Category Archives: Risk Factors

Summary of the Pandemic, July 21st, 2021

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.

Origin:  Controversy over the origins of the SARS-2 virus began very early in the pandemic.  The most common theories were that the virus arose naturally at a live animal market in Wuhan China, where animals from a wide variety of species are sold.  The predominant theory is that the SARS-2 virus arose in bats, then transferred to another animal, perhaps a pangolin, before moving to humans.  This has been the most accepted theory for the majority of the pandemic, promoted by the WHO, the CDC, and American media. 

The lab leak theory, the idea that the virus arose from the Wuhan Institute of Virology, was present from the beginning, but was heavily disfavored by official channels for most of the pandemic.  On May 23, 2021, the Wall Street Journal published an article that gave evidence for idea, followed closely by an article from Vanity Fair.  The articles normalized discussion of the theory and as of this writing, polls show that a majority of Americans believe that the virus came from the WIV.

Emails between several virologists, public health officials and Dr. Fauci strongly suggest that this group believed that the virus may have come from the laboratory as early as January 31, 2020.  However, this same group published a scientific article on February 9th supporting the natural origin theory.  The paper was at odds with discussion in the email correspondence.  If investigations show that the group published claims they knew to be false, this would represent a significant case of scientific fraud.

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, outdoor transmission of SARS-2 appears to be extremely 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 viral 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 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:

age
asthma or COPD
heart conditions
kidney conditions
liver disease
high blood pressure
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.  N95, KN95, and KF94 respirators are effective at filtering close to 95% of virus.  A good mask is well fitting and filters the air moving in an out of your mouth and nose.  The commonly used surgical masks and other loosely fitting masks do not filter air and I don’t recommend using them.

Social Distancing: Aerosolized virus can travel through the air. Staying 6 ft away from others helps prevent infection. Social distancing may be more important for droplet transmission, like the flu, than for aerosol transmission in which microdroplets can stay suspended for much longer and travel much further.

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. Supplementing Vitamin C and Zinc is also recommended.

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.

I’ve been traveling all over the country, and have been in dozens of airports, gas stations, and stores.  I get tested regularly and have always been negative.  Here are the precautions I use:

1) Wear a mask or face covering indoors in public.  Now that vaccines are available, I no longer avoid unmasked people indoors, but as an unvaccinated person, I still wear mine.
2) Keep 6 ft away from others. (I basically ignore this one if other precautions are in place, especially on an airplane!)
3) Avoid indoor gatherings, especially ones in which singing or shouting is likely. This is now voluntary now that we have vaccines, as an unvaccinated person, I still follow this rule.
4) Outdoor gatherings are fine, even without masks, if everyone maintains a distance. I have hosted several outdoor gatherings.
5) While many restaurants are open for limited indoor seating, I personally am still not comfortable eating indoors at a restaurant. I enjoy eating outdoors at restaurants, however.
6) Wear an N95 or KN95 mask when going to more high risk areas like airports or public areas where people may gather. These masks are rated to filter out 95% of viral particles. In my opinion, surgical masks and especially neck gators are nearly worthless in these settings.
7) I never take my mask off on the plane, and find an isolate spot in the airport to eat or drink on layovers.

Vaccinated people can relax many of these rules!  Vaccines are 90-95% effective, so you still have a small chance of infection.

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. They can take longer to process because they need specialized equipment that most small labs don’t have, so most of the wait time is just for shipping to a specialized facility.

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. These tests are cheap and fast, but are more prone to false positives and false negatives than PCR tests.

Antigen: These tests use a very similar technology to Antibody tests, but instead of detecting a patients antibodies against virus, they use antibodies to detect viral proteins in a sample. An “antigen” in immunology lingo is just a protein that can induce an immune response. So in this context, an “antigen” is a SARS-2 protein that can be bound by an antibody. Like PCR tests, these tests detect an active infection, because they detect viral proteins currently in the body.

Isothermal amplification:  The Abbott ID Now COVID tests uses this relatively new technology.  These tests are similar to PCR but more prone to false negatives. 

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.

Antibody Dependent Enhancement:  I’ve written about this a lot and I won’t describe it in depth here.  In short, this pathway allows some viruses to create more severe disease on the 2nd time infecting a person than the first.  It is theoretically possible, perhaps even likely with SARS viruses, which is why I have been careful to avoid infection and why I’m not going to get the vaccine unless perhaps my work requires it.

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.

