this pattern.  Also several new variants of the SARS-2 virus are more infectious than the original strain and likely factor in these new surges.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus Countries, March 29th, 2021

Important new video with Dr. Shane Crotty:  MedCram has posted a new video interview with Dr. Shane Crotty, an immunologist in San Diego. His work looks into immune system responses to vaccination as well as native infection.  He has several very interesting points to make about SARS-2 immunity and vaccines. First, he says that those infected with SARS-2 do have significant lasting immunity for many months, although it does go down a bit over time.  Different people can respond very differently, however, and reinfection is possible in some.

Regarding vaccines, he said that those who have been infected have a good but not great immune response, but it is significantly boosted by a single vaccine dose, gaining an immune response higher than those vaccinated alone. So there is a good reason to be vaccinated if you have already been infected.  Of course, if you’ve been infected, you may choose to wait until at-risk people have been vaccinated before you get a vaccine booster.

As for variants, he says there are 2 broad categories of variants, those similar to the UK variant (now commonly called B.1.1.7), and those similar to the South Africa variant (B.1.351).  Both new strains are more infectious than the original Wuhan strain.  The big difference between them is that those who have had SAR-2 are immunized against the UK strain, but not the South Africa strain.  Also, the Astra-Zeneca vaccine does not protect well against the South African strain, and the Pfizer and Moderna vaccines appear to be less effective as well.  The good news is, the Johnson and Johnson and Novavax vaccines do appear to protect against the South Africa strain. This suggests that although the South Africa strain is different, it isn’t so radically different that we have nothing to fight it with. 

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Update, April 6th
A new small study from Pfizer suggests that their vaccine does work on the South Africa variant. The patient number in this trial is small, so they still don’t know exactly how effective it is.
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Soberingly, the South Africa strain has reached the US, so if we see a surge in the next few weeks, this strain may be at least partially responsible.

Impact on ADE?  If you’ve read my posts on ADE, then you know that the danger from ADE may come when a different strain arises.  With the South Africa strain arriving in the US, we may be able to see if ADE will have an impact with SARS-2 in the next few weeks and months.  So far, new death numbers have come down with Wave 3, and there is no apparent impact from ADE on case severity.  I will certainly be watching to see if this changes.

Graph is by me, from data collected from Johns Hopkins University COVID site.

Don’t fear, but be smart,
Erik

What is Science?

This is a long post about the philosophy of science. I probably should have written this one a long time ago, but here it is. 

During the pandemic, we’ve often heard scientists and commentators say “I’m just following the science.”  Confusingly, we’ve heard people on all sides of the issues say this, pro-maskers, anti-maskers, vaccine fans, vaccine detractors, people who love Hydroxychloroquine, and those who think it kills people.  Very often, when people have used the word “science” in the last year, they’ve used it in a way that you DIDN’T learn in high school biology class (thanks, Mr. Walker!).  So what do people mean when they say this, and how can you evaluate what they are saying?

When you hear the word “science” on the news or in discussions on the pandemic, other definitions are often smuggled in. I’ll give you a few different ways people use the word “science”, and then I’ll talk about how you can evaluate science related discussions.

1) In actuality, science is a method for measuring things in the natural world, and using reasoning and the scientific method to make, falsify, and confirm hypotheses about natural things.  Science has been phenomenally successful about describing aspects of the natural world, as well as producing useful applications for communication, travel, health, manufacturing, the arts, and nearly every conceivable human endeavor.  The incredible success of science has given it enormous cultural power as well, and many ascribe to it powers that it does not have. By definition, science measures and describes the natural world, but cannot describe many common aspects of reality, questions like “what is justice?” or “what is the meaning of life?”. 

While many contributed to the Scientific Method, the steps were formalized by Francis Bacon.  The steps include 1) the formulation of a question, 2) the development of a hypothesis, or a guess about what actually happening, 3) a prediction about what impact the hypothesis may have on a system, 4) doing experiments to test the hypothesis, and last 5) analyzing results, to include falsifying or confirming the hypothesis and forming a new question.

The scientific process is not a slow gradual accumulation of truth.  It’s often ugly, with long searches down the wrong path before finding the right one. Fields can experience sudden, jerky changes in direction.

2) The collection of facts currently believed by the majority of scientists.  When many in our current culture use the word “science”, this is what they mean. The phrase “settled science” often refers to this.  But scientific truth is not decided by a vote.  Yes, if a “fact” is believed by most scientists, it’s more likely to be true, but science history is full of people who had “weird” ideas that later turned out to be right.  By definition, topics under current study are not well understood, and there can be widely varying opinions about what’s going on. 

It’s always OK for a scientist to question current thought.  Trust me when I say that having a PhD does not mean that other scientists have to believe you.  I’ve heard shouting matches at conferences over what to believe about seemingly simple things.  

Real “Truth” transcends opinion.  Things are true whether you believe them or not. Science is the search for the truth about the natural world, not the search for ways to force your view on others.

Which leads to…

3) The collection of facts currently believed by scientists who agree with me.  When things are murky and not well understood, which is quite often in active fields, there can be 2 or more models of how a system is working. Sometimes the evidence that is out in the world can appear to be contradictory. This may be because some of the evidence is wrong, or because conclusions based on the evidence is wrong, or because a crucial piece of evidence is still missing, or because the system is just more complicated than anyone is aware of. At this point, a good scientist will try and rethink the available evidence or perhaps design a new experiment to try and get at something still unknown.  Instead, some people, even good scientists in a moment of weakness, will simply declare that their view is correct prematurely.  Scientists must always seek to be more persuasive, and not just shout louder.

