Category Archives: Treatments

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!

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

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

America’s Frontline Doctors Video

A quick note, I posted an update yesterday, but I accidentally only sent it to one person, so for the weekly update, check your feed for yesterday morning, or check my timeline.

Many people have asked me about a video that was posted yesterday by a group called “America’s Frontline Doctors”.  The original video has since been removed from Facebook, YouTube and the group’s website has even been dropped by the host, Squarespace. All this to say, you may have a hard time watching it if you want to.  I found a different version.

As I’ve said before, politics and science should never go together.  Whenever a scientific issue becomes political, it becomes very difficult for free scientific inquiry to move forward, and nearly impossible for non-scientists to figure out what the truth is. So I’m sorry to those of you who are confused and are trying to pursue the truth. The video was put together by the Tea Party Patriots and Breitbart News, 2 right leaning organizations.  This is a red flag for me because I know that the message will have a political angle, and that I’ll need to watch with extra care.  As I said in my July 14th post, however, just because you disagree with someone in general doesn’t mean they have nothing good to contribute to the discussion.  Especially with politically charged issues, we need to get information from a variety of sources in order to be as informed as we can.  I know for many of us, it’s nearly impossible to have time for that, so we often just pick someone we trust to get our information from.  I definitely have political opinions, but whenever a scientific issue comes up, I do my best to set those aside and look at the evidence.  I hope this has been valuable to you.  You may have noticed that some of my thoughts about the Coronavirus have been “left-wing” and others have been “right-wing.”  I’m doing my best to be objective.  And yes, I consider it a tragedy that opinions on scientific issues can be categorized as either left or right.

I want to discuss some of the main points of the video and offer my informed but not expert opinion.  I am a Ph.D. molecular biologist specializing in infectious disease testing.  I am not a physician or an epidemiologist. I will give my opinion and also why I think that way.

Hydroxychloroquine (HCQ): The video focuses to a great degree on HCQ as a potential “cure” for the Coronavirus.  As soon as President Trump mentioned it as being potentially helpful for treating Coronavirus, it became a subject of immediate and hot controversy.  Democrats seemed to reflexively dismiss HCQ, and Republicans seemed to reflexively support it.  President Trump dug in his heels and seemed to support its use before all the evidence was in.  Obviously, this is not how science should be done.  Careful and well-reasoned studies should be done, and conclusions made based on evidence. Early studies seemed to support both conclusions. Opponents claim that HCQ doesn’t work and is even harmful to patients, causing heart problems in some.  Supporters claim that HCQ works when given early in the disease, and with Zinc and perhaps azithromycin.

Dr. Immanuel made an impassioned case for the use of HCQ, having successfully used it to treat over 300 patients.  This kind of evidence is what scientists call “anecdotal”.  Anecdotal evidence, basically stories, is often not considered scientific because in a large pool of people, you can find stories supporting all kinds of claims.  Anecdotal evidence also usually does not carefully consider other factors that may contribute to a conclusion.  An example would be “I ate ice cream and then I got attacked by a shark, so eating ice cream leads to shark attacks.”  This is obviously a silly example, but many pieces of anecdotal evidence you hear suffer from the same lack of critical thinking.  However, this is not at all to say that anecdotal evidence is not useful!  These kinds of stories may not be scientific per se, but can often trigger more rigorous studies that prove the claims of a story.

Several scientists I’ve heard from will point out that HCQ is useful when given early and given in combination with Zinc, and also in appropriate dosages.  I actually agree that some of the studies arguing against HCQ use have given it too late or in inappropriately high dosages.  I would like more rigorous studies to be done, however at the moment, I think HCQ is well worth consideration by the medical community. Other treatments also exist and may actually be better, such as the MATH+ protocol I described in my summary post on June 22nd, Dexamethasone, Remdesivir, and perhaps Budesonide.  For the HCQ protocol, it appears that Zinc is actually most responsible for anti-viral activity, with HCQ mostly helping Zinc enter cells to interact with the virus.

Some have pointed out that Dr. Immanuel has some beliefs that are well outside accepted scientific views.  As I pointed out before, even folks who you generally disagree with can bring helpful information to the table.  Her HCQ experience may be true despite her unorthodox beliefs. So even if you justifiably don’t consider a person reliable, you should resist the urge to dismiss them outright.

Lastly on the issue of HCQ, physicians have the right to use drugs “off-label” meaning they are granted by their medical degree the right to try medications in ways that are not necessarily supported by the literature or guidelines.  This right is granted in the interest of patients, because careful studies can take a prohibitively long time to be published, and to encourage the development of helpful new protocols.  In my opinion, government agencies should not be restricting the use of HCQ by doctors at this time.