Supportive care: Most treatment is supportive care, treating symptoms while the patient recovers naturally.  Anti-inflammatory medications are often used to prevent the immune system from over-reacting to the virus.

Ventilators/nasal cannula:  While widely used early on, some doctors now state that ventilators carry risks that may be unacceptable for COVID patients.  Many doctors now favor oxygen therapy using a nasal cannula, using ventilators only as a last resort breathing if labored. 

Remdesivir: This antiviral was used widely for much of the pandemic, but many sources now claim it has limited effectiveness.

Dexamethasone: Steroid used to treat patients with low oxygen levels.

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.  Treatment with Ivermectin is likely more beneficial in a wider range of disease state than HCQ.

Ivermectin: A anti-parasitic medication used since 1981, Ivermectin has reportedly been used by doctors around the world, notably India and Mexico, to reduce COVID fatalities.  Reports claim that Ivermectin is beneficial in a wide range of disease state, from pre-disease prevention to late stage disease.  Like Hydroxycholoroquine, promising data was often labeled “misinformation” by outlets in Western countries, and western doctors were strongly discouraged from prescribing it.  Thus, experimentation with Ivermectin was hindered and the drug’s potential is still unknown. 

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.

Several vaccines against SARS-2 were finally released to the public in December of 2020.  The vaccines released to the public are in 2 types:

Attenuated vaccine: This type has been commonly used for decades for a variety of viruses. The technique makes a severely weakened form of the virus that still makes viral proteins that provoke an immune response.  With this type of vaccine, the patient is infected by a weak form of the virus that they quickly recover from, usually with no symptoms other than occasionally the flu like symptoms that are your body’s natural response to invasion.

mRNA vaccine: This is a brand new technology that has been worked on for years.  The SARS-2 vaccines are the first ones that have been introduced to the public using this technology.  The vaccine includes a piece of mRNA inside a lipid bilayer that mimics the cell wall.  The mRNA is inserted into the cell where it is translated into a copy of the viral Spike protein.  These vaccines are 90-95% effective against infection, and even those infected have less severe symptoms.  However, they are not 100% effective, so some infections of vaccinated individuals has occurred.

As has often happened, the vaccines have generated significant controversy.  As you know, I have been careful to avoid being infected and also getting the vaccine because of the potential of ADE.  My concern with the vaccine actually has nothing to do with the new mRNA technology, I actually have no reservations about the mRNA vaccines.  From an ADE perspective both the attenuated vaccines (Johnson & Johnson) and the mRNA vaccines (Pfizer and Moderna) produce Spike protein that may trigger an ADE response should a new strain of SARS virus appear, not a variant, a new SARS strain, like a “SARS-3”.

When the vaccines were released, rumors of side effects, sometimes severe, arose immediately.  For some time, I minimized these as a risk of any vaccine.  All vaccines carry the risk of side effects and even death.  However, a video podcast featuring Robert Malone, the inventor of mRNA vaccine technology, convinced me that the Spike protein itself has toxic properties of its own, separate from the vaccine technology used. This is because the Spike protein can bind to cells all over the body and may have wide ranging effects.

Despite ADE and issues with side effects, I actually still believe some will benefit from the vaccine.  These include the following groups:

Anyone over 60
Anyone with 1 or more risk factors:

obesity
certain auto-immune diseases
use of NSAID medications
heart, lung or kidney condition
immunocompromised patients (HIV, cancer and transplant patients)
respiratory condition such as asthma or COPD.

Frequently working with the public
Musicians who sing in indoor settings
Medical personnel

Again, I am not a physician, so check with your healthcare provider while making decisions about getting the vaccine or changing your medication.

If you’ve had the vaccine or had COVID and are concerned about ADE, remember that it will only become a factor if a significantly new strain arises (“SARS-3”). If this happens, then the procedure for you would be to be very careful initially, then get the “SARS-3” vaccine as soon as possible. The new vaccine will protect you from the new virus. In the future, vaccines against Coronaviruses will be produced even more quickly than this time.

The vaccines have pros and cons.  I’m in support of vaccines for some but not necessarily for others.  Each person needs to weigh the risks for themselves.  I am not for companies or government agencies coercing individuals to get the vaccine.

Herd Immunity:  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.  The idea is useful, but in my opinion, efforts to push people into getting vaccinated to achieve herd immunity are misplaced. Before a vaccine is available, the only way to reach herd immunity is to expose large numbers of people to the virus, which is counter productive.  Now that the vaccine is available, those who are concerned should just get the vaccine themselves and not harangue others about getting it.  Gentle persuasion may be convincing, but haranguing rarely is. Given even the pre-pandemic resistance to vaccines, a forceful effort to vaccinate is likely to back-fire.

