Category Archives: Treatments

Case Update: April 20th, 2021, Vaccination in SD County, Herd Immunity

This is a case update. I’ll also discuss vaccination in San Diego County and herd immunity in general.

New cases may have plateaued in the US, but new outbreaks are apparent in some states. Michigan was the standout state for new cases, but endcoronavirus now suggests outbreaks across the Rust Belt, Northeast, Northwest, Colorado, and Florida. In most counties, actual numbers are small, but are obviously much larger in urban areas. If we are in a 4th wave, it appears to be much smaller than Wave 3, probably impacted by increased vaccination.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, April 19th, 2021
Endcoronavirus State Level Map, April 19th, 2021

New case loads remain low in California and San Diego, likely at least partially because cases were so high during Wave 3 in the Fall and Winter.

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.

Internationally, new cases are very high worldwide. The new high cases numbers are likely impacted by the new variants such as B.1.1.7 (the UK variant) which is more infectious than the original Wuhan strain, and now dominates in many countries. Brazil and India are particularly hard hit. Canada’s current wave is as high as their Winter wave, but the numbers there are in general much lower than for the US.

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

Vaccination in San Diego County: According to the County, about 37% of County residents are now fully vaccinated, with 60% having had at least 1 dose. Vaccination is now available to anyone 16 and up who wants to be vaccinated. If you want to be vaccinated, you can find a location on their website.

San Diego County Media Briefing, April 14, 2021

Herd Immunity: First, just a reminder that I am not an epidemiologist. Early in the pandemic, many recommended herd immunity as a way out of the pandemic. At the time, I argued that exposing a lot of people to a disease to protect people from a disease was counter productive. Now that we have a vaccine, herd immunity is a viable option for moving forward. For a population, herd immunity can be effective, although the percentage of people who need to have immunity to reach this is dependent on the disease and usually surprisingly high. On an individual basis, if you’re concerned about catching the virus, it’s far better to just get vaccinated at this point than to worry about if we’ve reached herd immunity.

Don’t fear, but be smart,
Erik

Case Update: April 13th, 2021; ADE and What You Should Do if there’s a SARS-3.

This is a case update. I’ll also talk briefly about ADE and it’s impact on the current pandemic and the potential impact on the next SARS virus, if one ever happens.

Cases in the US continue to rise slightly. Outbreaks continue in Michigan, with some new cases also in the Greater New York Metro area and the Texas panhandle. Why is Michigan having such a hard time? Frankly, I’m a little mystified, especially since Michigan has been in strict lock-down through much of the pandemic. It’s now well known that the viral load upon infection has a large impact on the severity of COVID symptoms. Those who get a low viral load upon exposure have lower symptoms. I will speculate and say that perhaps some states with very strict lock-downs caused people to interact in ways that encouraged larger viral loads upon infection, like being with groups of people in private homes. Again, I’m just speculating. This may also explain the large and sustained number of cases in LA county this Fall and Winter.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, April 13th, 2021

California and San Diego County both have come to an equilibrium, with approximately 3000 and 200 new cases a day respectively. Neither appears to have experienced an Easter related bump in cases. The new lower caseload in the US is likely related to vaccination and natural immunity, and is likely to become lower still as we head into Spring and Summer.

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.

Internationally, the caseload continues to increase, almost to Winter peak numbers.

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

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!

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

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

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

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

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

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

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

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

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

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

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

_____________________________
Update, April 6th
A new small study from Pfizer suggests that their vaccine does work on the South Africa variant. The patient number in this trial is small, so they still don’t know exactly how effective it is.
_____________________________

Soberingly, the South Africa strain has reached the US, so if we see a surge in the next few weeks, this strain may be at least partially responsible.

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

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

Don’t fear, but be smart,
Erik

Case Update, March 3rd, 2021; When will the Pandemic be Over, New Variants and Vaccines

This is a case update.  I’ll also talk about when the pandemic may be considered “over”, and briefly discuss the new SARS-2 variants.

For the US, the downward trend in new cases has paused.  New cases have been steady for the past 2 weeks.  The daily new cases continue to be higher than the first wave, and almost as high as for the second wave this summer.  The new case map from endcoronavirus shows recovery, but this particular map only shows changing trends.  The small number of counties in red may be misleading, because many of these counties are rural, so represent very few actual cases.  If you look at the top 10 counties for new cases in the country, there is still a significant number of new cases in several counties.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, March 3rd, 2021
Endcoronavirus County Level Map, March 3rd, 2021

We continue to see a downward trend in California and San Diego County. However, the new case numbers remain higher than they were during the 1st wave.  

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.