4) The collection of facts currently believed by me, right now.  This definition is common for those who believe an outlier view.  It’s not bad to have a view that is outside the current orthodoxy, this is how scientific breakthroughs happen, but a person in this position must seek even more to persuade with evidence, not just be dogmatic.  Do more internet work, read more literature, or design another experiment.

5) An atheistic worldview, as in “I believe science”. Science is great at discovering information about the natural world, but it can’t answer the big questions. What some call “science” in this way is really “naturalism”, the belief that only matter and energy exists. It rejects any worldview that includes a transcendent or supernatural component. Science alone does not support this worldview, because by definition, science can’t “prove” the non-existence of things outside the known universe. Other philosophical structures are necessary to support this view.

So how do you figure out what’s really true about a scientific opinion being presented.  This can be difficult, but it can be a little easier to figure out if someone is abusing “science.” Here are some clues that science might be being misused.  You’ll have to dig deeper to be sure:

  1. A real scientific argument includes a conclusion supported by evidence.  Does the person talking give any evidence for their position? Often, people just make an assertion, a claim without evidence.  This is OK if they can back it up, but very often they can’t.  Ask “can you clarify that?” or “how did you come to that conclusion?”
  2. When questioned, a person should have evidence for their claim. If instead they call you anti-science, or *phobic or *ist, then they are abusing science.
  3. If a story or comment starts with “X person is brilliant and has been in the business for years”, this is often a red flag for me.  While a person’s qualifications are important, they must still present evidence.  A title or degree is not enough for them to be automatically believed.  The more glowing the terms used to describe a source, the more I’m suspicious that they are about to spout nonsense.
    Yes, these even applies to me.  If you tell someone “This Facebook friend of mine is a real scientist and he says <something really smart>”, you should rightfully expect your friend to ask what evidence I had for my claim. If you don’t know, then re-read my post, or just message me!  I’m happy to work through it with you, and I’ll tell you outright if I’m just speculating.
  4. News articles are OK, but they are only a starting place.  If a person references a news article, they still have homework. What news outlet? What evidence did the author use? Journalists often misunderstand or misrepresent information from scientific sources.
  5. Real evidence can be a scientific paper, a study learned about on the radio (who presented it?), or a comment by an authoritative source (who is the source?).  Each of these can in principle still be wrong, but they have more weight than other sources.
  6. Often, we gain knowledge about the world from someone we trust, an authority on the matter.  This is a fine way to learn things. Your parents were the first authority that you used for learning much of what you needed to know.  But authorities, even good ones, are not always right.  You learned this about your parents when you were a teenager. It’s OK to pick someone you trust as an authority on scientific matters, but still don’t believe everything you hear.  The CDC, the WHO, Dr. Fauci, the President (either one), yes even me, have been right about some things and wrong about some things during COVID. During an evolving situation, expect opinions and “facts” to change as more information is gathered.  Your favorite authority doesn’t know everything.

Of course, the debate on several COVID related topics have become politicized, which can make it difficult for scientists to do good work, and often VERY difficult for lay people to know the truth. I feel for you. It can be really difficult for folks to figure out what’s true about something that’s not in their field.  I feel the same way about climate change, an important topic of frequent debate that’s not in my field.  Don’t feel dumb if you have trouble figuring out what’s going on.  Lots of folks are abusing science, trying to make you agree with them.  Hopefully I’ve given you a few tips on how to discover the truth.  Here’s an article on how to communicate scientific things!

Don’t fear, but be smart,
Erik

Fall Wave “Animation”

Below is an “animation” of sorts, photos from endcoronavirus, about a week apart, with one photo from June, and then a series starting in September. I’ve said that the Fall wave started in the North and then moved to the South as the wave progressed. I think you can see this in this series of photos. You can also see a flare up in new cases in January, right after Christmas.

Counties are colored based the change in cases, not the number of cases. Red is increasing cases, orange is falling or constant cases, yellow is cases almost under control, dark green is cases under control, light green is no cases.

Erik

June 9th, 2020
September 15th
September 23rd
September 30th
October 13th
October 21st
November 1st
November 11th
November 19th
November 24th
November 28th
December 5th
December 10th
December 12th
December 21st
December 29th
January 5th, 2021
January 10th
January 18th
January 25th
February 1st
February 10th
February 18th
February 24th
March 3rd
March 10th
March 15th
March 23rd

Case Update: December 12, 2020; Important news on Vaccines and ADE!

Here’s an overdue case update. Cases continue to rise for the US, California, and San Diego County. The timing of the current US peak makes it clear that the bump is directly related to the Thanksgiving holiday, starting less than a week after Thanksgiving, and after cases had started to come down. LA County currently has more that 100,000 active cases, more than twice the number than the next highest county, Cook County, the home of Chicago.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.

New case peaks have left the Northern states and are now centered in the Southwest and Northeast.

Endcoronavirus County Level Map, December 12th, 2020

San Diego County now has 24,000 active cases, far higher that the 4,000 we had at the low point between peaks 2 and 3.

Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.

More on ADE and Vaccines: Some potential very good news for me on the vaccine front. For months I’ve been warning about ADE, the phenomena that some viruses can be even more dangerous in a second infection than the first. Karen Parrott, a former colleague at Quest Diagnostics, often provides me with interesting COVID related stuff. This week she sent me a podcast featuring Paul Offit, the developer of the first Rotavirus vaccine and an author of many books on immunology and vaccine production. I am not an immunologist but he is. More importantly, he’s the first authoritative person that I’ve heard in the media speak at length on the ADE issue and how it relates to COVID. He claims in the attached clip (time stamped at 14:40) that the current vaccines do not appear to trigger the ADE pathway in animal models, and human trial subject never displayed the signs that ADE was involved in secondary exposures. This difference from SARS-1 and MERS may be related to the fact the SARS-2 is much less virulent than these other 2 viruses.

