Category Archives: Quarantine

The Next Pandemic

In yesterday’s post, I outlined some of the factors that resulted in the very high COVID case rate in the US. Today I will discuss how we can prepare for the next pandemic.

I have a PhD in molecular biology, and I specialize in infectious disease testing. I am not a physician or epidemiologist. I have an informed but not expert opinion.

Identifying the threat:

First, most new infectious diseases do not pose a global threat.  SARS-2 was so dangerous because of its high infectivity, long incubation time, and asymptomatic spread. Most diseases do not have these parameters.  Whenever a new disease comes around, and they will, we should soberly and cautiously assess the real threat.  Coming to the wrong conclusions about the threat will lead to the wrong conclusions about combating it.

There have been several important new infectious disease outbreaks in the last few years, including Hantavirus (1993), SARS (2003), Avian Influenza (2004), H1N1 Swine Flu (2009), Ebola (2013), Zika (2015), and of course HIV in the 80s.  They all have different disease parameters which make them behave very differently.  Most of these diseases did not have global impact.  The first SARS for example was much less infectious than SARS-2, but much deadlier, so it was contained quickly and didn’t spread much beyond Asia.  HIV can be spread by asymptomatic victims for a full 8-10 years, avoids the immune system, and evades vaccination efforts, so it has become endemic in much of the world.

The following parameters determine how a new disease will behave:

  • Mechanism of spread
  • Infectivity
  • Asymptomatic/ambulatory spread – can the victim walk around and spread disease?
  • Incubation period
  • Fatality rate
  • Vector – what carries the virus to a new host
  • Non-human reservoir – diseases that come from non-humans are harder to control and cannot be eradicated.

Obviously, we cannot respond to different diseases in the same way. Part of the reason we failed to contain the virus was that we used measures that were designed for viruses that spread by droplet transmission against a virus that spreads through aerosol transmission.  Using the wrong measures was less effective.

Much of my concern with the SARS-2 virus was the Antibody Dependent Enhancement issue, which is very uncommon among viruses, so is not usually a concern.

Be cautious.
Whenever a new threat arises, it is wise to be extra cautious until information can be gathered.  Although many of our precautions turned out to be unnecessary, I still support taking extra precautions early on.  Remember that early estimates were that the fatality rate for COVID was 3.68%.  With the 82 million confirmed cases in the US, this would have been over 3 million deaths if the fatality rate had really been this high.  As it stands, we have had almost 1 million COVID related deaths, a death rate of approximately 1.2%.  Yes, I know we can debate how many of these are deaths really resulted from COVID and how many infections there really were.  But we cannot discount that COVID had an enormous impact.

What if COVID were deadlier? Or what if it had selectively killed children, or caused more long-term symptoms like polio did? Things would have been much different.

All this to say, I think caution was warranted in the beginning of COVID, and we should continue to be cautious in future pandemics. On the other hand, we should also learn to abandon precautions that are not effective.  Maintaining ineffective precautions wastes resources, causes extra economic and social suffering, and causes people to lose confidence in government agencies.  It started to become clear to me by May of 2020 that lockdowns were ineffective, and that transmission was happening mostly indoors, but I still see people wearing masks outside to this very day.

Persuasion, not coercion:
From the beginning of the pandemic, public communication was terrible.  Official guidelines were confusing and often contradictory.  Far worse, explanation or evidence was rarely given for policies.  Instead, disagreement was met with accusations of being anti-science, rather than persuasion.  This approach contributed to the loss in confidence in official channels. 

Going forward, officials need far better communication skills when dealing with emergencies.  Give evidence rather name-calling, and respect the population enough to tell the whole truth.

Then came the vaccine mandates.  Many people I know were coerced into getting vaccinated against their will, and many others were fired.  All at a time when information about the vaccines was being hidden from the public.  This is unacceptable, and no way to run an emergency.

