Friends, Sorry for the long wait for a new update, I’ve been helping put together a new COVID lab, and I’ve been working long days for the past week. Today, I’ll give the update, then talk about a new study concerning masks.
Update: New confirmed cases continue to go down for the US, California and San Diego County. For California, the numbers are kind of flat. The reporting system in California was broken for much of last week, but the state says it’s working again. Death rates are coming down from their second peak. Comparing the new daily case numbers and the new death numbers make it clear that the virus has become much more survivable than it was in March and April.
New study on droplet transmission from various masks: A study was pre-published a few weeks ago that studied droplet transmission from various popular masks (Fischer EP, et al., Low-cost measurement of facemask efficacy for filtering expelled droplets during speech, Science Advances, pre-released August 7, 2020). The study used a system in which a speaker wearing a mask would say a prescribed phrase several times into a box through which a laser was shining. A camera would then capture droplets that were illuminated by the laser. The study used a relative scale for mapping mask benefit, with the N95 getting a relative score of 0, and no mask at all getting a score of 1. See the results in the photos.
Surgical masks did the second best after the N-95, and a 2 ply cotton mask with a sheet of polypropylene (like blue Shop Towel) fabric did third. I’m particularly happy to see the cotton and poly mask do so well, because that’s what I use! Performing poorly are knitted masks, bandanas, and especially the neck gaiter, which actually did worse than nothing! The authors speculate that this is because the fleece material may break up larger droplets into smaller ones instead of stopping them.
Shout out to my sister-law Penny who has made hundreds of masks in her home. The 2 ply cotton masks she makes have a pocket for inserting a filter or piece of poly like I use, and these masks did very well in this study! For extra credit, say the phrase “masks she makes” ten times fast.
I have never been a fan of the surgical mask because of the large side spaces that allow air to pass easily into and out of the mask from the side. I was surprised to see these masks do so well in this study. The answer may be in the experimental design, which captured droplets coming from the front of the mask, but excluded ones from the side. I would like to see a study that captures that too! This just shows that experimental design matters, and just because a study shows something, doesn’t mean the study was designed to detect all relevant things!
Mask wearing has become controversial, but the data supports the idea that masks reduce viral transmission, and that lower viral load on exposure leads to better medical outcomes!
Here’s the weekly update. The US, California, and San Diego County continue to improve. New confirmed cases continue to drop. I have to qualify this however, since California had a problem with their cases reporting system for much of last week. It’s back working normally, but cases may still be erratic in number for the next few days. This may impact the San Diego numbers as well.
According to Rt Live, more than half the states in the US now have an Rt of below 1.0 again. This suggests that those states are on the downslope of the last peak, and virus is slowly going away in those states. This is great news.
I spoke to testing professional this week who said that viral load, the number of viruses in a patient’s test sample, started coming down in April, when mask wearing became common place. This supports my claim that even if a person gets exposed to the virus, they receive less virus if they’re wearing a mask. This may also be why the virus has been more survivable in the past few months.
I have a grab bag of things to discuss today, starting with the weekly update, a note about the new KN95s, a new version of the Coronavirus (D614G), and where outbreaks are located, at least in San Diego County.
The positive trend continues! Cases are dropping in the US and San Diego, and are flat in California, which is actually better than it sounds, since the state has been steadily increasing in cases since mid-April. Active cases continue to decline in San Diego. Even in Los Angeles County, the epicenter of new cases in the entire country for the last few months, new daily confirmed cases are finally coming down.
KN95 masks: I’ve started to see a new kind of mask being worn, the KN95. They are rated to filter out 95% of virus particles, but are made and certified in China and carry the European CE mark. The FDA has allowed their use in the US as an emergency measure. They fit a little less snugly than an N95. Perhaps their greatest benefit is that they’re available. If you’re still using a surgical mask consider upgrading to the KN95, which will be an improvement!
A KN95 mask.
