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.
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.
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.
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.
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!
A version of the America’s Frontline Doctors video: NOTE: The below video was removed by YouTube a day after this blog posted.
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.
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.
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.
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.
Today I’m going to discuss the JP Morgan study on transmission (among other things), how the Moral Matrix effects how people see the fight against the virus, and the boom stage in many Southern Hemisphere countries.
Frankly, when I think about anti-coronavirus efforts, I have tended to lump lockdowns and social distancing together, especially since many use these terms interchangeably. Notably, the study separates these 2 concepts and suggests that will social distancing (staying a distance away from people in public) may be valuable, lockdowns (staying in your home) is not.
You might say there have been 2 primary models for dealing with the pandemic in the last month after we’ve flattened the curve, but have not brought the numbers down, at least not in the US. I’ll call those models the Lockdown and the Re-opening models. Some want to continue the lockdowns to keep everyone safe from the virus, others want to re-open right away without restrictions. For several weeks, I have been gravitating toward a third Adaptive model. Of course, there can be many flavors of this model. Personally, I think masks, even bad ones, are far better than nothing, especially when worn by everyone, and can help us get back out of our houses and help us re-start the economy with reasonable safety. So I’m very open to the idea that the lockdowns have not been beneficial. Some of you will disagree.
The JP Morgan study is at odds with the endcoronavirus.org study, which recommends brief, very strict lockdowns. It could actually be that these 2 studies actually agree, depending on the time frame you’re talking about. I do think the lockdown was very helpful in the initial “boom” stage of the epidemic here in the US, but may have lost its usefulness later.
The Moral Matrix: ZDoggMD is a physician and medical YouTuber with a very silly screen name, but who posted VERY interesting video on how different people see the pandemic we are all facing. Using Jonathan Haidt’s work on the Moral Matrix, he talks about how different people’s moral framework shapes how we are viewing different efforts to address the issue. I was aware of Haidt’s work, but not had yet applied it to the pandemic in my mind. As someone who is sometimes exasperated with people who disagree with me (as they are with me I’m sure), this video is helping me remember to see their point of view. If you’re exasperated with your friends or family, I HIGHLY recommend you watch this video.
Upsurge in the Southern Hemisphere: Lastly, I just want to mention that many countries which have been relatively little effected until now, are now experiencing a big upsurge in cases. These countries include Russia, Brazil, and Mexico, and many are in the Southern Hemisphere, which is in the late Autumn months right now. Let’s hope they are able to get things under control quickly.
Don’t fear, but be smart!
PS. We went hiking in nearby Calaveras Park today for the first time in months, without our masks. There were a lot of people on the trail, and most were well behaved. When I can’t avoid someone on a narrow trail, I use an old SCUBA diving trick for ascending without getting the bends. Just close your mouth and blow slowly out of your nose as you pass someone. You’ll gently move any virus away from your nose! To maintain my friendliness, I greet people early, with plenty of time to start this little maneuver!
The number of news cases has been erratic in the last week, but at least in the US, it continues to trend downward. I’ve started collecting the number of new cases in the US and California, and while I’m not sure how to integrate that data into my Excel spreadsheet yet, I can tell you that more tests definitely mean more new confirmed cases. So some of the erratic graphs were seen are definitely because of more testing. In the long run, I expect to see new cases come down drastically as we continue to increase testing.
Rt.live is showing that 45 of 50 states have an Rt value below 1 yesterday. This is great news, as it shows that in most states, the virus is slowly disappearing. I’m watching with great interest to see how the states that have started re-opening do. Keep up the great work! We are having an impact!
Also included is a very interesting video I ran across, Simulating an Epidemic, showing a non-scientific computer model of possible epidemic outcomes given different approaches. Keep in mind, this model is NOT attempting to show what will happen in the COVID epidemic, just some theoretical things that might happen given different approaches. He does NOT attempt to prove that any of these things are what’s happening.
The most interesting parts for me were when he compared 2 methods that have been used in different places. At 6:00 minutes, he talks about the Detect and Isolate method, which I favor. This is were you find an infected person and quickly quarantine them until they have recovered. He argues that this is the most effective method in an epidemic like the current one. We haven’t been able to do this, really, because of our lack of testing in the beginning. My fervent hope is that if we get a second wave in the Fall or Winter, we will be ready for this approach.
At 16:50, he talks about a method that I think we are kind of using, the shelter in place, but with trips to central locations. He says that without other measures, these locations become a source of new infections. This is probably not happening as badly in real life because so many are wearing masks to the store!
Friends, This one is going to be a little mathy. Several people have sent me the video titled “Dr. Erickson COVID-19 Briefing”. I’ve watched the first 12 minutes of the 52 minute video. Dr. Erickson argues that we have a large number of current cases, and that when comparing this number to deaths, he calculates the fatality rate at between 0.03 and 0.07%. This is less than the typical flu. He uses data from his home county of Kern County in California, NYC, the US, Spain, and others. Unfortunately, Dr. Erickson makes a critical error in his calculations.
For the US, he says we have 802,000 confirmed cases (around April 20th) and around 4 million tests. This would give him a positivity rate of 20% for the country. He then calculates that we then have 64 million cases in the country and only 45,000 deaths, giving us a fatality rate of 0.07%
The mistake he makes is that he assumes that tests given represents a random sampling of the population. Anyone who has tried to get a test and failed knows that not everyone who wants a test gets one. And not everyone requests a test either. Dr. Erickson has what’s called a sampling bias. You have to make sure you have a sample that represents the group you want test if you want to say anything about that group. Instead of testing the general population, Dr. Erickson is testing just people who meet the criteria for testing by the CDC or other health care body. This group is far smaller, and far more likely to have the virus than the general population. He over-estimates the number of COVID cases, by maybe 10 fold.
Several studies, some not yet published, have tested random selections of the population using PCR and antibody tests (see references 1, 2, 3, below). In those studies, fatality rates range from 0.12 – 0.7%, 2 – 23x higher than Dr. Erickson’s estimate. Also, the studies by Bendavid and Sood (2, 3) suggested that approx. 4% of the populations of Santa Clara County (San Jose) and Los Angeles were infected in early to mid April. So 96% of the population is still susceptible. At the 0.12 – 0.7 death rate, that’s 6,000 – 37,000 potential deaths for those 2 places alone. Even these studies, with fatality rates far higher than Dr. Erickson’s, have been criticized for an estimate that is too low because of sample bias (4).
We won’t really know how many people have had it until there is wide spread testing. South Korea has done extensive testing, and their fatality rate is 2.24%. This might be in the ballpark of the rate in the US.
So I have to reiterate, SARS-2 is not the average flu. In addition to being up to at least 5x more deadly, it’s also 4x more infectious. The very good news is, our efforts are paying off, and the daily rate of new cases for the US is now just 2.46%, down from a terrifying 46% on March 19th. It’s right for some living in rural areas to wonder if they can begin the process of going back to normal. Some can, but it needs to be done carefully and watchfully, with lots of testing for exposure, not just for symptoms (See my April 9th and April 22nd posts). The entire state of Minnesota plans to do just that. We can watch in real time to see how it goes for them. We don’t want another Albany, Georgia! Urban areas like coastal California and the Acela Corridor will have to wait awhile longer.