Here is a link to my post on science communication:

Restoring Trust:
Both the CDC and FDA hid information from the public.  In order to restore confidence, senior leadership needs to be replaced and new leadership should explain how things will be better in the future.  Is likely to happen?  No, it is not.

Government agencies need to be far more transparent.  Lack of transparency forces people to wonder what is going on, and create their own theories.  Government agencies often decry conspiracy theories, but they had a big role in creating them.

Freedom of speech, censorship, and misinformation had a major role in the public discussion over the pandemic.  Doctors and scientists were frequently censored, shunned, or fired for sharing ideas that went against WHO or CDC guidelines. This includes ideas like the lab leak hypothesis that later turned out to be likely.

Freedom of speech is a foundational principle of American life.  It’s in our DNA, as some would say.  We are not America without it.  Some will say that too much freedom of speech leads to misinformation and conspiracy theories.  While it’s true that this freedom allows the spread of falsehoods, it also allows all ideas to be debated, true ideas to be raised up, and false ideas to be discredited. Freedom of speech is the solution to misinformation, not the cause.  Most of the leaders in world history that wanted to control freedom of speech had something to hide. It is essential that we maintain this basic right.

State emergency powers:
As discussed in yesterday’s post, the US federal government has surprisingly little power to deal with a public health crisis.  The CDC can develop guidelines, but most of the real work is done at the state and local level.  State officials need to step up and realize it’s their responsibility to respond well.  Citizens need to hold state and local officials accountable.

The US needs to maintain manufacturing capacity for certain essential items like personal protective equipment, testing kits and equipment, and medications.  Tax incentives need to exist to encourage companies not to send these functions overseas.

In addition, we should have national and state stockpiles of certain equipment.  I know many hospitals and labs are now creating stockpiles of their own.

Most countries that did well produced lots of COVID testing early.  In the US, the CDC tried to manage all the testing themselves, and quickly became overwhelmed.  By the time private labs were allowed to develop their own tests, it was way too late.  Testing capacity didn’t become nearly adequate until at least July of 2020. Next time, the CDC needs to allow testing by private labs right away.  Ideally, anyone who wants a test and anyone potentially exposed to an agent should be tested.

Quarantine, not Lockdown:
Countries that did well did not quarantine healthy individuals, although some of these countries had more restrictions during the big Winter waves.  Instead, only COVID positive people should be quarantined.  This is only effective when tests are readily available.

Later in the pandemic, some outlets acknowledged that most infections were happening in private settings.  Basically, people would get infected outside, then bring COVID home to infect everyone in the household.

Here is a very interesting video using computer models to show why our model of lockdown was not effective.  Computer models are only as good as they are programmed to be, so this is only for demonstration purposes, and is not data.

Contact tracing:
Contact tracing was very successful in some countries, but the long incubation time of COVID made this difficult.  Successful programs involved tracking of individuals by cell phone and credit card data, practices that would probably not be tolerated in the US. Such programs would need to be voluntary to not trigger the creepiness factor and violate constitutional rights.

I was a big proponent of wearing a medical grade respirator (N95, KN95, or KN94) indoors during the pandemic.  Because COVID spread as an aerosol as well as droplet form, cloth and blue surgical masks were ineffective.  Simpler masks can be effective against colds and flu, however.  So the choice of mask depends on the agent in question.  CDC guidelines need to reflect the method of spread of the agent in question. 

So what should Dr. Fauci have said early on?  Something like this:

N95 masks offer the best protection against infection by the SARS-2 virus. However, our current supply is very low, and we desperately need to save these masks for our medical professionals.  Please do not purchase N95 masks at this time.  In the mean time, there are some options that will help reduce the risk…

In actuality, of course, I didn’t see an N95 in a store from March 2020 until at least February of 2021, so I couldn’t have bought one if I’d wanted to!

