Category Archives: Re-opening

Restaurants and More Businesses Re-opening in San Diego and other California Counties

On Wednesday, San Diego County announced that the county will be moving further into California’s Step 2 re-opening plan.  This means restaurants will be opening for modified seating with some other restrictions, and many more businesses will able to open as well.  To sum, customers will still need to maintain 6 ft separation, and everyone will need to wears masks while shopping.  Restaurant guests will need to wear masks while not at their table.  Tables in restaurants will need to be moved so that seated customers are at least 6 ft apart.  Tables that cannot be moved will need to have barriers between them.  Restaurants can also expand outdoor seating!

I’m excited for this change, but it will be important for the public to follow these new guidelines. We want to keep making forward progress!

Don’t fear, but be smart!


Case Update: May 19th, Some California Counties Re-open Further, San Diego Recovered Patients

This is a case update for the previous week.  As we’ve seen before, new cases in the US are slowly trending downward (currently around 21k confirmed cases per day), slowly trending upward in California (around 2k confirmed cases per day), and flat in San Diego County (around 125 confirmed cases per day).  As we discussed from statistics last week (May 12th post), many of these are likely real cases, and not just because of additional testing.

Active cases after 5/15 are based on data released by San Diego County. Points previous to 5/15 are calculated based on the assumption that recovery time after detection is 16 days.

Rt Live reports that all but 2 states have an Rt value below 1.0, meaning that the virus is slowly disappearing in that state.  You may notice if you look on that site, however, that several states, including California, still have slowly upward trending cases, even though they have an Rt value below 1.0.  This appears to me to be a discrepancy.  Possible explanations for this may be that the Rt Live’s algorithm is too generous and miscalculates Rt for some states, or that the Rt value needs to be much lower than 1 for a downward trend to be seen.  We can certainly hope that we will see improvement in these states soon.

Some counties in California will be able to move further into Step 2 of re-opening (Step 2b?). Unfortunately for many of us, none of these counties are in Southern California!

My friend who works at San Diego County Public Health, Brit Colanter, has posted an update slide deck that the County has released, and will update regularly.  The county is continuing to have more testing available to the public and is now releasing the number of recovered COVID patients.  As of last night, total confirmed cases in SD is 5946, and current active cases is 1926.  So more than half of our confirmed cases have recovered!  That’s great news!

As we continue into recovery and more businesses open, please continue to wear masks in public, and continue to distance whenever possible!  The CDC was slow to recommend masks, and it’s true that masks are not 100% effective, but if everyone is wearing masks that are 50% effective, this will go a long way toward minimizing transmission. See my May 5th post for more info and for mask designs! I’m a big fan of wearing masks in public, and it may be the key to opening more businesses.

The more we keep new cases low, the faster we can continue the re-opening process!

Don’t fear, but be smart!


Rt Live

California, Resilience Roadmap

County by county guidance

San Diego County Update Slides

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!

Dr. Erickson’s Video and the Fatality Rate

Originally posted on April 25th, 2020 on Facebook

This one is going to be a little mathy. Several people have sent me the video titled “Dr. Erickson COVID-19 Briefing”. I’ve watched the first 12 minutes of the 52 minute video. Dr. Erickson argues that we have a large number of current cases, and that when comparing this number to deaths, he calculates the fatality rate at between 0.03 and 0.07%. This is less than the typical flu. He uses data from his home county of Kern County in California, NYC, the US, Spain, and others. Unfortunately, Dr. Erickson makes a critical error in his calculations.

For the US, he says we have 802,000 confirmed cases (around April 20th) and around 4 million tests. This would give him a positivity rate of 20% for the country. He then calculates that we then have 64 million cases in the country and only 45,000 deaths, giving us a fatality rate of 0.07%

The mistake he makes is that he assumes that tests given represents a random sampling of the population. Anyone who has tried to get a test and failed knows that not everyone who wants a test gets one. And not everyone requests a test either. Dr. Erickson has what’s called a sampling bias. You have to make sure you have a sample that represents the group you want test if you want to say anything about that group. Instead of testing the general population, Dr. Erickson is testing just people who meet the criteria for testing by the CDC or other health care body. This group is far smaller, and far more likely to have the virus than the general population. He over-estimates the number of COVID cases, by maybe 10 fold.