Variants:  During the course of the pandemic, several variants have arisen that have a slightly different Spike protein sequence from the original Wuhan strain.  Confusingly, naming conventions have changed several times, making it difficult to keep them all straight.  As a general rule, the variants have all been more infectious than the Wuhan strain, but have not been more pathogenic.  Fortunately, the vaccines have been effective against all of the variants, although are not as effective against some variants.

The Delta Variant: The UK/Alpha variant caused waves of new infections in some countries and was more infectious than the original Wuhan strain.  In late 2020, a new variant arose in India, the India/Delta variant.  This variant was significantly more infectious than other strains and has caused huge peaks in cases in several countries.  As of this writing, several countries are still experiencing waves of new cases most likely due to the Delta Variant, including the United States.

While the Delta Variant has caused large numbers of new cases and an increase in hospitalizations, data suggests it may be less pathogenic than the Wuhan or UK variants.

Current Status: In late Spring, at least in the US, life began to get back to normal, with approximately 50% of the US population vaccinated, much lower new case numbers, and reduced restrictions. Currently however (July 21, 2021) a wave of infections, likely caused by the Delta variant, is causing concern and some calls for new restrictions.  Several other countries scattered across the globe are also currently experiencing peaks in cases.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a linear format and includes only the Fall/Winter 2020, Spring ’21, and Delta Variant peaks.
Endcoronavirus County Level Map, July 20th, 2021
Daily new confirmed cases in India, from data collected from Johns Hopkins University COVID site. The Delta Variant peak is the large one on the right. Notice the sharp upward and downward trends. The new persistent daily case numbers are higher than before the Delta peak began.

The Future: Since vaccination started in the US, there have been many fewer new cases.  This has led many to basically go back to behaving normally.  The Delta Variant is rightly causing concern, but I’m still hopeful that the current peak in new cases will be short lived. In other countries with Delta related waves, the peak has been very sharp, with quickly increasing, then quickly decreasing case numbers. However, I’ve started to be a little more cautious in public again, while we wait for the increase in cases to slow.

Several other countries are still experiencing an elevated case load.  The pandemic won’t be truly over until cases are low in all countries.  I’m hopeful that this will happen this year, but it’s certainly too early to know for sure.  So far, all new variants have been susceptible to the vaccines and natural immunity.  There is a small chance however, that we may see new versions that are not.  If this happens, SARS may become endemic, circulating seasonally like the flu does.  So far, I don’t see evidence that this will happen.

In the future, we may have a “SARS-3” a new virus from the SARS family that will be similar, but different enough to trigger the ADE pathway.  If this happens, those of you that have had COVID or been vaccinated should be very careful to avoid infection initially, then get the “SARS-3” vaccine as soon as it is available.

In a future post, I’ll give my recommendations for what should be done differently if a new pandemic should arise.

Don’t fear, but be smart,
Erik

Case Update: April 27th, 2021; Indoor Transmission, New CDC Guidance

This is a case update. I’ll also talk about a new paper discussing indoor transmission as well as new CDC guidance.

This US is recovering from the 4th wave.  Yes, the wave was much smaller than others, and if you don’t want to call it a wave, I won’t argue with you.  Michigan bore the brunt of new cases, but cases are going down.  Only Washington, Oregon, and Colorado are still experiencing higher case loads.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Endcoronavirus County Level Map, April 26th, 2021
Endcoronavirus State Level Map, April 27th, 2021

California and San Diego County continue to have fewer confirmed new cases.  In fact, California had just 661 new cases on Sunday.  The state hasn’t had fewer than 1000 new cases since almost exactly a year ago on April 28th. Yes, Sunday always has the fewest cases of the week, but it does indicate that cases are trending lower.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.

Internationally, a large peak is starting to improve. India has been particularly hard hit by the current wave of cases.  The higher cases are likely impacted by the more infectious new variants as well as slower vaccination rates.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus Country Page, April 27th, 2021

Indoor transmission: Several news outlets have been talking about a new paper on indoor transmission of SARS-2 published by a lab at MIT.  It makes several interesting points.  First, the paper points out that the Six Foot Rule was designed to mediate infection from large droplets like we see for the flu.  Large droplets usually only travel from a person to the ground in 6 feet or less.  SARS-2 on the other hand, appears to be transmitted as small droplets in an aerosol.  The micro-drops stay in the air much longer and can travel much further.  Transmission in indoor settings are a function of the number of people in a space, and the time of exposure.  Ventilation helps reduce transmission.