Most medical facilities in the US didn’t treat COVID until a patient was experiencing respiratory distress.  By then, treatment options were limited.  To their credit, intubation was largely abandoned by the medical community when it was learned that this treatment was largely ineffective.

However, controversy swirled over potential treatments that became disfavored by the medical community.  Doctors are usually granted the right to prescribe “off label” medications, meaning they can use medications for treatments outside the guidelines of the manufacturer.  But drugs like Hydroxychloroquine, Ivermectin, and others quickly become forbidden, and some doctors even got fired for prescribing them.  Research on these drugs were minimal.

I am not arguing here that these drugs are effective against COVID.  I’m simply saying that forbidding doctors from working with or publishing papers about these drugs was a big mistake.  While it is of course wise for a doctor to consider guidelines, treating a novel virus may require some “outside the box” thinking.

Let me know in the comments if I missed something important!

Don’t fear, but be smart!

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.


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,

Indoor Venues Approximately 19 Times more Dangerous than Outdoor Venues

Yesterday right after I posted, Mark Rasmussen sent me an article that ran in Science Magazine, one of the 2 most highly regarded science journals in the world.  It’s a news article, not a peer-reviewed journal article, but it attempts to pull together information from different sources, and I think clarifies the picture regarding SARS-2 viral spread. The take-away message of the article is that while the R0 appears to be between 2.5 and 3 (more on that later), it’s not true that the average individual will pass the virus on to 2 or 3 others.  Rather, most infected people don’t pass the virus on to anyone at all, rather a few infected people are “super-spreaders”, infecting a large number of people at once.  There are many documented cases of super-spreading, from choir practices, funerals, concerts, fitness classes, and meat packing plants.  The commonality appears to be indoor locations with lots of people in a small space, with some of them shouting or singing.  While the risk in outdoor venues isn’t zero, indoor venues account for 19 times the number of super-spreading events, according to a Japanese study.

According to the article, SARS-2 has a tendency to cluster in this way more than other respiratory diseases such as the flu or colds. This may be partially because of the “viral load” effect mentioned in the Erin Bromage article I posted on May 12th.  In that article, it appears that the initial number of viruses an individual is exposed to partially determined if they will be infected, and how sick they will get.  This also explains why so many medical workers in Italy got very sick or died in the early stages of the pandemic.  Many medical procedures such as intubation create a bloom of floating virus from a sick patient, exposing unprotected workers to high viral loads.

The science article suggests that while the virus is still dangerous and outdoor venues are not completely without risk, it may be appropriate to relax restrictions on some outdoor activities.  So here’s my informed but not expert advice on how to adapt to life with COVID:

  1. Staying at home all the time may no longer be the best approach, although it was probably very helpful in the early stages of the pandemic.  Going outside to get some fresh air and exercise is probably a good thing, although still not without risk.
  2. When doing outdoor activities, it’s probably OK to not wear a mask, but maintain at least 6-10 ft from others you don’t live with.  Locations with a gentle breeze will help move virus away from you!
  3. At work or shopping, wear a mask when around others to reduce the viral load that you are wafting into air should you be infected without your knowledge.  Any reduction in viral load will help.
  4. If you suspect you may have been exposed, contact your physician and see if you can get a test.
  5. If you have a yard, invite a few friends over for lunch or dinner at a safe distance. Since Summer is starting, an evening outdoor dinner will be a welcome break from the isolation.  You may want to have your guests bring their own food and utensils. Don’t invite a large number of friends, and sorry to say, don’t invite those friends who can’t resist hugging everyone! Young children may require supervision to be safe.
  6. Now that restaurants are open in California, I would personally only be comfortable with outdoor seating at the moment.  If you’re comfortable, visit your favorite local restaurants to give them some business, sit outside, and leave your server a big tip if you’re able!
  7. I am a church goer, and I want to see my peeps again, but singing in a congregation is still a high-risk activity.  Churches will need to be creative to open up again safely.  Consider lower density services without singing, and/or hold services outdoors.