This makes me more optimistic that the vaccine will be safe from an ADE perspective. I won’t be able to get the vaccine for some time, but I am more willing to get it now than ever before. Several physicians I know are eager to get it as soon as it is available. This is great news!

In the interest of full disclosure, I will point out the some patients receiving the vaccine the UK have experienced some injection site irritation, especially in those with allergies. This is actually somewhat normal for vaccines, and appears to pass within a few days.

In addition, now that mRNA vaccines have been produced for the first time, future development of this new kind of vaccine should be even faster than this time!

Don’t fear, but be smart,
Erik

Antibody Dependent Enhancement

Originally posted July 7th, 2020

I’m going to bring up an issue that I’ve been avoiding talking about for some time. I’ve been avoiding talking about it because it’s not a certainty, and also because the possibility will be scary for some. The reason I feel compelled to talk about it now is that many are having a hard time understanding why I am still so concerned about the virus when the fatality rate is low and dropping, and folks want to get back to normal life. I’m even hearing about young people having COVID parties in which people gather with a sick individual so they can all get infected and be immune from the virus thereafter.

Before I share this, I’ll also say that the medical community is doing a better job treating patients with COVID, and the disease is becoming more survivable. In addition, we now know a lot about how the virus is spread, and if a person wants to remain uninfected, they can do that, while still getting together with friends and family, and still working and getting on with life. You can be reasonably certain you will not get infected if you do the following:

1) Wear a mask or face covering in public. Avoid places with unmasked people.
2) Keep 6 ft away from others.
3) Avoid indoor gatherings, especially ones in which singing or shouting is likely.
4) Small outdoor gatherings are fine, even without masks, if everyone maintains a distance. Have guests bring their own food.
5) While many restaurants are open for limited indoor seating, I personally am still not comfortable eating indoors at a restaurant. I enjoy eating outdoors at restaurants, however.

Antibody Dependent Enhancement: Several years ago, scientists were developing a vaccine against Dengue Fever, a mosquito borne disease which causes debilitating joint pain in patients. Some time after trial vaccination, several vaccinated patients died suddenly of Dengue Fever. This became the most studied example of Antibody Dependent Enhancement (ADE). Normally, for the annual flu let’s say, a person gets infected by the flu, is sick for a few days, and the immune system develops a response by creating antibodies against that specific strain of the flu. If they are exposed again in a month, nothing will happen. If the patient is exposed to a different strain the following year, they may still get sick, but the antibodies they developed the year before may help them have less severe disease and recover more quickly. Part of the immune response is that some immune cells display antibodies on their surface to capture new invaders.

With Dengue and some other viruses, the first stages are normal. A person gets infected and develops a response. If they get re-infected a month later, nothing happens. But if they get infected with a slightly different strain months or years later, instead of being protected, the virus attaches to antibodies displayed on immune cells and uses the antibodies as a site of entry into the immune system. The immune system is quickly infected, and the patient has a more severe disease with the second infection. Some estimates are that disease may be 3-4 x more severe in these patients.

As it turns out, SARS-1, which arose in 2002, and MERS, which has small outbreaks every year, are both Coronaviruses and both appear to be able to use the ADE pathway. This raises the possibility that SARS-2, the current virus, can also use the ADE pathway. This means that a person infected for a second time with a different strain of SARS-2, or any other Coronavirus for that matter, may be at much higher risk for severe disease.

This is why I’m not in favor of pursuing herd immunity as a pathway out of this crisis, because it will prime people for ADE related problems if a similar strain should strike next year.

This is not a new idea. If you search for “ADE” or “Antibody Dependent Enhancement”, you will see many articles, some peer reviewed from respected journals, on the phenomena. Dr. Fauci has even referenced it using the term “enhancement” when talking about vaccine development.

Why haven’t the government public health departments been more open about this? They tend to make statements only based on what they can be reasonably certain of, which is why they have been so slow to react to many aspects of the current crisis.

Again, it’s not certain that ADE will play a role next year. It’s too early to know. I’m informing you of the possibility so you can make wise decisions for you and your family.



Update: November 20, 2020

Since writing the above post, things have changed a little. There have been a handful of known cases of people being re-infected with SARS-2. In some of these patients, symptoms were worse, while in others, symptoms were less severe. In all of the well characterized cases, the 1st and 2nd strains that infected them were different, suggesting that it’s not a re-infection by the same strain, but a new infection by a different strain.

We’ve had at least 2 main strains in the US, SARS-2 which arrived in January or February, and a strain called D614G which probably arrived in April or May and likely caused the 2nd wave in June and July. The D614G strain is likely more infectious than the original SARS-2 strain, but is perhaps less virulent, since the fatality rate during the second wave appears to have been lower. In fact, there may have been several strains circulating around the world and the US for much of the pandemic.

How does this all relate to ADE? The fear with ADE is that a 2nd infection will cause worse symptoms than with the first infection. This may still be true. But we’ve had several circulating strains and so far, no real evidence the re-infections have universally been worse. So it appears for now that the ADE experiment is already going on, and that perhaps the phenomena will not have as great an impact as I feared. I am currently cautiously optimistic that ADE will not cause significant additional mortality.

This also has some impact on the vaccine discussion that is currently ongoing. If ADE will not have a significant impact, than the vaccine may be safer that I previously thought, and I have become cautiously optimistic about the success of the vaccine.

