Category Archives: Testing

Case Update: February 10th, 2021

This is a case update. New case numbers continue to plummet for the US, California, and San Diego County. New case numbers are now similar to those in early November. Obviously, the number are still not zero, so we still have work to do, but we have good news. As an interesting side note, the endcoronavirus map of new cases reveals a little pocket of new cases spreading out from Austin, Texas! Other parts of the country are generally improving, and the central part of the country is doing particularly well.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, February 10th, 2021
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.
Graph is by me, from data collected from Johns Hopkins University COVID site. This graph shows reported tests. Laboratories are currently required to report both to the ordering physicians and also report positives (without identifying information) to the CDC as well as county and state public health. Some labs have been late reporting to public health, which is why you see some days which have either a very high or very low number of tests.

Of course, we just had the Superbowl, which I count as an American cultural holiday. We may have had some new infections associated with gathering in peoples homes. If so, we may start to see numbers coming up starting on Friday or Saturday. After Thanksgiving and Christmas, new cases started to increase a little less than a week afterward.

During the year, we’ve seen testing capacity come up slowly but steadily from just a few hundred a day when the CDC was trying to do all the testing themselves in March, to around 1.5 to 2 million per day in December ’20 and January ’21. Now that new cases are starting to come down, testing is just starting to head down as well. If you are a medical professional, especially in testing, you may begin to find it easier to buy pipette tips in the next month! We can only hope!

Don’t fear, but be smart!
Erik

Case Update, January 27th, 2021, Anaphylactic Shock in 0.0011% of Vaccine Recipients

This is a case update. I’ll also briefly discuss some cases of anaphylactic shock in some vaccine recipients. The US, California, and San Diego County are all experiencing a continuing decrease in new confirmed cases! The center of the country seems to mostly have recovered from the 3rd wave according to endcoronavirus, and the coasts are improving as well.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, January 25th, 2021
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.

Anaphylactic shock in some patients: According to Paul Offit, in a YouTube interview (at 2:30 in the linked video), a number of vaccine recipients have experienced anaphylactic shock after being vaccinated. All vaccines carry some risk of this phenomena, but the COVID vaccines appear to produce this at about 11x the rate of the flu vaccines. This is about 11 patients per 1 million vaccinations, about 0.0011%. Dr. Offit thinks this allergic reaction is likely caused by Poly Ethylene Glycol (PEG), a component of many vaccines, also used in many other products, including Dr. Pepper!

The good news is that anaphylaxis is easily treatable using an epi-pen. If you are prone to allergic reactions, let your provider know before getting the vaccine.

Don’t fear, but be smart!
Erik

Case Update: January 10th, 2021

This is a case update. I’ll also briefly discuss some more new variants, and a testing equipment shortage. For the US, cases continue to increase. Day to day case rates have been very erratic for the past several weeks. This is partially because many testing facilities don’t report on holidays, so that there is an artificially low case number on holidays, and an artificially high case number the day after. The arrows in the case number graph for the US show Thanksgiving, Christmas, and New Years Day. Wave 3c, the wave starting after Christmas day, is still increasing in confirmed case numbers.

Graph is by me, from data collected from Johns Hopkins University COVID site. Arrows indicate Thanksgiving Day, Christmas Day, and New Years Day.
Graph is by me, from data collected from Johns Hopkins University COVID site.

New cases continue to be focused in the East and Southwest. In particular, new case numbers have plateaued in California, but numbers are still quite high, with 4 of the top 5 counties being in California.

Endcoronavirus County Level Map, January 9th, 2021
Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, January 9th, 2021
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.

New confirmed cased numbers are continuing to increase in San Diego County, with no clear separation between Fall, Thanksgiving, and Christmas waves.

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

More new variants? I mentioned the new UK variant a few weeks ago. Since then, I’ve heard reports of new variants also arising in South Africa and Colorado. I don’t have much information on those yet, but the more people who are infected, the more likely a new strain will arise.

Equipment shortage. For those outside the medical community, just a little inside knowledge. The crisis has revealed many of the items that are limiting in our efforts to combat the virus. For the medical testing industry, many common materials have been very difficult to obtain, leading to long wait times for testing. There is a short supply of testing instruments, detection kits, RNA extraction machines, extraction kits, plastic plates used to contain testing reactions, and even plastic tips used to move small volumes of liquid in the lab. If you place an order of tips today, they may not arrive until April or May! This is part of the reason testing has been so slow and new labs difficult to start. I’m told that part of the issue is that there are only a few factories in the world that make medical plastics, and they are all overwhelmed. As a country, we’ll have to rethink our supply chain now and in the future.

Don’t fear, but be smart!
Erik

Case Update: July 22nd, 2020.

Friends,

Happily, there is some good news about the virus this week.  For the US and California, the number of daily new cases suggests that for both regions, we may have hit a peak in new cases.  Sunday or Monday is always the low number for the week, but the number of new cases on those days usually predicts the peak for the rest of the week.  For both, this week’s low is near or below last week’s low, suggesting that the high for the week will be near or lower than the high for last week. 

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

San Diego has been flat since early July.  New cases aren’t going down yet, but they aren’t going up anymore either.  In addition, the number of active cases in San Diego is probably going down, after a peak of almost 8000 active cases.  Unfortunately, California overtook New York for the number of confirmed cases in the country this week, and LA County has the most new cases in the entire country, and has 40% of confirmed cases in California.

Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Some data points of “Active Confirmed Cases” are from SD County, others are calculated.

As we discussed in May 12th post on new cases, comparing the number of tests and new cases can tell us if all the new cases are just related to new testing.  An R2 number between 0.95 and 1.00 shows strong correlation, “proof” that two things are related.  The tests vs cases for the US since early July give an R2 of 0.78. This suggests that though many of the cases are real, at least some are because of new testing. In California the R2 is 0.44, a much weaker relationship, meaning more of the new cases are not just due to more testing.

An R2 number of above 0.95 suggests good correlation, a number of 0.78 suggests that while there is a contribution from increased testing, some of the increase is real new cases. Graph is by me, from data collected from Johns Hopkins University COVID site.
An R2 number of above 0.95 suggests good correlation, a number of 0.44 suggests that while there may be some contribution from increased testing, much of the increase is real new cases. Graph is by me, from data collected from Johns Hopkins University COVID site.

Rt Live shows that more states have an Rt number of less than 1.0, indicating that the virus is slowly going away in that state.

From Rt Live

I have some African readers, so I’ll point out that the number of new cases appears to have peaked in Nigeria, DR Congo, Malawi, and South Africa, as well as in Brazil, a country which now has the 2nd highest number of confirmed cases, behind the US. Let’s hope we can keep this progress going!

New daily confirmed cases for Nigeria. Graph is from Johns Hopkins University COVID site.
New daily confirmed cases for the Democratic Republic of the Congo. Graph is from Johns Hopkins University COVID site.

Don’t fear, but be smart!
Erik

Case Update: June 30th

This is a case update. Unfortunately, we are experiencing an explosion of new cases in the US, California, and San Diego County this week, continuing the trend that started a few weeks ago. For all of these regions, this week brought record highs for all three regions. California reached approximately 66k active cases, and San Diego County has doubled it’s active caseload to 4,222 in just the past week.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Active Cases are calculated based on the assumption that all patients with cases confirmed more than 17 days previous have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Some data points for Active Cases come from San Diego County Health, while others are calculated.

Why is this happening? Probably for multiple reasons. First, as things re-open, some businesses and individuals are not following guidelines for safe reopening. San Diego County had 7 super-spreader events in the last week, 4 at restaurants, and 1 at a private residence. You may have seen a story in the news this week about a bar in Michigan in which 85 college aged people were infected in a single evening. As you might imagine, they were not wearing masks, and were not practicing social distancing. The recent protests and riots almost certainly have had an impact as well.

In my May 12 post, I explained how you can tell if testing is having an impact on confirmed cases by graphing daily tests against daily new confirmed cases. In the last few weeks, the R2 number has risen into the 0.5 range for the US and California. An R2 number of 0.95 “proves” correlation, but a number in the 0.5 range suggests some contribution by increased testing. These graphs suggest that increased testing has contributed some of the new cases numbers, but some of the new cases are simply new infections as well.

An R2 number of above 0.95 suggests good correlation, a number of 0.59 suggests that while there may be some contribution from increased testing, much of the increase is real new cases.
An R2 number of above 0.95 suggests good correlation, a number of 0.51 suggests that while there may be some contribution from increased testing, much of the increase is real new cases.

There is some good news. That is that if you are careful and follow the below guidelines, you can be reasonably certain you won’t catch COVID:

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

An epidemic is like a brush fire. When it dies down, we can start to be complacent, but diligence is still required. We are experiencing this new burst of cases because we have let our guard down. Hopefully, we can get things back under control soon.

Maybe take a break. After all the troubling news of the past month, a friend of mine complained that he is feeling depressed and not doing well. While I encourage everyone to follow the news and to be engaged with public life, studies show that over consumption of social media can lead to depression and anxiety. If you feel depressed, or your blood pressure is high, or you’ve been ranted to your wife more than she would like (I know someone like that), you may benefit from a news and/or social media fast. Consider taking a day or more off a week to let yourself calm down and get back to normal. In our information age, we can receive all the bad news of the world at all times, and we aren’t designed to carry that burden.

Don’t fear, but be smart.
Erik

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Best option: An N95 mask with no valve.

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

Handwashing:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Don’t fear, but be smart,
Erik

San Diego County Residents Encouraged to Get Tested for COVID-19

My friend who works for San Diego County Health, Brit Colanter, just posted that all San Diego County residents are encouraged to get tested for COVID-19. Check with your health care provider first to see if they will give you a free test. If not, check the below website, or call 2-1-1 for an appointment at a County Site. State run testing sites are located in Escondido, El Cajon, Chula Vista, San Ysidro and Southeastern San Diego. Check the website for a phone number or link to get an appointment at a state site.

These are likely the Abbott, ID Now rapid COVID test.

Getting a test gives you peace of mind, but also helps scientists understand the real rate of infection in the County!

Happy Testing!
Erik

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,

Erik

Re-opening, How Many New Cases?, endcorona.org 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!

Endcorona.org compares responses: I discovered a new website the other day, endcorona.org, 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, endcorona.org 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!

Erik

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!

Erik