Regarding the R0 value for SARS-2.  I saw a CDC website last week that gave the R0 value as 2.5.  After 10 minutes of looking, I couldn’t find this site again. The Sanche paper I’ve referenced before (High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2, EID, July 2020), published in the official CDC journal, Emerging Infectious Disease, gave the R0 as 5.7.  So the CDC itself seems confused about what the R0 number is. My guess is, it’s somewhere between 2.5 and 5.7.  That was a joke.  Obviously, this range is far too large to be useful, and 2.5 and 5.7 are very different as applied to an R0 number.  2.5 is a very infectious disease, 5.7 is a super-infectious disease.

I’ve mentioned this before, but I want to remind everyone.  Herd immunity is only a goal when a vaccine is available.  Seeking herd immunity when there is no vaccine is not a good idea, because it will put large numbers of people at risk.  Additionally, I am generally very pro-vaccine, but because of the risks of side-effects with this particular virus, a vaccine may not be available for several years.  We will need to adapt to this reality.  My hope is that we will start seeing daily cases come down this Summer.

Don’t fear, but be smart,

JP Morgan Study on Lockdowns, The Moral Matrix and Pandemic, and the Viral Upsurge in the Southern Hemisphere

Today I’m going to discuss the JP Morgan study on transmission (among other things), how the Moral Matrix effects how people see the fight against the virus, and the boom stage in many Southern Hemisphere countries.

JP Morgan has produced a study suggesting among other things that lockdowns are ineffective in fighting Coronavirus (see also a summary from Daily Mail).  The reasoning for this is primarily that transmission is most common in households if a member becomes infected. 

Frankly, when I think about anti-coronavirus efforts, I have tended to lump lockdowns and social distancing together, especially since many use these terms interchangeably.  Notably, the study separates these 2 concepts and suggests that will social distancing (staying a distance away from people in public) may be valuable, lockdowns (staying in your home) is not. 

You might say there have been 2 primary models for dealing with the pandemic in the last month after we’ve flattened the curve, but have not brought the numbers down, at least not in the US.  I’ll call those models the Lockdown and the Re-opening models.  Some want to continue the lockdowns to keep everyone safe from the virus, others want to re-open right away without restrictions.  For several weeks, I have been gravitating toward a third Adaptive model.  Of course, there can be many flavors of this model.  Personally, I think masks, even bad ones, are far better than nothing, especially when worn by everyone, and can help us get back out of our houses and help us re-start the economy with reasonable safety.  So I’m very open to the idea that the lockdowns have not been beneficial.  Some of you will disagree.

The JP Morgan study is at odds with the study, which recommends brief, very strict lockdowns.  It could actually be that these 2 studies actually agree, depending on the time frame you’re talking about.  I do think the lockdown was very helpful in the initial “boom” stage of the epidemic here in the US, but may have lost its usefulness later.

The Moral Matrix: ZDoggMD is a physician and medical YouTuber with a very silly screen name, but who posted VERY interesting video on how different people see the pandemic we are all facing.  Using Jonathan Haidt’s work on the Moral Matrix, he talks about how different people’s moral framework shapes how we are viewing different efforts to address the issue.  I was aware of Haidt’s work, but not had yet applied it to the pandemic in my mind.  As someone who is sometimes exasperated with people who disagree with me (as they are with me I’m sure), this video is helping me remember to see their point of view.  If you’re exasperated with your friends or family, I HIGHLY recommend you watch this video.

Upsurge in the Southern Hemisphere: Lastly, I just want to mention that many countries which have been relatively little effected until now, are now experiencing a big upsurge in cases.  These countries include Russia, Brazil, and Mexico, and many are in the Southern Hemisphere, which is in the late Autumn months right now.  Let’s hope they are able to get things under control quickly.

Don’t fear, but be smart!