Update: December 12th, 2020

More on ADE and Vaccines: Some potential very good news for me on the vaccine front. For months I’ve been warning about ADE, the phenomena that some viruses can be even more dangerous in a second infection than the first. Karen Parrott, a former colleague at Quest Diagnostics, often provides me with interesting COVID related stuff. This week she sent me a podcast featuring Paul Offit, the developer of the first Rotavirus vaccine and an author of many books on immunology and vaccine production. I am not an immunologist but he is. More importantly, he’s the first authoritative person that I’ve heard in the media speak at length on the ADE issue and how it relates to COVID. He claims in the attached clip (time stamped at 14:40) that the current vaccines do not appear to trigger the ADE pathway in animal models, and human trial subjects never displayed the signs that ADE was involved in secondary exposures. This difference from SARS-1 and MERS may be related to the fact the SARS-2 is much less virulent than these other 2 viruses.

This makes me more optimistic that the vaccine will be safe from an ADE perspective. I won’t be able to get the vaccine for some time, but I am more willing to get it now than ever before. Several physicians I know are eager to get it as soon as it is available. This is great news!

In the interest of full disclosure, I will point out the some patients receiving the vaccine the UK have experienced some injection site irritation, especially in those with allergies. This is actually somewhat normal for vaccines, and appears to pass within a few days.

Now that mRNA vaccines have been produced for the first time, future development of this new kind of vaccine should be even faster than this time!

Update: April 13th 2021

ADE and the next SARS virus: I wanted to explain a little more about my continued concerns about ADE. As the pandemic progresses and we have numerous variants circulating around the world and the US, ADE does not appear to have had an impact on the current situation. This is certainly good news. If it did have an impact, we would be seeing additional deaths from the new variants, which we do not.

My continued concern comes because ADE impacts our ability to fight the NEXT virus. SARS viruses (SARS, MERS, SARS-2) have the ability to easily infect the immune systems of those previously infected with closely related but different strain of the virus. If a future strain of SARS comes out, let’s call it SARS-3 for now, ADE may become a big deal. I stress that this is only theoretical at this point. SARS was moderately infectious, but also very pathogenic, giving all known patients severe symptoms and killing 10%. It was actually less dangerous globally, since outbreaks tended to be detected early and quickly snuffed out. SARS-2 is highly infectious, but much less pathogenic. It’s greater global impact came from it’s very high infectiousness and very long incubation time, being passed even from pre-symptomatic patients. The tendency of all viruses is to become more infectious and less pathogenic over time, a pattern followed by SARS and SARS-2. If we have a SARS-3 someday, it will likely be even more infectious than SARS-2, but less pathogenic. On the other hand, MERS is more pathogenic than SARS, so this pattern doesn’t always follow. The next time another SARS coronavirus breaks out, we will need to be very careful initially until we understand the parameters of the new virus.

So what do you do if you had COVID or had a COVID vaccine if a SARS-3 comes out? If that happens, vaccine production will likely be much faster than this time. Be very careful with the virus initially, and get the new vaccine as soon as it is available to you, because you may be at greater risk for severe symptoms. I know some of this is confusing and counter-intuitive! Feel free to ask questions below!

More than ever, don’t fear, but be smart,
Erik


A selection of relevant papers:

ADE and it’s potential impact for SARS-2:ade-and-sars-2 Download



ADE in SARS-1:ADE and SARS-1 Download



Overlapping symptoms for SARS, MERS, and SARS-2:ade-sars-mers-sars-2-liu_et_al-2020-journal_of_medical_virology Download



Is COVID-19 receiving ADE from other coronaviruses?ADE_and_COVID Download



Possible mechanism for ADE:ade-mechanism-jvi.02015-19 Download

Case Update: October 13, 2020; Voting, Re-Infection, 3D Structures

I’ve been traveling a LOT recently and just skipped last week’s update. Sorry for the long delay.

The US continues a slow trend upward in new confirmed cases. According to endcoronavirus, most of these new cases are arising in the Northern states, although the upward trend seems to be creeping south. This seems to confirm my suspicion that the new uptick in cases is caused by colder weather, and people being indoors together more often. If this suspicion is correct, we may be in for a long broad 3rd wave of cases this winter. You may remember that the Southern states (California all the way to Florida) drove new cases this summer. During the summer of course, people in Southern states tend be indoors with their air conditioners more often. This is my theory for the time being.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, October 13th, 2020

After the end of the 2nd wave, California is experiencing a persistent 3000 new confirmed cases a day, and San Diego County has a persistent 300 new confirmed cases a day. Unfortunately, I’m firmly convinced at this point that COVID may be with us at least until next Spring. As you know if you’ve been reading my posts, I think we will need to adapt to this situation, and open up our economy and normal life as much as possible, while still taking precautions.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.

As I’ve mentioned before, I am doing a lot of traveling these days, and get tested almost every week, and I’m always negative so far. I use air travel and go into all kinds of gas stations and stores. I do the following:

1) Wear a mask or face covering in public. Avoid places with unmasked people.
2) Keep 6 ft away from others. (I basically ignore this one if other precautions are in place, especially on an airplane!)
3) Avoid indoor gatherings, especially ones in which singing or shouting is likely.
4) Small outdoor gatherings are fine, even without masks, if everyone maintains a distance. Have guests bring their own food.
5) While many restaurants are open for limited indoor seating, I personally am still not comfortable eating indoors at a restaurant. I enjoy eating outdoors at restaurants, however.
6) Wear an N95 or KN95 mask when going to more high risk areas like airports or public areas where people may gather. These masks are rated to filter out 95% of viral particles. In my opinion, surgical masks and especially neck gators are nearly worthless in these settings.
7) I never take my mask off on the plane, and find an isolate spot in the airport to eat or drink on layovers.