Several studies, some not yet published, have tested random selections of the population using PCR and antibody tests (see references 1, 2, 3, below). In those studies, fatality rates range from 0.12 – 0.7%, 2 – 23x higher than Dr. Erickson’s estimate. Also, the studies by Bendavid and Sood (2, 3) suggested that approx. 4% of the populations of Santa Clara County (San Jose) and Los Angeles were infected in early to mid April. So 96% of the population is still susceptible. At the 0.12 – 0.7 death rate, that’s 6,000 – 37,000 potential deaths for those 2 places alone. Even these studies, with fatality rates far higher than Dr. Erickson’s, have been criticized for an estimate that is too low because of sample bias (4).

We won’t really know how many people have had it until there is wide spread testing. South Korea has done extensive testing, and their fatality rate is 2.24%. This might be in the ballpark of the rate in the US.

So I have to reiterate, SARS-2 is not the average flu. In addition to being up to at least 5x more deadly, it’s also 4x more infectious. The very good news is, our efforts are paying off, and the daily rate of new cases for the US is now just 2.46%, down from a terrifying 46% on March 19th. It’s right for some living in rural areas to wonder if they can begin the process of going back to normal. Some can, but it needs to be done carefully and watchfully, with lots of testing for exposure, not just for symptoms (See my April 9th and April 22nd posts). The entire state of Minnesota plans to do just that. We can watch in real time to see how it goes for them. We don’t want another Albany, Georgia! Urban areas like coastal California and the Acela Corridor will have to wait awhile longer.

Don’t fear, but be smart!

1. Sutton et al., Universal Screening for SARS-CoV-2 in Women Admitted for Delivery. April 13, 2020. NEJM,
2. Bendavid et al., COVID-19 Antibody Seroprevalence in Santa Clara County, California, April 11, 2020, preprint by medRxiv
3. CBS report on upcoming study
4. Experts demolish studies suggesting COVID-19 is no worse than flu

PS. If you want me to watch something later in Dr. Erickson’s video, please tell me what the time reference is. I really don’t want to watch the whole thing!

What is the Fatality Rate?, Antibody tests, Re-opening

Originally posted on April 22nd, 2020 on Facebook

This is a little longer post, this time with lots of science. I’ll talk about new measures of the fatality rate, some of the new Antibody testing, and also about the new re-opening guidelines. As always, consult with your doctor when making health care decisions!

First, very briefly, I’ll just say that we have seen a big up-tick of cases in the last few days. I’m trying to be optimistic about this and assume for now that this is because of increased testing. The large labs have been purchasing new instruments of different types to broaden their offerings.

There have been a handful of studies trying to discern the number of asymptomatic cases. One recent study in New York tested all pregnant women coming in to deliver. It showed that at least in this sampling, there we about 7x more asymptomatic women testing positive for COVID than symptomatic women (Sutton et al, Universal Screening for SARS-CoV-2 in Women Admitted for Delivery. April 13, 2020. NEJM, If this is roughly correct, then most confirmed cases numbers you see can be multiplied by 8 to get the real number of cases, as least until testing becomes more comprehensive. This also means the real fatality rate may be approximately 0.7%, about 5x higher than the typical flu.

Some have suggested that the fatality rate for COVID is the same as the flu, but this is the low end of new estimates, and for now, my guess is that it is higher. I think 0.7% is a good estimate for now. The rate for the typical flu 0.14%. Keep in mind that the Ro value for SARS-2 is about 5.7, much higher than the flu at 1.28.

On to Antibody tests! There has been a lot of excitement recently about antibody tests, and I have promoted them in my posts as well. As many of you know, the PCR based tests look for viral RNA in nasal swabs and detect an active infection. They are very sensitive, but they are more expensive, and need to be performed at specialized sites. Because the virus mostly lives in the lungs, nasal swabs don’t always collect virus from an infected person, and the false negativity rate has been estimated to be around 29%, at least initially. This is very high.

Antibody (Ab) tests detect an immune response by the patient by isolating antibody from the blood. Most detect 2 kinds of antibodies. IgM antibodies are produced during infection, and start appearing after about 3 days. IgG antibodies are produced later, at about 7 days, but continue to be produced for weeks to months after infection. The antibody tests are often less sensitive than the PCR tests, and they do not work during the first few days, since antibodies are not produced that early.