New strain D614G: A new strain appeared in the US and worldwide probably in May or June. Called D614G, it carries a mutation at the 614th position of the Spike protein. This mutation makes the virus more infectious by 4-5 times, and may have contributed to wave Ib of the virus that we saw in June and July. Dr. Deborah Birx, White House Coronavirus Response Coordinator, has speculated that this mutation may be why we saw more widespread virus outside urban areas during the last jump in cases.
Coronaviruses are RNA viruses. Enzymes that replicate RNA tend to be very error prone which is why RNA viruses change so rapidly. This is true for Coronaviruses as well as for the flu and for HIV. We can continue to expect more naturally occurring mutations in the future. The good news is, over the course of years, viruses generally become less virulent and more mild.
The location of outbreaks in San Diego County: San Diego Public Health has published a graph on the locations of outbreaks as part of their regular slide package. Out of 134 the top most common places for outbreaks are restaurants with a bar (40), businesses (27), the healthcare environment (15), and residences (9), further down the list, faith based organizations and government offices are tied at 5. As a business traveler myself, I’m happy to see that hotels are only at 3. Restaurants without a bar only had 5 events.
Things are starting to get better! But remember that an epidemic is like a wildfire, getting containment doesn’t mean it’s over! We need to remain diligent in order to put it down for good. Keep up your efforts!
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.
Some more good news this week. The United States has unambiguously reached the peak of wave 1b, and daily new confirmed cases are slowly going down. Daily deaths have risen slightly, trailing the higher new cases by a few weeks, but are still relatively low.
The situation is much the same in California and San Diego, with new daily cases coming down and daily deaths rising slightly. Active cases are probably starting to go down as well.
Testing continues to rise and it is having some impact on the increasing confirmed numbers. The higher testing is definitely a positive thing and will help us get a more accurate picture of what’s going on.
Happily, there is some good news about the virus this week. For the US and California, the number of daily new cases suggests that for both regions, we may have hit a peak in new cases. Sunday or Monday is always the low number for the week, but the number of new cases on those days usually predicts the peak for the rest of the week. For both, this week’s low is near or below last week’s low, suggesting that the high for the week will be near or lower than the high for last week.
San Diego has been flat since early July. New cases aren’t going down yet, but they aren’t going up anymore either. In addition, the number of active cases in San Diego is probably going down, after a peak of almost 8000 active cases. Unfortunately, California overtook New York for the number of confirmed cases in the country this week, and LA County has the most new cases in the entire country, and has 40% of confirmed cases in California.
As we discussed in May 12thpost on new cases, comparing the number of tests and new cases can tell us if all the new cases are just related to new testing. An R2 number between 0.95 and 1.00 shows strong correlation, “proof” that two things are related. The tests vs cases for the US since early July give an R2 of 0.78. This suggests that though many of the cases are real, at least some are because of new testing. In California the R2 is 0.44, a much weaker relationship, meaning more of the new cases are not just due to more testing.
An R2 number of above 0.95 suggests good correlation, a number of 0.78 suggests that while there is a contribution from increased testing, some of the increase is real new cases. Graph is by me, from data collected from Johns Hopkins University COVID site.An R2 number of above 0.95 suggests good correlation, a number of 0.44 suggests that while there may be some contribution from increased testing, much of the increase is real new cases. Graph is by me, from data collected from Johns Hopkins University COVID site.
Rt Live shows that more states have an Rt number of less than 1.0, indicating that the virus is slowly going away in that state.
I have some African readers, so I’ll point out that the number of new cases appears to have peaked in Nigeria, DR Congo, Malawi, and South Africa, as well as in Brazil, a country which now has the 2nd highest number of confirmed cases, behind the US. Let’s hope we can keep this progress going!
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.
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.
Dear Friends, This is a case update. I’ll also have an important message about antibody dependent enhancement.