Voting: If you haven’t heard, there is an election coming up. As with many issues, mail-in voting has become a politicized issue. The New York Times recently had a story expressing reservations about mail in voting, claiming that mail in ballots are more likely to be disqualified than in person voting. This is because filling out and mailing in these ballots can be complicated and prone to errors that disqualify these ballots. Some stories even claim that people have been sanitizing their ballots, ruining the ink and disqualifying be ballot. It is therefore my recommendation that everyone vote in person if possible. Follow the above precautions, and I’m confident you can do so safely. Dr. Fauci claims that in-person voting is safe if proper precautions are taken.

Reinfection: There is a recently published study of a confirmed case of re-infection in an American man. Apparently, this is the first confirmed and well characterized case in the US, although there have been other suspected cases. His symptoms were more severe with the second case, suggesting that my fears of ADE may be warranted. However, there have been only 22 confirmed cases of reinfection world wide, so it’s still apparently a very rare phenomena. The paper also states the 2nd infecting strain is distinct from the first, consistent with the ADE model.

The paper suggests that there may have been dozens of circulating strains since the beginning of the pandemic. While this case of re-infection appears consistent with ADE, the rarity of the re-infection phenomena along with the many circulating strains suggests that ADE, while theoretically possible, may not have large real-world significance.

New 3D structure: Last, for those of you who want a deep dive, the New York Times has a nice story with a collection of 3D structures of the virus from different sources.

Don’t fear, but be smart!
Erik

Summary: What we know so far, June 22, 2020

This long post will be a summary of what we have learned so far about the Coronavirus, and I’ll make some predictions about what to expect next.  Since I’ll be sharing so much information, I won’t give references for everything here. I also have to make the disclaimer that new studies are constantly being done, and some of the below information may need to be revised later. To make my standard disclaimer, I am not an epidemiologist or a physician.  I have a Ph.D. in molecular biology, and my specialty is infectious disease testing. On much of the below, I have an informed but not expert opinion.

Coronaviruses: Coronaviruses are a large group of viruses unrelated to the flu.  What we think of as the common cold, are actually member of several classes of viruses like Adenovirus, RSV viruses, Rhinovirus, and several Coronaviruses.  Many Coronaviruses cause diseases no more virulent than the common cold.  However, just like novel flus can cause extra trouble, so can novel Coronaviruses.  The first SARS virus was much more lethal that the SARS-2 virus, but because SARS had a short incubation period and made almost every infected person sick, it was much easier to contain.  The Middle East Respiratory Syndrome (MERS) Coronavirus infects a few people every year, and is very lethal, with a fatality rate of 34%, but it also has not made a global impact.  The reason SARS-2 is so dangerous is that it’s VERY infectious (Ro of between 2.5 and 5.7) and has a VERY long incubation time (2-14 days), making it very hard to track.  Plus, it’s at least 2x as deadly at the annual flu.

Name: The official name of the virus is SARS-2-CoV (for Severe Acute Respiratory Syndrome-2 CoronaVirus).  The official name for the disease it causes is COVID-19 (for COronaVIrus Disease-2019).  You may notice that the term SARS actually sounds a lot like a disease.  You would be right.  So why did they need a different disease name than SARS-2, or SARS-19? I don’t know.

Spread:  Early reports were that SARS-2 mostly spread like a flu, with droplets spreading from coughing or sneezing.  It became apparent later that the virus was also spread through aerosols by laughing, singing, shouting, or even just talking in close proximity for long periods.  As further study was done, it appears that most infected people don’t infect anyone else.  Rather, most infections come from “super-spreader” events, in which a single person infects a large group of people.  This usually happens indoors (at least 19 times more likely) during activities like fitness classes, funerals, concerts, and choir practices.  While outdoor activities aren’t completely immune to these events, they are much more rare.

Viral load upon exposure appears to be an important determinant of how severe a case will be.  Basically, this means that if you’re infected by a “low dose” of virus, your disease is likely to be less severe.  I have several physician friends who have stated that it seems to them that cases in the hospital are less severe than they used to be.  One likely reason for this is that since more people are wearing masks in public than early on, those who are infected are being infected by a lower viral load.

Early studies demonstrated that viable virus can exist on objects for hours or days.  However, it does not appear that a substantial number of people are being infected because they have touched a contaminated object. 

The WHO made a confusing claim recently that asymptomatic people cannot spread the virus.  While this is technically correct, they were not clear that “asymptomatic” is a technical medical term meaning someone who does not have, and will never have, symptoms.  Another group is “pre-symptomatic”.  These are people who currently don’t have symptoms, but will develop symptoms in a few days.  As it turns out, pre-symptomatic people do spread virus, and are likely responsible for up to 80% of new cases. So yes, people without symptoms can and do pass the virus to others.

Risk Factors:  Many believe that only old people are at risk. While it’s true that age is a dominant factor, other risk factors are important, and younger people have also experienced severe symptoms.  Other risk factors include respiratory conditions like asthma or COPD, heart conditions, kidney conditions, liver disease, diabetes, obesity, auto-immune disease, use of NSAID anti-inflammatory medications, being immunocompromised (HIV infected, undergoing cancer treatment, under medication for a transplant), vitamin-D deficiency, type A blood (Type O appears to be protective), inadequate sleep.

Always check with your doctor before changing your medications. I have an auto-immune disease and take daily anti-inflammatories, but my doctor has advised me to continue taking these unless I experience COVID symptoms.

Make sure your doctor is aware if you have any of the above conditions.

Symptoms: Many people who have SARS-2 experience no symptoms, or experience mild flu symptoms.  If you have ANY cold or flu symptoms, contact your doctor and see if you can be tested.  If you live in San Diego County, and your doctor cannot offer you a test, call 2-1-1 to get a free test from SD County Public Health.  If you have additional symptoms like shortness of breath (you just can’t seem to get enough air), loss of smell or taste, nausea or diarrhea, contact your health care provider or an urgent care immediately.