When will this be over?  The 3rd wave this Fall and Winter is winding to a close, which makes many speculate on when the pandemic will be over.  I’m going to speculate on this, and what criteria we may use to determine this, but remember that I am not a physician or epidemiologist.  This is my informed but not expert opinion.  I am a molecular biologist specializing in infectious disease testing.

The most significant event happening right now that will impact the progress of the pandemic is the ongoing vaccination program going on in the US. We are currently into Phase 1B, vaccination of all individuals over 65. If you are over 65, I encourage you to consider vaccination.  Check in with your local health department to find out how you can be vaccinated.  You know I have some concerns about the ADE issue, but on balance, those over 65 will almost certainly benefit from the vaccination despite these concerns. As more vulnerable people are vaccinated, we will continue to see a drop in new cases, as well as a further drop in severe symptoms and mortality. Soon, we will enter Phase 1C, in which anyone over 16 with COVID risk factors will be able to receive the vaccine. 

Once everyone who is vulnerable has been vaccinated, this may rightfully be considered the “end” of the pandemic in the minds of many.  We should also pay attention to the number of COVID deaths. In order for the pandemic to be considered truly over, the number of deaths must be very low as well. I’m not willing to speculate yet on exactly what “very low” means.  Keep in mind also that many other countries do not yet have the vaccine, so vaccination in the US alone will not end a global pandemic!  Even after the epidemic in the US is over, travel to and from other countries may still be restricted.

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.

Variants: We have seen several SARS-2 variants arise over the last few months.  Most of these variants have made the virus more infectious but not more pathogenic.  This is because they alter the Spike protein, the viral protein that is used to infect our cells.  This is also the protein that the immune system, and the vaccines, target to neutralize the virus.  However, the vaccines currently in use appear to still work on most variants.  The exception to this is the South African variant (501.V2) which some suggest may evade the current vaccines.  Concerns about this are strong enough that Moderna is currently working on a vaccine against 501.V2.  This variant is already present in many countries, including the US.

The Second Shot: I haven’t been vaccinated yet, but I’ve heard several accounts of people feeling significant flu like symptoms after their second COVID vaccination. It’s actually not unusual to have flu like symptoms after a vaccination. Flu like symptoms are your body’s normal response to an invasion and many of the symptoms we experience are designed to help you fight an infection. That’s why so many infectious diseases produce “flu-like symptoms”. So unless your symptoms are severe, or your fever is over 102°, you don’t need to get medical attention. If you are prone to allergic reactions after a vaccine, inform your healthcare provider before you get one.

So we have lots of good news, but we need to continue to be diligent!

Don’t fear, but be smart!
Erik

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

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

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

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

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

Endcoronavirus County Level Map, December 12th, 2020

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

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

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

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

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

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

Don’t fear, but be smart,
Erik

New Vaccines and ADE

Vaccines – Because of this week’s announcement about vaccines, lots of folks are asking me about it.  I’ll give you my thoughts.  I am not an immunologist, I’m a molecular biologist specializing in infectious disease testing, so my thoughts on vaccines are informed, but not expert.

As I’ve discussed before, I’ve been pessimistic about COVID vaccines, mostly because of the phenomena of Antibody Dependent Enhancement, or ADE (link below).  This is the phenomena in which some virus can use antibodies against a similar but not identical virus to infect the immune system and cause more severe disease.  As this relates to a vaccine, a person given a vaccine could gain immunity against virus very similar to the vaccine given, but less similar strains may still infect and cause more severe illness.  This has been my concern about both vaccines and the herd immunity approach. 

In the past few months, however, a trickle of known cases have come out about people who have been reinfected with SARS-2. Some of these patients have had worse symptoms, and some more mild.  It’s also evident that they are not being infected with the same strain they had before, but by a different strain.  If all this is true, then the ADE experiment is already being done.  And it looks like while some experience more severe illness, not all do, and reinfection appears to be rare, despite several circulating strains.

This week Pfizer announced that studies with their vaccine show 90% effectiveness in preventing COVID infection.  My hesitation with vaccines has always been about ADE.  It’s still not well known if ADE will play a significant role, but if it doesn’t, then perhaps there is reason for hope.

All medications and vaccines carry the risk of side-effects and harm.  However, I’m actually becoming cautiously optimistic about a COVID vaccine.

Some technical info about vaccines.  There are actually several kinds of vaccines.  Various developers tried different pathways to a COVID vaccine, and several kinds are in trials right now.

Killed vaccines – These are vaccines that have been deactivated or broken down into various parts and then injected into the body.  They cannot replicate and degrade in the body, so parts are attached to molecules called adjuvants that serve to boost their visibility to the immune system. 