Cases continued to rise unchecked in the US, California and San Diego County in the last week, although the long holiday weekend did have impacts on reporting. Some good news is that the number of deaths reported in the US has been slowly declining despite the case increase. Keep in mind however, that deaths will lag behind cases by as much as 2 weeks, so we may yet see an impact from the higher caseload. The number of deaths have been trending flat in California.
Rt Live is reporting that all but 8 US states or territories have Rt values above 1.0, meaning that the virus is expanding in those states.
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.
This is a case update. Unfortunately, we are experiencing an explosion of new cases in the US, California, and San Diego County this week, continuing the trend that started a few weeks ago. For all of these regions, this week brought record highs for all three regions. California reached approximately 66k active cases, and San Diego County has doubled it’s active caseload to 4,222 in just the past week.
Why is this happening? Probably for multiple reasons. First, as things re-open, some businesses and individuals are not following guidelines for safe reopening. San Diego County had 7 super-spreader events in the last week, 4 at restaurants, and 1 at a private residence. You may have seen a story in the news this week about a bar in Michigan in which 85 college aged people were infected in a single evening. As you might imagine, they were not wearing masks, and were not practicing social distancing. The recent protests and riots almost certainly have had an impact as well.
In my May 12 post, I explained how you can tell if testing is having an impact on confirmed cases by graphing daily tests against daily new confirmed cases. In the last few weeks, the R2 number has risen into the 0.5 range for the US and California. An R2 number of 0.95 “proves” correlation, but a number in the 0.5 range suggests some contribution by increased testing. These graphs suggest that increased testing has contributed some of the new cases numbers, but some of the new cases are simply new infections as well.
An R2 number of above 0.95 suggests good correlation, a number of 0.59 suggests that while there may be some contribution from increased testing, much of the increase is real new cases.An R2 number of above 0.95 suggests good correlation, a number of 0.51 suggests that while there may be some contribution from increased testing, much of the increase is real new cases.
There is some good news. That is that if you are careful and follow the below guidelines, you can be reasonably certain you won’t catch COVID:
1) Wear a mask or face covering in public. Avoid places with unmasked people. 2) Keep 6 ft away from others. 3) Avoid indoor gatherings, especially ones in which singing or shouting is likely. 4) Small outdoor gatherings are fine, even without masks, if everyone maintains a distance. Have guests bring their own food. 5) While many restaurants are open for limited indoor seating, I personally am still not comfortable eating indoors at a restaurant. I enjoy eating outdoors, however.there may be some contribution from increased testing, much of the increase is real new cases.
An epidemic is like a brush fire. When it dies down, we can start to be complacent, but diligence is still required. We are experiencing this new burst of cases because we have let our guard down. Hopefully, we can get things back under control soon.
Maybe take a break. After all the troubling news of the past month, a friend of mine complained that he is feeling depressed and not doing well. While I encourage everyone to follow the news and to be engaged with public life, studies show that over consumption of social media can lead to depression and anxiety. If you feel depressed, or your blood pressure is high, or you’ve been ranted to your wife more than she would like (I know someone like that), you may benefit from a news and/or social media fast. Consider taking a day or more off a week to let yourself calm down and get back to normal. In our information age, we can receive all the bad news of the world at all times, and we aren’t designed to carry that burden.
This is a Coronavirus case update. New confirmed cases continue to climb for all three regions that I monitor closely, the US, California, and San Diego County. Calculated active cases in California are now at approximately 50,000 active cases, up from 20,000 at the height of the first peak in early April. Los Angeles County continues to dominate the caseload, with 51% of total confirmed cases in LA County.
Internationally, Brazil just crossed the 1 million confirmed case mark, and is #2 in total confirmed cases behind the US. Brazil’s new daily cases may have hit it’s peak, however, so new cases may finally be slowing down. Russia and India are next in total cases.
Over the past week, San Diego County Public Health has reported several small outbreaks in restaurants and businesses. As we re-open, it will continue to be important to wear masks and social distance while in public.
doubloondiagnostic.com 