In severe cases, the virus can do wide spread and permanent damage to multiple organ systems.  Early treatment is necessary to prevent the most severe symptoms.

Precautions:  While lockdowns may have been effective in the US during the early stages of the pandemic, especially at a time when masks were hard to come by, recent evidence suggests that lockdowns provide only a moderate benefit over other means of control.  Here’s what appears to be beneficial:

Masks: Masks are not all the same and some are better than others.  Their main benefit is that they stop, reduce, or slow the travel of virus from infected people.  This prevents surrounding people from infection, or lowers the viral load of exposure.  Some, but not all, also prevent the wearer from inhaling airborne virus. N95 style masks without a valve are best if you can obtain one.

Best option: An N95 mask with no valve.

Social Distancing: Aerosolized virus can travel through the air. Staying 6 ft away from others helps prevent infection.

Handwashing:

Adequate sleep: Sleep is very important for a wide variety of body functions, including the immune system.  Get 7 – 8 hours of sleep per night.  A 26 minute power nap during the day is also beneficial if needed.

Vitamin D: Several studies have suggested that patients with the most severe cases of COVID also have the lowest levels of Vitamin D.  Because of our often indoor lifestyle, most Americans are Vitamin D deficient to some degree.  The best way of getting some Vitamin D is to make it yourself by going outside in shorts and a T-shirt for 30 minutes a day.  This is because Vitamin D is manufactured in our skin in response to sunlight.  If it’s not practical for you to do this, consider a Vitamin D supplement.  Darker skinned people are more likely to be Vitamin D deficient in the US.

Home isolation: If you have cold or flu symptoms, contact your doctor immediately and see if you can get a test.  Tests are much more available that early in the pandemic, and you should be able to get a test by request.  Also, if at all possible, isolate yourself from the rest of your family until you can be tested as negative.  Many new infections are taking place among family members.

Testing: There are several kinds of tests, and they tell you different things.

PCR: These tests use material collected from the nose and need to go to a specialized laboratory for processing.  They are very sensitive and specific, and indicate whether the patient is currently infected. This is the most common kind of test.

Antibody:  These tests detected antibody from a patient’s blood to see if the patient has been infected for at least a few days.  IgG tests may also tell if a patient was infected weeks or months previous, but are no longer infected.  Some patients do not mount an immune response that will provide long term antibody.

Isothermal amplification:  The Abbott ID Now COVID tests uses this relatively new technology.  These tests are similar to PCR and are both sensitive and very fast. 

If you have cold or flu symptoms, contact your doctor immediately and see if you can get a test.  Testing is much more available than it was early in the pandemic.  San Diego County is encouraging anyone who wants a test to be tested.

Treatments:  Treatment for COVID is complicated and not all patients can be treated in the same way.  Additionally, treatments are evolving rapidly, and your doctor many not treat you in the ways listed below.

Ventilators:  Some doctors now state that ventilators carry risks that may be unacceptable for COVID patients.  Many doctors now favor a nasal cannula, using ventilators only as a last resort if breathing is labored. 

Hydroxychloroquine, Azithromycin, Zinc: Several doctors from several countries have reported success with this combination.  Studies on the effects of these drugs have as yet still been non-conclusive.  Some positive studies suggest that Zinc is the main virus fighter of the treatment, with Hydroxychloroquine allowing better penetration of Zinc into cells.  Unfortunately, the debate on the efficacy of this regimen has taken on a strongly political tone, which almost always interferes with the scientific process.  Now pundits, as well as scientists, weigh in on this regimen.  I’m still holding a “wait and see” posture with this treatment.

MATH+: This regimen uses Methylprednisolone (an anti-inflammatory), Vitamin C, Thymine, and Heparin, as well as optional other treatments including Vitamin D and Zinc.  Early reports suggest success with this treatment.

Vaccines: Each spring, scientists learn which flu is likely to be prominent by the following Fall.  They make some guesses and create a vaccine for the flu season.  The manufacture process takes a few months. But it’s only this short because they already know how to make a flu vaccine.  Development of a brand new type of vaccine takes between 4 and 30 years!  There are many methods to make a vaccine, and scientists must try many of them before finding one that works.  Then they must try the vaccine on patients and make sure they are relatively safe.  Every vaccine carries some risk of side effects.

Early estimates for a Coronavirus vaccine were around 18 months.  My guess is that this is too optimistic.  Personally, I wouldn’t count on a vaccine for at least a few years.  In addition, some studies have suggested that Coronavirus vaccines in particular may cause side effects that may make vaccine development challenging.  My standard practice for my family is to wait on new drugs for a few years before using them myself. While I pro-vaccine in general, I would personally recommend waiting for a few years before getting a Coronavirus vaccine.

Herd Immunity: Some are promoting herd immunity as a way to move through the crisis faster.  The idea of herd immunity was popularized in pre-pandemic discussions on vaccines, promoting the idea that the more people are vaccinated, the more protection for those who can’t be.  This is a good idea when a vaccine is available, but not when there is no vaccine.  Putting many people in harm’s way to protect fewer others is not wise and is not standard medical practice.

The Future: Of course, it’s impossible to know what will happen next. My initial prediction was that the first wave would be over by July, and at this point, this doesn’t look likely.  New confirmed cases have started to rise or rise faster in the 3 areas I monitor most closely, the US, California, and San Diego County, and cases are rising fast in some countries previously unaffected, especially Brazil, Russia, and India. So I’m starting to think we may not be out of the first wave before the Fall season.

In addition, RNA viruses, such as Coronavirus, can mutate very quickly because the proteins used to copy their genomes are very error prone.  This means that a virus may change to a new form that can re-infect a person who has already had a previous version. Some reports suggest that this may already be happening with SARS-2. Some good news is that on the very long term (years), novel viruses tend to evolve to be less virulent, because it’s not in the “interest” of the virus to make the host very sick. The message is, we may need to adapt to a new reality for the next few months or years.  We can’t really afford to be “locked down” anymore, but mask wearing and elbow bumps may be a part of the landscape for some time.