PS. We went hiking in nearby Calaveras Park today for the first time in months, without our masks. There were a lot of people on the trail, and most were well behaved. When I can’t avoid someone on a narrow trail, I use an old SCUBA diving trick for ascending without getting the bends. Just close your mouth and blow slowly out of your nose as you pass someone. You’ll gently move any virus away from your nose! To maintain my friendliness, I greet people early, with plenty of time to start this little maneuver!

Re-opening, How Many New Cases?, Compares Responses, Viral Spread

I have a variety of resources to share with you today. 

Re-opening: First, after many states have started to re-open, Rt Live is showing that all but 3 states have an Rt value below 1. This means that for most states, each infected person is passing the virus to less than 1 other person, and the virus is slowly disappearing in that state.  The states with an Rt above 1 are Minnesota, Maine, and Nebraska.  After a poor initial response, I’m happy to say that New York State is doing very well now, and daily new cases are low in New York. In California, my home state, the number of new cases is flat, approximately 1700 cases per day since the middle of April.

How many real new cases?  This is going to be a little mathy!  I told you I was going to start tracking the number of tests, and I have been doing that since April 27th.  This will help us know how many of the new cases are just because of more testing, and how many are actual new cases.  I’ve plotted the new cases against the new tests.  For each day, a point comparing the new cases and new tests is shown. If new testing matters, then a day with a high number of tests will also have a high number of new cases. To find out if this pairing exists, we can do a statistical test called the R2 test (pronounced “R squared”, also called the correlation coefficient).  This test creates a best fit line with the data and that creates an R2 value.  This value is a measure of how well the 2 parameters (new tests and new cases) are correlated.  I show a hypothetical graph in which the 2 sets of data are well correlated.  A perfect correlation will have a score of 1.0, while a set of data with no correlation at all will get a score of 0.0.  For scientists (at least the ones in diagnostics, like me) a correlation is considered “true” if the R2 value is above 0.95.  You could also say that the correlation is 95% likely to be true.

Now on to our data. I started plotting on April 27th.  5 days later, the graph for the United States got an R2 value of 0.6559.  This suggests that new cases and new tests are 66% likely to be correlated for this time period.  In real world terms, this probably means that some new cases are because of new testing, but some aren’t.

Interestingly, as of yesterday, a graph like this for the US gets an R2 value of just 0.0117.  This is very low and suggests that there is now no correlation between new testing, and new cases.  This means that new cases we see now are probably “real” new cases, and not just pre-existing ones that are just being found because of new testing.  For California, the correlation between new cases and new testing was never very high.  Right now, the R2 value is only 0.0039 for California, suggesting that most new cases discovered are “real” new cases.  What this means going forward is that we probably have enough testing now to locate new cases.  As we go forward, I expect we will start to see a steeper decline is new cases.

Good news!  This good news comes with a warning, however!  Those living in the West will easily understand a comparison to a brush fire.  Right now, we are in the “containment” stage.  We have the fire surrounded, and were at the beginning of the end, but if we walk away now, the fire will start to spread again.  We need to stay on task and keep fighting the fire!  I am all for re-opening, but we need to remain diligent.  Wear a mask when you go out into public, and continue to keep your distance from others!  If your workplace re-opens, you will probably want to wear a mask, wash your hands frequently, and sterilize your workspace often. I am probably going to start traveling for work again soon, and I’m very glad that everyone will be wearing a mask on the plane! compares responses: I discovered a new website the other day,, from the New England Complex Systems Institute.  The group compares the responses and results from different countries.  First, “green” countries responded very well, and were able to get the virus under control quickly.  Aside from the good response, I also notice that most of these countries have relatively small populations.  You may notice that China also appears on this list.  Most experts agree that the data coming from China is not reliable, and they probably have many more cases than they are reporting. After intermediate cases in yellow are countries in red that need more action.  This includes the US.  If you’ve been reading my posts, you’ll recognize the “flat” curve of the US.  Yes, we’ve flattened the curve, but we haven’t been able to knock down our case load yet.  Other countries with similar flat curves include Canada, Finland, Indonesia, Panama, Poland, Sweden, and the UK. Other countries had low cases at first, but are now experiencing explosive growth in new cases, including Brazil, Mexico, and Russia.