School reopening:  In some ways, there is reason to re-open schools in the Fall.  It appears to be true that children under 10 do not get infected at high rates, do not carry a high viral load when infected, do not get severe disease, and do not seem to spread virus to others.  So there is a case to be made for reopening schools for young children.  However, because of the ADE issue I’ve written about before, I am not currently in support of re-opening schools in the Fall.  Just to recap, ADE (Antibody Dependent Enhancement) is the phenomena in which some viruses can use antibodies presented on immune cells to infect those cells and cause more severe disease.  So a second infection with a similar strain can lead to much worse symptoms.  SARS-1 and MERS, cousins of SARS-2, can both use this pathway, so with current evidence, it seems likely that SARS-2 will as well.  But we won’t know for sure until another SARS strain develops and we see how people respond to it. I will point out in full disclosure, that almost no-one is talking publicly about ADE.  Dr. Fauci has mentioned it, but just in passing.  So I could be out to lunch about this, but it is a major concern of mine. I have had a few epidemiologists mention in private conversations that they think ADE is a real issue, but they aren’t comfortable talking publicly about it either. 

Sweden and Herd Immunity: Dr. Dan Erickson, who made a video back in April, also spoke.  I was critical of his original video because his analysis of the death rate used the wrong number for total cases.  This time he spoke mostly about the lock-downs, and most of his comments were more measured.  He argued against lock-downs and suggested Sweden as a model.

I am also critical of lock-downs as they were done in much of the US, with people asked to stay home at all times.  However, I am not supportive of the Swedish model either, in which few precautions are taken.  While I am not for people staying at home, and I think people should find ways to get back to work, I also think people should wear masks while indoors in public.  Small outdoor meetings are fine, even without masks, but large outdoor gatherings with closely packed people are dangerous in my opinion.  Again because of the ADE issue, I am not in support of the idea of obtaining herd immunity as a way out of the crisis.

Masks: Some have taken away from the video the idea that we should not wear masks.  I didn’t get this from the video. Dr. Gold explicitly said she thinks masks should be worn indoors, but not necessarily outside. I agree with this approach.

As you can see, I agree with some aspects of the video, and disagree with others. When possible, study all sides of the issues, and make the best most reasoned choices for you and your family.

My basic rules are as follows:

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.

Don’t fear, but be smart!

Erik

A version of the America’s Frontline Doctors video:
NOTE: The below video was removed by YouTube a day after this blog posted.

My recent summary post.

My comments on Dr. Erickson’s original video.

Masks

Antibody Dependent Enhancement

Science Communication

July 28th Update

Case Update: July 14, Budesonide

This is a case update. For the US and California, cases continue to rise. The number of daily deaths have begun to rise as well in the last week, running about 3 weeks behind the rise in daily confirmed cases.

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.

The news is better in San Diego. Daily new cases has flattened and may even be going down. A caution is always that Sunday and Monday are always low days of the week in terms of new cases, so you have to be careful about saying things are getting better on a Tuesday! The number of active cases in San Diego may be flattening as well.

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.

After a spike in cases in Imperial County, east of San Diego, hospitals in El Centro have become overwhelmed and COVID patients are being sent to San Diego, Orange and other counties. This stresses the importance of keeping case loads low so as not to overwhelm hospitals and ICU deparments.

Texas Medical Association Chart: The Texas Medical Association released a very helpful chart giving the relative risks of different activities.

If you’ve reading my posts, you won’t be very surprised by the entries, they are pretty consistent with what I’ve thought myself.

The information was obtained by polling Texas doctors, so the data probably reflects what they know about their own patient’s histories, and also probably some opinion.

Budesonide: A very interesting video was posted last week featuring Dr. Richard Bartlett. He claims to have a very effective new treatment, using a nebulized anti-inflammatory normally for asthma, Budesonide. It will be very interesting to watch if others have success with this method.

The video introduces another topic that is very timely. If you watch the whole video, you’ll notice that Dr. Bartlett has some views about the virus that I don’t share. However, I think the video is still worth watching. Often these days, people dismiss people with whom they disagree on any topic. In reality, it’s very common to be able to take at least some truth from those with whom we disagree. In fact, on complicated topics, I find that with almost anyone I read or watch, even people I respect highly, there is often some topic that I think they’re wrong about. If I refuse to learn from people that I disagree with, I’d have to quit listening to most of the people I respect! With all that’s going on in the US right now, we will need to listen to and learn from all kinds of people to move forward. Even if you disagree, learning a person’s position will help you understand the topic better.

Don’t fear, but be smart!
Erik

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Best option: An N95 mask with no valve.

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

Handwashing:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Don’t fear, but be smart,
Erik

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