Don’t fear, but be smart,
Erik

Masks: What’s the Deal?

The messaging on masks has been very confusing.  For several weeks, the CDC said the public doesn’t need masks, then finally, the surgeon general was demonstrating how to make a mask out of a T-shirt. I’m convinced that the CDC was so slow to recommend masks simply because they have been so hard to come by.  But the delay in recommending masks has caused a lot of confusion. 

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Section added 2/22/21: Masks have produced a lot of controversy, but I am a big fan of mask wearing indoors. This does several things, it usually prevents infection if you’re wearing an N95 or KN95. However, studies suggest that even if you get infected, a masks will help you have a lower initial viral load on exposure, greatly reducing your symptoms! I personally always wear a mask indoors, and I rarely eat indoors right now.

Outdoors are a different story. Unless you are in a tightly clustered large group of people, you probably do not need to wear a mask outdoors! Some municipalities encourage or require mask wearing outside, but this is usually unnecessary. I am not saying you should ignore local requirements! I’m just saying that when you are going for a walk, a hike or a bike ride, a mask is not necessary.
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First, let’s talk about the words you’re hearing now!

Cloth Face Covering: A “cloth face covering” (I’ll say CFC for short here) is not technically a mask as the CDC defines it, and is not considering Personal Protective Equipment (PPE) from a medical perspective.  This a t-shirt, bandana, buff, or anything else that can be used to cover your nose and mouth.  The virus can still get both into your nose or mouth, or leave your body through these coverings, but it’s much better than nothing.  A lot of people who are trying to be responsible, but can’t find a mask to buy, are using these coverings.  If you hear someone saying they don’t work, they mean that they aren’t completely effective, but they are much better than nothing! Even if you sneeze, a face covering will capture larger droplets, slow the velocity of the sneeze, and help protect those around you.  If all you have is a CFC, you should still wear it when you go out!

According to Fischer et al, gator style masks may be even worse than wearing nothing at all, since they may break up droplets into a smaller size that stays in the atmosphere longer! So avoid a neck-gator style mask!

A surgical style face mask.

Face mask: A “face mask” is a filtering mask that covers the nose and mouth, but does not seal around the nose and mouth.  This includes the blue surgical mask that you see a lot of today.  These masks are designed to prevent material from medical worker’s  face and nose from getting to a patient during a procedure, while still allowing somewhat normal breathing.  They filter incoming air to some degree, but there are large gaps at the sides of the mask, so there are not very effective at preventing infection by SARS-2.  Coughing, sneezing and singing will still expel air from the sides while wearing these masks!  They aren’t completely effective, but they are certainly better than nothing, and will prevent transmission through simple talking. If you have one, please wear it!

UPDATE: Now that KN95 masks and some N95s are available (see below), I can no longer recommend wearing these masks.

Respirator: These masks seal against the sides of the face cover at least the nose and mouth.  They are designed to filter the air and prevent particles from entering the nose and mouth.  N95s prevent 95% of viruses from getting through and are the preferred mask for medical workers in most situations right now.  Unfortunately, they have been in very short supply since the beginning of the pandemic, so the public is being asked not to purchase these for now.  Doctors tells me that N95s are not adequate protection while performing certain procedures on COVID patients!  One told me a story about 14 medical workers being infected by a single patient during a procedure!  This work requires a Powered Air-Purifying Respirator (PAPR).  These masks cover the entire face and also blow air into the mask, pushing virus out.

An N95 with a valve.

If you have an N95 with a valve in the front, these masks will still vent air when you cough or sneeze, so be aware that it will not protect others from virus coming from you! N95s with no valve are the best choice for protecting both you and those around you. Again, hold off on purchasing these until there are in greater abundance.

An N95 with no valve.

I see a lot of very nice looking fitted masks with a little round filter in the front.  These filter out large particles like dust or large droplets, but not necessarily small virus particles.  While much better than nothing, these are not necessarily N95 masks! Read the product information carefully when buying these masks.

KN95 Masks: A new style of mask is being sold in the US now, labeled KN95. These masks are made in China and designed to filter out 95% of viral particles, like N95s. However, they are certified by a Chinese agency, and not by the FDA or CDC. They have been allowed to be sold in the US on an emergency basis. Users say they fit more loosely than N95 masks.

KN95 mask.

There are lots of studies showing the effectiveness of these masks, and unfortunately I don’t have one ultimate study to share with you.  Suay, a clothing company in LA, did a study suggesting that normal blue shop towels (like Tool Box Shop Towels or Zep Industrial Towels) do a much better job at filtering than cotton, and are a cheap and available alternative to an N95 when sewn into a mask. My sister-in-law Penny is part of a team that makes masks for the local hospitals in Bozeman.  These are homemade masks with a pocket for a HEPA filter. She’s sending me some, and I’m going to add a Shop Towel to mine! Both designs are posted below.

Here’s a few tips for wearing your mask:

  1. Your CFC or mask must cover your mouth and nose.  Leaving your nose hanging out, or simply wearing it as a chin mask is not adequate! 
  2. When adjusting your mask assume both your hands and the mask are contaminated.  Wash your hands before AND after adjusting.
  3. 30 min of UV light effectively kills SARS-2 virus.  In the bright sunlight, it may only take a few minutes.  I sterilize my mask by leaving it in the sun for a half hour after a shopping trip.  If you have a cloth face covering or mask, machine washing is a better choice.