After analyzing the responses of these countries, recommendations include the following, many of which you’ll recognize:

  1. Lots of testing to identify new cases.
  2. Isolating infected individuals, even from family members!
  3. Strict lockdowns.  The stricter the lockdown, the shorter it will be.
  4. Travel restrictions, even within the same country.
  5. Adequate health care capacity.
  6. Safe practices for essential services.
  7. Masks in public for everyone.

Viral spread: Erin Bromage, an Associate Professor of Biology at U Mass Dartmouth, has a very nice article on his blog describing how the virus spreads. It is well written for non-scientists and has lots of links to original research.  The take home lesson is that the virus spreads particularly well in-doors.  In addition, cough, sneezing, and to a lesser degree shouting, singing, and even talking are all risk factors in spreading virus.

That’s all for now!

Don’t fear, but be smart!


COVID Vaccine, Herd Immunity, and California Re-Opening

Today I’m going to wade into the piranha filled waters of the vaccine discussion. I’m also going to talk about the issue of herd immunity, and my advice for re-opening.  I’m not prepared for a discussion of the MRM vaccine that has been raging for the last several years, I’m going to discuss vaccines in general, and the hopes for a COVID vaccine in particular. I will say to start out, that I’m a big fan of vaccination in general, but each vaccine is different, and I may not be in favor of a particular vaccine.

Vaccines: I’m not an immunologist and I haven’t made vaccines myself, I’m just sharing with you what I’ve learned from an informed perspective over the last few months.  When I first started sharing about COVID, I said something wrong, that it would take at least a few months to create a vaccine against COVID, which seemed like a long time to many.  This was based on the time it takes to develop a flu vaccine every year.  In the Spring and Summer, scientists find out that strains are likely to cause flu later that year, and they begin making a vaccine. This process takes several months. As it turns out, it’s only this fast for flu because there is a standard way to make a flu vaccine, they just need to know what strains will be likely to arise in the Winter. And sometimes they are wrong. 

Unfortunately, however, there isn’t just one way to make a vaccine.  There are many different ways, and it can be different for every virus or bacteria.  So for every new infectious disease, a vaccine must be developed from scratch, testing all these different methods.  The process can take from 2 to sometimes as long as 30 years!  Some scientists have said that Dr. Fauci’s prediction of a vaccine by next Summer is actually very optimistic! In my informed, but not expert opinion, we should not count on a vaccine for this current COVID-19 crisis.  However, the vaccine work being done will likely help with future outbreaks.  At least part of Dr. Fauci’s optimism is that a lot of red tape is being cut to speed the process, and that’s good, but less development time will also mean more risk for the final product.

Herd immunity: I have heard many people promoting the idea that herd immunity will help us get out of the crisis. Even some governments have been promoting this idea.  Herd immunity is a useful discussion for diseases for which there is a vaccine, but in my opinion, it is not something we should be striving for now with COVID.  We shouldn’t put a bunch of people in danger to keep fewer different people out of danger. Herd immunity requires a lot of people to be immune, and that number is different for every virus.  I’ve heard the numbers 50 – 70% for COVID thrown around.  That’s a majority of the population!  Why would we risk exposing the majority to the virus to save the minority? To be crass, it’s kind of like saying that once the pool is full of bodies, no one else will drown.