MZ Bazant and JWM Bush, PNAS2021 Vol. 118 No. 17
MZ Bazant and JWM Bush, PNAS2021 Vol. 118 No. 17

The authors also point out that the likelihood of transmission outdoors is very low.  One paper they reference has data from 7,324 transmission events, only 1 happening outdoors.  They also say that masks have much more effectiveness in preventing transmission than lockdowns or social distancing, adding more evidence that the virus spreads as an aerosol.

Are you surprised by the papers conclusions? If you’ve been reading my posts, then probably not. I’ve been writing similar things since May 27th of last year. So why are people talking about this now? I certainly have my opinions, and I’ll bet some of you can guess.  Meanwhile, several news outlets are saying that the CDC is about to release new guidance that vaccinated individuals can now go outdoors without masks.  At the risk of running counter the CDC, I’ll just mention that I’ve been going outdoors without a mask since March of last year, at my most concerned. I almost always wear a mask indoors, but almost never wear a mask outdoors.

Don’t fear, but be smart,
Erik

Case Update, April 6, 2021; More on Vaccines, Auto-Immune Disease.

This is a case update. I’ll also add something to last week’s discussion of the South Africa variant and vaccines, and also talk briefly about autoimmune disease.

Last week, cases in the US looked like they were rising, but this week, it’s more ambiguous. New cases in the US are the same or maybe even a little lower than last week, so I can’t point to a clear trend right now. A spike in new cases persists in the Eastern Michigan at the moment, as well as higher new cases in several other Eastern states.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, April 5th, 2021
Graph is by me, from data collected from Johns Hopkins University COVID site.

New confirmed cases are also slightly up from last week in California and San Diego County. If we have a bump in cases because of Easter, it will start to show up on Wednesday or Thursday.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are reported by San Diego County. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.

Update, Vaccines and the SA Variant: Last week I discussed the effectiveness of several vaccines on the South Africa variant (B.1.351). I said that the Astra-Zeneca vaccine works poorly against the vaccine and that the Pfizer and Moderna vaccine were still poorly understood. New data from a small study Pfizer released in early April suggests that their vaccine is effective against the SA variant, though the study is too small to say how much. The Moderna vaccine is not particularly effective against the SA variant, but they are testing a booster against the SA variant right now. The Johnson and Johnson vaccine is 75% effective in the US, and 57% effective in South African patients (as reported by J&J).

Auto-Immune Disease and COVID: It appears that those with auto-immune diseases, like me (celiac disease), may suffer more severe symptoms from COVID. There is some suggestion that this may be because of consistent use of NSAID medications to counteract inflammation. Most doctors will suggest remaining on anti-inflammatories unless COVID symptoms appear. Check with your doctor before changing any medications. I am continuing to take my NSAID medications. By the way, Ibuprofen (Advil) is an NSAID, so if you’re taking an NSAID regularly, take Tylenol instead of Advil for routine pain so as to not double up on NSAIDs.

Unfortunately, there aren’t really studies yet to determine if auto-immune sufferers are at greater risk from getting the vaccine. In my non-expert but informed opinion, the risk of SARS-2 infection for auto-immune sufferers is likely higher than the risk of a reaction from the vaccine. Since the COVID vaccines only present the Spike protein to the immune system, they’re likely no more risky than any other vaccination. If you tolerate other vaccinations well, you’ll likely tolerate this one too. My recommendation would be for auto-immune sufferers to get the vaccine. Of course, check with your doctor first. If you choose to get the vaccine, I strongly suggest getting it at a medical facility that can monitor you rather than in a mass vaccination center.

Don’t fear, but be smart,
Erik

PS. FB doesn’t like it when I discuss vaccines! They often add a note about vaccines when I discuss it, referencing info from the WHO. While comments FB has added recently are accurate, I generally don’t regard the WHO as a good source of information about COVID, since they are overly influenced by certain political entities and have occasionally been very wrong. The CDC is better, but it often very slow to present new information.