In addition to preventing infection, masks appear to reduce the viral load in newly infected patients, leading to less severe symptoms! So even if you get infected while wearing a mask, your symptoms are likely to be less severe!

As we think about re-opening the economy, face coverings, even the bandana type, will really help keep new infections low.  So wear a mask when you go out in public! Any improvements will hasten the day when businesses can re-open. I am awaiting data to see what the infection rate is at businesses in which employees wear masks. Hopefully, this data will come out soon.

Don’t fear, but be smart!

Erik

Masks effective in protecting healthcare workers, Bartoszko et al.

Study on the best masks, Fisher et al.

Mask may reduce symptoms and even provide some immunity, Ghandi et al.

Science Communication, and Being Persuasive

Originally posted on April 27th, 2020 on Facebook

Friends,
This post doesn’t have much science in it, it’s about why I started posting about the virus, and something about my philosophy on communication. If you’re not interested in that, feel free to skip it.

Much of the reason stems from how scientific information is often communicated to the public. So often a scientist or public official shows up on a news show, and basically gives a conclusion, but no real data. Instead of giving a persuasive case, they just make a claim without much support. Because of this, many in the public have been confused or lost trust in what they learn from the media.

On March 9th, I started posting to Facebook, since I don’t yet have a blog. If you’ve been one of my Facebook friends for a long time, you know that I rarely post, really only to change my profile picture for Talk Like a Pirate Day! I felt it was important to give some data in a digestible way, so people would have some understanding of what was going on. I just wanted to show some data so people could understand why SARS-2 was not like the typical flu.

I started out by giving my credentials, since many of you, especially my high school friends, may not have even known I was a scientist. And yes, it might have helped me get my foot in the door with some of you. However, one of the things I don’t like about our public discourse, is how many scientists expect that their credentials means that they must be believed by the public. Being an expert isn’t enough to automatically be believed. You still have to show your data and show why it supports your conclusion. Anyone who has been to a scientific conference or even a journal club knows that experts often disagree. You can’t just say “I have a PhD” to a room full of PhDs. So when experts try to make a case to the public, they still need to show data, and how they came to their conclusion. Unfortunately, because they often just have 60 seconds on a news show, they don’t have time for that. What too often happens, is that they just make a claim without support, and say that if you don’t believe them, you’re just a <news anchor, YouTuber, insurance salesman> or you’re just anti-science or racist or whatever. This is just lazy, and ironically, is anti-science. Scientists must make observations, show data, and be persuasive. Taking short cuts like name-calling isn’t persuasive, and it just makes your opponent irritated and unwilling to listen. In fact, if your opponent knows how to argue, you’ve just clearly told them that you can’t make your case. You lose.

Here’s what I do: I show a piece of data, then say what it means. I’m prepared to tell you where the data come from, and how I manipulated it if I did. If I quote a source, I give a reference. This shows I have reliable information, and also relieves me of some of the burden, since I’m just reporting what someone else said. I also think graphs are much easier to digest than tables, and tables are much easier than numbers in a paragraph, so I make content visual when I can.

If a news story makes a scientific claim, I try to find the original source, since journalists often oversimplify, misunderstand, or misrepresent scientific information. Politics and science make a terrible combination. As soon as a scientific issue gets politicized, it becomes difficult for scientists to figure out the truth, and nearly impossible for the public to. If you want to understand a scientific issue that has become political, you’ll have to read widely on all sides of the argument. Most people just don’t have time for that.

Here are a few of my rules for being persuasive. If you’re one of my lunch buddies from Quest, you know I did this well sometimes, and also failed sometimes!

  1. If you can’t support a claim, don’t talk until you can. Go study and come back.
  2. If you do speak, don’t just lean on your credentials or criticize someone else for not having any. You both need to be persuasive. And if you have data and can support your claim, you don’t need a degree, although training certainly helps to develop these skills. I am a molecular biologist, specializing in medical testing. I am not an epidemiologist or a physician*.
  3. If someone asks you to support your claim, and you find that you can’t, you may need to change your position!
  4. Ask clarifying questions. This may give you time to think, and also helps you learn their position. It’s OK to have an entire discussion in which you only learn their position.
  5. Don’t accept the burden of proof. When someone makes a claim, many will just offer an opposing claim. When you do that, you’re accepting the burden of proof! Don’t do that! Just ask them where they heard it, or why they believe it. A lot of people can’t tell you either of these things.
  6. If you don’t know something, say you don’t know. Making something up undermines your credibility! You may lose a discussion in the short term, but you’ll build trust.
  7. Don’t hide important information. This of course is a favorite trick of media and politicians. It’s a handy way to deceive your audience without technically lying. However, if you’re caught doing this, you completely undermine your credibility. Plus, you can’t really hide the opposing facts, you just bury them alive. They’ll eventually come out like a zombie and eat your brain.
  8. Your job is not to “win”, it’s to be persuasive. Jerks aren’t persuasive. Play the long game! It’s OK to lose a discussion if you can earn another discussion by being respectful.
  9. Find common ground and build from there. If you can show your opponent that you’re on the same team, you have a head start.
  10. If you find that someone is more interested in being insulting than seeking truth, it’s OK to disengage. Some also give you a burden of proof so great, it’s impossible to meet it. They may not be seeking the truth, and there are some people that you will never convince. Relax! It’s not your job to convince everyone!
  11. Don’t post angry! Take a walk, have lunch, maybe even sleep on it, and think before you respond to something obnoxious. You will lose credibility if you say something destructive. While live conversations are always better, social media allows you to think before you post!

Don’t fear, but be smart!
Erik

*A medical license grants the legal right to order tests, interpret results, prescribe medication, and give medical advice. Also, your doctor knows your medical history, and the particular tests and medication you’ve taken. So always consult with your doctor when making medical decisions!