As you might guess, combining PCR and Antibody tests may give a good indicator if and even when an asymptomatic person was infected. Below is a table of possible interpretations of test results, assuming testing is accurate. Always confirm results and discuss with your doctor when making health care decisions! The FDA regulates testing in the US, and several tests have received Emergency Use Authorization (EUA) status. This is not FDA approval, but allows tests to be performed under emergency conditions. Several labs have started to perform antibody testing along with PCR. At first, Ab tests will be given in combination with PCR tests to see if health care workers have already been infected. If you want an antibody test, you’ll need to check with your doctor to see if you meet availability criteria. Many other companies have tried to offer tests without EUA status, including at home tests. Many of these tests have very high false negativity rates, and are basically no good! As of this writing, I would not use any at home test kit. Before taking any test, check with your doctor, or confirm with the FDA or CDC websites to see if a test has EUA status.

Re-opening: The federal government has released guidelines on the re-opening process. These are recommended guidelines, and most states are likely to adopt them, but the final decision will be up to the Governor of each state. I’ll provide the link below. In short, to enter the first phase of re-opening, states or counties must show a downward trajectory of cases and symptoms for 14 days, and must have certain hospital capacities and infectious disease surveillance procedures in place. Each additional phase can be entered if these conditions continue to be met for an additional 14 days. Some states or counties may already meet the criteria for phase 1, and some states plan to enter phase 1 on May 1st. Looking at the criteria, the guidelines seem reasonable to me, and I hope Governors will learn from the experiences of other countries and states while making these decisions.

Until next time, don’t fear, but be smart!

FDA Emergency Use Authorizations:

Federal Reopening Guidelines:

When should we re-open? Opposite valid interests

Originally posted April 13th, 2020 on Facebook

This will be a longer post, so buckle up!

While I certainly have political opinions, I’ve been trying to minimize them for the purposes of these posts, in order that more of you will be willing to read! Today, some of you may be able to figure out where I stand on some things, although I’ll still try to keep the controversy to a minimum. This last weekend, there were protests in many cities of the US asking for the economy to be opened up. Of course, most of these requests took the form of slogans shouted or written on signs, rather than specific policy proposals. I’m very sympathetic to the need of many to get back to work so they can provide for their families, pay the rent, etc. I also share the frustration that much of the information provided by the media and government agencies is untrustworthy or incomplete. This is why I write these posts!

I want to reiterate the differences between the typical flu and the SARS-2 virus:

The R0 value (a measure of infectiousness, see my April 13th post) for the flu is 1.28. For SARS-2, it’s 5.7, 4.5 times higher!

The incubation time for the flu is 2-4 days, for SARS-2, it’s 2-14 days, and asymptomatic people are often contagious!

Yes, the fatality rate for both is impossible to know. And it’s probably over-estimated for both, since we don’t know the number of infected people with mild to moderate symptoms for either disease. But estimates are that the fatality rate for the typical flu is 0.14%. The current rate for COVID-19 in the US is 5.36% (deaths/confirmed cases), 38 times higher.

In short, SARS-2 is not the typical flu.

We have to concede that in an event like this one, there are many valid interests that are in some ways are opposed to each other. People at risk want to stay safe. Doctors and nurses want to treat their patients, but also face constant exposure of themselves and their families to the virus. Those in government do not want to expose their constituents to unnecessary risk. On the other hand, many have lost their jobs and need to get back to work. Mental health workers worry that their patients cannot withstand prolonged isolation and stress. Employers wonder if they have to lay off more people or close their businesses. All of these are real concerns, and they can’t be dismissed.

It will be difficult moving forward to strike a balance between these competing interests, and no solution will be perfect. We need to understand that most are doing their very best to manage a very difficult situation. There is lots of blame to go around, but remember that the nature of the virus has never been completely clear. For myself, I gave a talk at my church on March 13th (Posted here on March 18th). During the previous week, I was trying to determine if the virus was spread by droplet transmission (coughing and sneezing), or by aerosol transmission (shouting, laughing, singing, even talking). At the time, most outlets including the CDC said it was only spread by droplet transmission, but a few scientists were warning that it may be aerosol. Should I really be giving a talk on virus safety to room full of people? It appeared at the time that it would be OK, so I moved forward. Luckily for me, the decision was made to cancel gatherings, and my talk was recorded for the web. As it turned out, the SARS-2 virus is much more infectious that originally thought (see my post from April 13th), so add me to the list of people who were wrong! Thank God I didn’t have a crowd in the room during my talk!