Case Update: December 21st, 2020; Allergic Reactions to Vaccines in a Small Number of Patients

This is a case update and I’ll also discuss recent news about vaccines and allergic reactions.Cases continue to rise dramatically in parts of the United States, particularly, the Southwest, the East Coast, and South. The Northern states, where the third wave began, are continuing to improve, some counties are getting new cases under control.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, December 21st, 2020
Graph is by me, from data collected from Johns Hopkins University COVID site.

California is doing particularly badly, with the highest new case loads occurring in 5 California counties in the top 10 counties for the country. LA County alone has 170,000 active cases (new cases in the last 2 weeks), more than 3 times that of the next county, San Bernardino County.

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 Johns Hopkins University COVID site.

San Diego County is in 7th place for new cases in the country with 33,000 new cases. Cases continue to increase despite new restrictions on outdoor dining.

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.

I never go indoors without a mask on, but still frequently eat at restaurants outdoors and do a lot of hiking. I almost never wear a mask outdoors. I get tested nearly every week, and am always negative. Here in SD County, I’m noticing a lot of people wearing masks outside, and often get the stink eye from them when I’m not wearing a mask outside. Especially if there’s a breeze, I believe it is unnecessary to wear a mask on a hike! Data shows very few outbreaks occurring outside, at least in non-crowded environments. One Japanese article claimed a 19 fold smaller likelihood of becoming infected outside, and other articles saw no transmissions outdoors, according to an article in Science Magazine.

Allergic Reactions to Vaccines: As of this writing, 6 people have been reported to have suffered from severe allergic reactions after receiving a vaccine against the SARS-2 virus. This is out of 272,000 vaccinations given so far, or about 0.002% of vaccinations. The CDC has issued a guidance that those with known allergies to vaccines or injectable medications should not get vaccinated. Those with allergies to food, pets, venom, or latex are still safe to receive the SARS-2 vaccine. For those with latex allergies, know that most medical facilities have changed to non-latex gloves because of allergies to latex.

Mild allergic reactions such as site redness or pain are more common, but will resolve on there own within a day or 2.

I am currently encouraging the elderly or those with significant risk factors to get vaccinated when you can, and to inform your health care provider of your risk status so you can “get in line” for your vaccine.

Don’t fear, but be smart!
Erik

Antibody Dependent Enhancement

Originally posted July 7th, 2020

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

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

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

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

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

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

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

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

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

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



Update: November 20, 2020

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

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

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

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

Update: December 12th, 2020

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

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

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

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

Update: April 13th 2021

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

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

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

Update: August 26th, 2021

Delta already using the ADE pathway? A doctor friend of mine sent me a pre-print paper from a lab in Japan. Please note, this is a pre-print paper and has not yet finished peer review! The paper describes experiments using antibodies derived from patients infected with the Wuhan strain, as well as with the Delta Variant. They then studied binding of these antibodies to artificial viruses. The paper argues that Delta variant viruses are less neutralized by vaccines against “wild-type” or Wuhan strain vaccines. While the “wild-type” antibodies against Wuhan can neutralize a region of the Delta Spike protein called the Receptor Binding Domain (RBD) (Figure 1C), other antibodies binding to another region of Delta Spike protein actually enhance infectivity. Figure 1D from the paper shows negative levels of “neutralization” for antibodies that bind the N-terminal domain of the Spike protein. The paper calls this “enhanced”. Yes, this is the ADE I’ve been talking about.

Figure 1 from Liu et al 2021.

They suggest that with rapid changes in COVID variants, a new version of Delta is going to be able to use the ADE pathway in the near future, when Wuhan era antibodies will no longer be able to neutralize a mutated Delta strain.

To sum that all up in simpler language, it basically says that Delta is more infectious because it is partially using the ADE method of infection. Future versions may be less prone to be neutralized by Wuhan antibodies, making them fully enhanced. If this happens, we may have more severe disease in those who get infected with this new enhanced Delta.

They conclude by saying a booster against the Wuhan strain will not be effective in improving protection from Delta, and that a new vaccine against Delta will be required.

The material in the paper may help to explain why we have been seeing lowering levels of vaccine effectiveness in some countries.

Just to be very clear, they are not saying that this new enhanced Delta exists now, just that it may exist in the future.

I will pay close attention to this issue. If you have already been vaccinated or had COVID, a new Delta vaccine will be your best defense against possible ADE arising from a possible enhanced Delta.

If an enhanced Delta arises, and you have had Wuhan COVID or a Wuhan vaccine, and you haven’t had Delta, then you may be at greater risk for severe disease.