Reopening: More states continue to begin the reopening process. I actually strongly support this, as long as people continue to take care as they interact in public!  Even California has entered Phase 1 (CA calls it Stage 2) today, Friday May 8.  The stages CA will use, as well, as the announcement for the May 8th reopening were announced by Twitter by the Governor.  Not my favorite method of making an official announcement, but there it is.  Re-openings have a much higher chance of being successful if we continue to take care! Continue to wear masks in public, and continue to distance when appropriate (see my May 5th post).  I’m hopeful that we can advance quickly through the stages if people continue to take precautions.  Also, it will be important for us to continue to expand testing, and for businesses to take advantage of expanded testing by screening employees as appropriate.  Some municipalities are starting to have drive through testing, including parts of San Diego (you must still have an appointment to be tested).  Check with your health care provider or public health department to see if and how you can be tested.  Keep watching how other states are doing!  We can learn a lot by observing what methods are working, and what methods are not!  I predict that outbreaks will occur in places that become relaxed too soon.

2nd Wave:  Again, I’m not an epidemiologist, and the following is an informed guess, not an expert assessment.  In my informed opinion, we will have second wave in the Fall or Winter, and history suggests it may be more severe than the first wave.  But I’m still optimistic.  Why?  Because I think that with expanded testing, we will be able to test far more broadly this Fall than we could in March and April.  This will help us identify and quarantine infected people rapidly, and will help us control the spread much better than in the first wave. For the 2nd wave to go well, we will need to stay diligent!

Don’t fear, but be smart!


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. 

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.

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!

Update, February 23rd, 2023,

Cochrane Report on the Effectiveness of Masks:  Jefferson et al released a meta-study through Cochrane Reviews on the effectiveness of medical masks (surgical masks) and medical respirators (N95) in public settings.  A meta-study is a study in which the authors gather information from published articles and try to draw conclusions from a large body of data. They do not gather a new set of data.

The Jefferson et al study reviewed 78 different studies, including data from pre-COVID flu outbreaks.  Their conclusions are sobering.  First, the authors suggest that there is virtually no benefit to wearing a medical surgical mask over not wearing a mask in most settings.  If you’ve been reading my blog for long, you will know that this conclusion does not surprise me.  Blue surgical masks have large gaps in the sides and do not filter air leaving the mouth and nose.  They were designed to prevent droplets from a medical worker from contacting a patient, not to prevent transmission of aerosol based agents.  This is a problem, since most mask wearing people in public during the pandemic were wearing surgical masks.  These people thought they were protected from aerosols, but they were not.

The study also concludes, however, that N95 masks didn’t perform much better.  In fact, for lab tested COVID, the difference was statistically insignificant, meaning that the difference between wearing N95s or surgical masks was so small, it could not be proven to be a real difference statistically. 

I have to point out that the Jefferson meta-study points out that many of the studies they reviewed had various failings that may have made them unreliable.  Much of the data was collected through self-reporting of participants, which is a source of inaccuracy, and participants were often non-random, making application to the general population difficult.  So some of the conclusions may have suffered from these kinds of errors.

As you know, I’ve been a proponent of wearing N95, KN95, or KF94 masks when indoors during the pandemic.  Unfortunately, N95s are tight and intolerable for most people for long periods, so most people didn’t want to wear them at all.  Those that did were not careful to make sure the mask fits properly, making the mask ineffective.  This is part of the reason I wore a KF94 (Korean) during the later stages of the pandemic when I had choices.

So have I been wrong this whole time?  Well, yes and no.  I wore a KN95 in all kinds of environments while traveling during the pandemic.  When I finally got COVID in January of 2021, I was not wearing my mask, working in a “gray area” environment with people that I later found out had COVID.  I was technically indoors, but the room had a lot of ventilation, so I thought I would be OK. Obviously, I was incorrect.  All this to say, I think my KN95 was effective for much of the pandemic.  On the other hand, I am a scientist in the infectious disease field, and have had a lot of experience wearing and fitting these masks to myself, so I am not a typical user.  It may certainly be that my experience does not translate to non-scientists.

If you still have not had COVID and are not high risk, I might say that the current version has an extremely low fatality rate, and it may now be worth the risk to say good-bye to the mask.  I know the large majority of you have done this already.

