Case Update: August 4th, 2020, KN95 masks, D614G mutation, where do outbreaks happen?

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.

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 San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Some data points of “Active Confirmed Cases” are from SD County, others are calculated.
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.
From Rt Live.

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.

From San Diego Public Health.

Another graph shows some of these outbreaks during June and July.  You’ll notice that July had about twice as many events.

From San Diego Public Health.

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!

Don’t fear, but be smart,
Erik

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 28th, 2020

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.  

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 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.

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.
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. Some data points of “Active Confirmed Cases” are from SD County, others are calculated.

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.

Don’t fear, but be smart,
Erik

Case Update: July 22nd, 2020.

Friends,

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. 

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.

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.

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. Some data points of “Active Confirmed Cases” are from SD County, others are calculated.

As we discussed in May 12th post 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.

From Rt Live

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!

New daily confirmed cases for Nigeria. Graph is from Johns Hopkins University COVID site.
New daily confirmed cases for the Democratic Republic of the Congo. Graph is from Johns Hopkins University COVID site.

Don’t fear, but be smart!
Erik

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

Case Update: July 7th, 2020; Antibody Dependent Enhancement

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.

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 San Diego County Public Health. See also regularly updated slides from SD County.
From Rt Live

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.

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 in SARS-1:



Overlapping symptoms for SARS, MERS, and SARS-2:



Is COVID-19 receiving ADE from other coronaviruses?



Possible mechanism for ADE:

Case Update: June 30th

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.

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 Cases are calculated based on the assumption that all patients with cases confirmed more than 17 days previous have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Some data points for Active Cases come from San Diego County Health, while others are calculated.

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.

Don’t fear, but be smart.
Erik

Case Update: June 23rd

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.

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 Cases are calculated based on the assumption that all patients with cases confirmed more than 17 days previous have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.

Rt Live reports that 29 of 51 listed US states and territories have an Rt of above 1.0, suggesting that the virus is spreading in those states.

From Rt Live.

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.

Daily new confirmed cases for Brazil, showing possible peak. Graph is from Johns Hopkins University COVID site.

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.

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

Case Update: June 17th

This is a case update.  New confirmed cases are starting to trend upward for the US again for the first time since about April 9.  In 19 US states, the Rt number is higher than 1.0, suggesting that the virus is spreading in these states.  On endcoronavirus.org, you can clearly see recent spikes of new cases in some states, and in many countries.

From RT Live.
From endcoronavirus.org.
From endcoronavirus.org.
Graph is by me, from data collected from Johns Hopkins University COVID site.

In California, the number daily new cases continues to accelerate.  San Diego has started to go up too.  San Diego County has started to publish the number of recovered patients.  My graph of cases in SD County now includes active cases, taking recovered people into account. Some of these points of data on my graph are given by SD County, the others are calculated by me based on the data points.  Looking carefully at the SD County data, the number of recovered people is approximately the number of total cases from 17 days previous.  The suggestion is that it takes approximately 17 days to recover after being confirmed as a COVID case, so I’ve made a similar calculation for California.  Just to be clear, in my graph of active cases in California, the data points are based on assumptions about recovery time, not actual data.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from San Diego County Public Health. Numbers from recovered patients are from a regularly updated slide presentation.

For San Diego, active cases have been hovering around 2,000 for several weeks, without much change, but for an increase in the last few days.  For California, we’ve seen a steady trend upward in active cases from 20,000 in early April, to 40,000 cases today.  There are of course lots of potential reasons for these increases, from gradual re-opening to the protests and riots stemming from the George Floyd incident.  I was once optimistic that the first wave of cases would be over this Summer, but new trends have called this into question.  I’m now feeling totally unable to predict how things will go.

Graph is by me, from data collected from San Diego County Public Health. Numbers for recovered patients are from a regularly updated slide presentation.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Active Cases assumes that those cases confirmed 17 or more days ago have recovered.

I heard a radio commentator talking about a recent study that I haven’t been able to find.  The study said that while Social Distancing account for maybe a 50% drop in new cases, the lockdown accounted for only a 5% additional drop.  Given the economic and social cost of the lockdown, the study suggested they were not on the whole worth the cost.  If you’ve seen the actual study, please post it in the comments!

So please continue to social distance and wear your masks in public!  But it’s time to figure out how we can get the economy running again!  We have big problems to solve, time to get to work!

Don’t fear, but be smart,
Erik