If you have had COVID since July 2021, you are likely already immune to the Delta variant, and this will not be an issue for you.

I am fully aware this complicated. Also, the CDC has rarely if ever discussed this possibility, so unfortunately, most of the people you talk to about this will not believe it. I am sharing this with you so you can make wise decisions for you and your family.

Some companies are already working on Delta versions of the vaccine. If you have had the current vaccines, or had COVID, you should get the Delta vaccines as soon as they are available.

Of course, discuss your medical history with your doctor before making medical decisions.

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


A selection of relevant papers:

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



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



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



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



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

Co-morbidities, vaccines

People have been asking me about a story that came out in the last few days about 94% of deaths having co-morbidities. The implication many have made is that most don’t really die from COVID, they die from something else, and they also happen to have COVID.It’s certainly true that contributing factors can make symptoms worse, and many of those with symptoms have another underlying issue. But I think it would be a mistake to think that this means COVID can be dismissed as no big deal. The fact is, the list of contributing factors is long, and includes the following:

age
asthma or COPD
heart conditions
kidney conditions
liver disease
high blood pressure
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)

A lot of people are on this list, including me, since I have Celiac Disease, an auto-immune disease. Think of it this way. If someone dies because they got pushed in front of a train, did they die because of the train, or because someone pushed them? Well, both. Getting shoved generally doesn’t kill you, but it does if you get shoved into a train.COVID on it’s own may not be very deadly on it’s own, but it is in combination with a lot of other conditions.

The good news is, COVID is getting more survivable as treatment gets better, and also perhaps since people are getting exposed to lower viral loads because of mask wearing. We should be concerned, but not fearful, and we can also be optimistic that things are getting better!

I’ve also been asked by several people recently about a vaccine. You may remember my post about ADE, Antibody Dependent Enchancement. It’s a rare phenomena in which a virus can use an antibody against a previous infection to infect the immune system (link to my original post below). This can make a second infection much worse than the first. This only occurs with a small handful of viruses, but SARS, MERS, and likely SARS-2 are some of them. Because of this phenomena, I am suspicious of vaccines against SARS-2, and will wait to see what happens before I get one for myself, or recommend others do. I am not an anti-vaccine person in general! I have gotten the annual flu shot many times! But SARS-2 is different. If someone involved with the vaccine creation process can convince me it’s safe, I will certainly let you know.

Don’t fear, but be smart!
Erik

Links:
June 22nd Summary
Antibody Dependent Enhancement

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

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

Rate of New Cases Down, US Confirmed Cases Surpass China’s

Originally posted March 28th, 2020

Good morning, Friends,
It’s good and bad news this morning. The good news is, our recent trend of a reduction in the rate of new cases in the US is holding! We’ve gone from being consistently in the 40% range, to consistently in the 20% range. This is good, but the bad news is, because our numbers are getting high, a lower daily percentage of new cases still means an increase in daily cases. Plus, in California, where many of you live, the rate has not trended down.

Unfortunately, the US now has more confirmed cases than any other country, surpassing China on Thursday.

So we doing better, but we need to to better still. The numbers are impacted by several things of course, one being our much improved testing rate. This certainly drives the numbers up, but I’m cautiously optimistic that the lock-down many you are experiencing will lead to big improvements soon. So keep it up! Your efforts are not in vain!

A few days ago, I mentioned that those with auto-immune disorders (like me) may be at higher risk. I still have not found an authoritative source for this. Since then, several news organizations have posted reports of people doing worse if they had taken non-steroidal anti-inflammatories (NSAIDs), including ibuprofen. Since auto-immune sufferers often take these medications, this may be part of the reason for their higher risk. This information is evolving, and will likely continue to change for awhile. Myself, I have quit taking one of my anti-inflammatory medications. Check with your doctor before you stop taking a prescription!

Don’t fear, but be smart!
Erik

PS If you’re wondering why testing in the US was so slow to get rolling, check out yesterday’s post.

Asymptomatic Transmission

Originally posted March 22nd, 2020 on Facebook

I know I’m not exactly Mr. Fun these days, but I have another little update. According to March 16th paper in Science, one of the worlds 2 leading scientific journals, asymptomatic people who are infected with the SARS-2 virus are about half as contagious as sick people. However, because there are so many of them, asymptomatic people account for 80% of new infections! (Li et al, Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2), March 16, 2020, Science Magazine).

The take away is, yes, even if you are not sick, you can spread the virus! So please stay home, and protect your neighbors!