Attenuated vaccines – These are live viruses that have been engineered to cause infection, but with no or mild symptoms.  Some are other viruses like Adenovirus which are symptom free, but produce viral proteins that your body can recognize and raise a response against.

RNA vaccine – This a brand new kind of vaccine that has been in testing for years.  Several SARS-2 vaccines are of this kind, and are the first potential viable candidates ever.  The patient is injected with a piece of RNA that codes for a viral protein. The RNA enters a cell and temporarily causes the cell to make the viral protein. RNA naturally degrades rapidly in the body and does not persist or permanently change the patient’s genetic material. This promising technique has the potential to generate new and more effective vaccines in the future.

Personally, I’m still taking a wait and see approach.  Vaccines will probably not be available to the general public for few months.  By then we may know more about how people are responding.

Don’t fear, but be smart!
Erik

Antibody Dependent Enhancement

Originally posted July 7th, 2020

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

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

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

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

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

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

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

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

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

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



Update: November 20, 2020

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

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

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

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

Update: December 12th, 2020

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

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

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

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

Update: April 13th 2021

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

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

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

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


A selection of relevant papers:

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



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



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



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



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

Case Update: November 1st, Quadruple Therapy, Air Travel, Symptoms in households with small children.

I have the weekly update, and I’ll also talk about a promising new treatment regimen and a surprising paper about children and COVID.

Update: Unfortunately, the US is experiencing a 3rd wave.  This is driven by new confirmed cases in the Northern states, likely because colder weather is driving people indoors.  I traveled to Anchorage and Minneapolis in the last few weeks, and I will tell you first hand that eating outside at a restaurant is not an option in those places, but the restaurants have lots of people in them.  They’re not full, mind you, they are following the current rules, but lots of people are indoors without masks on.  I’ve also been in plenty of airports, in “red” and “blue” states, in which people are filling the restaurants in between flights, with seemingly no regard to the virus.  No, I can’t tell you for certain that people are being infected in restaurants, but this is consistent with the idea that indoor activity is driving the increase in new cases.  Several European countries are also experiencing 2nd or 3rd waves at this time.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, November 1st, 2020

California has had a flat but persistent new case load for the past several weeks, but new cases are starting to increase here too.  This is likely most driven by new cases in LA County (18k), which has by far the most confirmed cases in California (308,000), and indeed has almost twice as many confirmed cases as the next highest county, Cook County, the home of Chicago (185,000).  Yes, counties in Northern California are experiencing the big upticks in cases right now, but the population and actual case numbers of these counties is so low that they cannot drive the increase in California.  Incidentally, Cook County currently has the most confirmed new cases of any US county at 24,000.

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.

San Diego County continues to have a stable but persistent new case load of about 300 new confirmed cases per day. There may be just a hint of 3rd wave starting in San Diego County right now.

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.

Air Travel: When I travel by air, I pretty much never take off my mask on the plane.  On layovers, I grab lunch to go at restaurant or convenience store, then go find an isolated spot to eat it.

Delta and Alaska are currently keeping middle seats open. United and American are not. The airlines claim that the air on the plane is filtered by industrial grade HEPA filters every 4 minutes. A pilot friend tells me that this is true. The intake vents are on the floor, and output vents are in the ceiling, like your personal vent, so air is constantly moving to the floor during the flight. If all this is true, then a commercial airplane is a relatively safe place to be!

New Treatment:  Doctors in India have developed a treatment combination that has shown great success.  Ivermectin is a drug that is commonly used for parasite infections, but is now being used for COVID.  It is being used in combination with Doxycycline, Zinc, and Vitamin D.  In a study, 93% of confirmed patients do not move on to severe disease while using this regimen, as compared to 58% who developed severe symptoms in the control group.

I’ve said before that Vitamin D has protective effect against the virus, so consider supplementing daily with Vitamin D, or getting out in the sun 30 minutes a day.  This is especially important if you have darker skin.  Also, supplement with Zinc and Vitamin C.

Less severe symptoms in households with small children: A pre-published study from Scotland claims that adults in households with small children get less severe symptoms if infected than those without small children!  This is a counter intuitive result of course.  We have known for some time that a low viral load on exposure can lead to less severe symptoms.  Also, it appears that most infected children carry a low SARS-2 viral load.  This paper puts these pieces together.  It suggests that adults with infected children are getting exposed to a lower viral load and having less severe symptoms that adults getting exposed to a higher viral load.  In fact, the paper suggests that the more children a household has, the less likely adults are to have severe symptoms!

Don’t fear, but be smart!
Erik