Again, I am not an epidemiologist, I am a molecular biologist specializing in infectious disease. But in my informed opinion, reopening the economy without great care is a mistake. A similar experiment has already been done. On March 11th, California Governor Gavin Newsom banned large gatherings including sporting events, church services, and university classes. On the same day, New York Mayor Bill De Blasio was encouraging people to eat out and enjoy themselves. As of this writing (April 19th), California has 31,000 confirmed cases, and New York City alone has 138,000, more than all but 6 countries (yes, I’m including China, the Chinese Communist Party is almost certainly heavily under-reporting their case load)1. For a time, New York hospitals were overwhelmed, and bodies were being temporarily buried on Hart Island. This is the possible consequence of going back to normal too quickly! If you choose to gather in large groups during this time (for example at protests in downtown San Diego), I would strongly encourage you to take extra care to isolate yourself from those at risk or those who may come in contact with them.

I am less sympathetic to those who want to get back to normal just so they can go to Disneyland or to their favorite restaurant. As we reopen the economy, we have to do so carefully. Theaters, restaurants, and amusement parks are among the last things that should be reopened.

We will need have adequate testing and hospital capacity to handle the additional case load. Each area will be different in this regard, and New York City should not be treated the same as Ennis, Montana. We will also need to have grace for one another, as well-intentioned mistakes will be made along the way. Ideally, we should also have contact tracing, contacting those potentially exposed to an infected person. This practice, along with aggressive testing, was used very effectively in Taiwan, So. Korea, and Singapore, to minimize caseload. Unfortunately, we are not yet able to do contact tracing in the US.

While I am very sympathetic to individual rights, and am in general for small government, we may need to voluntarily lay down certain rights for a time in order to protect each other. Pray for our leaders, regardless of party, and take care of each other!

I’ll have another post soon on the topic of antibody testing.

Don’t fear, but be smart!

Workers temporarily bury bodies on Hart Island in New York City

1 Editor’s note: As of the date of posting, the statistics here were correct. As of July 7, 2020, however, the situation has reversed. New York State as 398k confirmed cases, California has 284k confirmed cases. New York state daily cases are trending downward, while California daily cases have been trending upward.

Case Update: April 9, When can we go back to normal?

Originally posted April 9th, 2020 on Facebook

You may have heard lots of positive news in the press in the last few days about new lower rates of new infections in the US. If you saw my posts on March 30th and April 1st, you know that I was enthusiastic about some good news a little earlier than was warranted. So I wanted to wait a few days to see if the current positive trends would hold.

All that being said, I do have good news for you today! For the World, the US, California, and San Diego County, the rate of new cases as been below 10% every day since Sunday, April 5th! That’s great news. The actual daily new cases has been trending basically flat in the US since Sunday, and in California since April 1st. So the news is definitely good! There is even better news if you live in San Diego County. Daily new cases actually appear to have peaked on April 3rd, and are actually down since then.

Some in the media are discussing an end to our isolation, but I have to say that it is still very important that we continue to practice social distancing for a while longer. Our efforts are working, but we still have a lot of work to do!

My brother asked me when I thought it would be safe to go back to normal. I’ll preface my opinion by saying that I am not an epidemiologist. My opinion on this is informed, but I’m not an expert. In my opinion, we can go back to normal when:

  1. Our daily new cases are very low, a few a day.
  2. We can be reasonably certain that we know where every sick person is located, and that they are isolated.
  3. That we have enough testing capacity that we can test those who have been potentially exposed, not just confirming cases that appear to be COVID-19 cases by symptoms.

You can see that we have quite a ways to go to achieve these 3 criteria. So it’s important that we remain diligent! It is highly likely that we will experience a second wave of infections if we try to go back to normal too early.

A local physician told me last week, April 1st that wait times for testing was 12 days. Yesterday, Wednesday, April 8th, he said that results were coming back in just 2 days. So with new cases falling, we are able to test much faster. This will eventually give us capacity to test for exposure! I don’t know if public health officials are considering this yet.

So be encouraged, but be diligent! Your efforts are paying off!

Don’t fear, but be smart!