If you are at high risk, I still think an N95, KN95, or KF94 can be effective for you.  In order for it to be effective, however, you need to make sure it is properly fitted, making sure you don’t have gaps between your nose and cheek.  The mask should filter the air coming into your nose and mouth.

Since I had COVID last January, I no longer wear a KN94, and enjoy eating indoors in restaurants again.  I’ve basically been back to normal for a long time.

Dr. Visay Prasad has an excellent video describing some of the details of the meta-study.  He is an epidemiologist from UCSF. 

CDC report on filtration.

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.

San Diego County News

For those of you living in San Diego County, there is a lot of news on the evolving situation in San Diego and California.

First, San Diego County reports that the county has met 4 of the 5 criteria for entering Phase 1 of re-opening. We have had down-trending new symptoms and cases for the last 14 days. However, to meet the last criterion, the County needs to have more testing, PPE, and hospital capacity available in the county. Let’s hope this happens soon!

Also, after a brief beach opening for walking, swimming, and surfing, Gavin Newsome has closed all beaches and state parks effective today, May 1st.

Also on May 1st, face coverings will be required in San Diego County.

Please see the SD County news page for ongoing updates.

Don’t fear, but be smart!

Hugs, not Drugs: Oxytocin and Stress Reduction

Originally posted on April 7th, 2020


I still have some science for you today, but from a little different angle. Many of you know that we make a hormone, Oxytocin, that makes us feel good and is produced when we make physical contact with the people that we love, spouses, family, friends, etc. I was listening to a podcast the other day, in which a scientist was talking about how many of us are experiencing extra stress these days either because of isolation, or perhaps because of overexposure to some of those same loved ones! 😬

This scientist recommended 2 things: First, a 20 second hug every 2 hours! This produces Oxytocin, lowers Cortisol, the stress hormone, and makes us feel better. Your teenagers may think it’s totally weird, but I think they may secretly like it!

Second, he also said that we also get a shot of Oxytocin when we meet an old friend, or simply make eye contact with someone we care about. So when interacting with friends on line, seek to de-emphasize Facebook (yes, I get the irony), email, and phone calls, and emphasize FaceTime, Zoom, or some other tech that allows eye contact! This is especially important for those who are isolated during these times!

I checked all this with Dr. Scott Bunner, a psychiatrist friend of mine, and he said the hugging thing is pretty well known. He hadn’t heard of the eye-contact thing, but that it made sense to him.

So give grandma a FaceTime call! If you’re in the position to do so safely, help an elderly person get set up for Zoom! It will help us all get through this!

Don’t fear, but be smart!

Protecting Your Family – Dr. Dave Price

Originally posted on March 29th, 2020

This is a somewhat lengthy video which is very popular. This is an NYC doctor making a video for his family. He says a lot of the same things you’ve been hearing, but with a few twists.

First, while you can get infection from the air, as suggested by scientific journals, but only by sustained contact with a sick person. He thinks it’s fine to go shopping or go for a walk, if you follow the following rules:

  1. Wash your hands if you touch things. Touching your face with dirty hands is the main route of infection.
  2. Don’t touch your face with dirty hands!
  3. If you go out, where a mask, any mask. Most masks don’t do a very good job of protecting you from airborne virus, what they do is remind you not to touch your face! So any mask will do for this.
  4. Stay at least 6 ft from people.
  5. Have a small social circle, don’t be in large groups
  6. If you’re sick, isolate yourself from your family. Follow the above rules when interacting with your family.

He also says anyone older than 14 can get sick! Yes, older people are most affected, but plenty of people in their 20s and 30s are getting sick.

He also says that while asymptomatic people are spreading disease, those that do will probably themselves be sick 1-2 days later.

All of this is one guys experience, but I think it’s valuable.

Stay safe! Our efforts to protect each other are working!

COVID-19 Protecting Your Family with Dr. Dave Price