Case Update: October 21st, 2020

Friends,
Just a short update today. For the US, new case numbers continue to rise. Most new cases are centered in the Northern states, and new cases are spreading South. My guess is that the cold weather is driving these new cases, as people are spending more time indoors. Despite this, new cases are so far not producing an increase in fatalities.

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.
Endcoronavirus County Level Map, October 21th, 2020

California and San Diego continue to have a persistent number of new daily confirmed cases.

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.

Don’t fear, but be smart,
Erik

Case Update: October 13, 2020; Voting, Re-Infection, 3D Structures

I’ve been traveling a LOT recently and just skipped last week’s update. Sorry for the long delay.

The US continues a slow trend upward in new confirmed cases. According to endcoronavirus, most of these new cases are arising in the Northern states, although the upward trend seems to be creeping south. This seems to confirm my suspicion that the new uptick in cases is caused by colder weather, and people being indoors together more often. If this suspicion is correct, we may be in for a long broad 3rd wave of cases this winter. You may remember that the Southern states (California all the way to Florida) drove new cases this summer. During the summer of course, people in Southern states tend be indoors with their air conditioners more often. This is my theory for the time being.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, October 13th, 2020

After the end of the 2nd wave, California is experiencing a persistent 3000 new confirmed cases a day, and San Diego County has a persistent 300 new confirmed cases a day. Unfortunately, I’m firmly convinced at this point that COVID may be with us at least until next Spring. As you know if you’ve been reading my posts, I think we will need to adapt to this situation, and open up our economy and normal life as much as possible, while still taking precautions.

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.

As I’ve mentioned before, I am doing a lot of traveling these days, and get tested almost every week, and I’m always negative so far. I use air travel and go into all kinds of gas stations and stores. I do the following:

1) Wear a mask or face covering in public. Avoid places with unmasked people.
2) Keep 6 ft away from others. (I basically ignore this one if other precautions are in place, especially on an airplane!)
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.
6) Wear an N95 or KN95 mask when going to more high risk areas like airports or public areas where people may gather. These masks are rated to filter out 95% of viral particles. In my opinion, surgical masks and especially neck gators are nearly worthless in these settings.
7) I never take my mask off on the plane, and find an isolate spot in the airport to eat or drink on layovers.

Voting: If you haven’t heard, there is an election coming up. As with many issues, mail-in voting has become a politicized issue. The New York Times recently had a story expressing reservations about mail in voting, claiming that mail in ballots are more likely to be disqualified than in person voting. This is because filling out and mailing in these ballots can be complicated and prone to errors that disqualify these ballots. Some stories even claim that people have been sanitizing their ballots, ruining the ink and disqualifying be ballot. It is therefore my recommendation that everyone vote in person if possible. Follow the above precautions, and I’m confident you can do so safely. Dr. Fauci claims that in-person voting is safe if proper precautions are taken.

Reinfection: There is a recently published study of a confirmed case of re-infection in an American man. Apparently, this is the first confirmed and well characterized case in the US, although there have been other suspected cases. His symptoms were more severe with the second case, suggesting that my fears of ADE may be warranted. However, there have been only 22 confirmed cases of reinfection world wide, so it’s still apparently a very rare phenomena. The paper also states the 2nd infecting strain is distinct from the first, consistent with the ADE model.

The paper suggests that there may have been dozens of circulating strains since the beginning of the pandemic. While this case of re-infection appears consistent with ADE, the rarity of the re-infection phenomena along with the many circulating strains suggests that ADE, while theoretically possible, may not have large real-world significance.

New 3D structure: Last, for those of you who want a deep dive, the New York Times has a nice story with a collection of 3D structures of the virus from different sources.

Don’t fear, but be smart!
Erik

Case Update: September 30th, 2020

Here’s an update for today. The US, California, and San Diego County seem to have reached a “new normal” after the 2nd wave is over. All have a persistent rate of new cases, unfortunately higher than when the 2nd wave started. The US in fact is increasing in cases a little, with the Northern states having the largest new confirmed case load.

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.
Endcoronavirus County Level Map, September 30th, 2020

India now has 6.1 million cases as compared to the USs 7.2, and they are just reaching their first peak now, so they will probably surpass our case load soon. This is confirmed cases of course, and there’s no telling now many non-detected cases they have. Of the countries with the top 10 number of confirmed cases, 4 are in South America, Brazil, Colombia, Peru, and Argentina. Mexico is also in the top 10.

Don’t fear, but be smart,
Erik

Case Update, September 23rd, 2020, Existing Immunity, Reinfection, Strains and Vaccines

This is a weekly update, but I’ll also talk about apparent existing immunity in some people, reinfection, and the 2nd wave of cases and what this all may mean about Coronavirus strains.

The 2nd wave of cases is apparently over in many places in the US, although not all.  The US new confirmed case numbers have risen slightly in the past week.  While the southern part of the country, California all the way for Florida, was the epicenter of cases for several weeks, new cases are primarily arising in the North Central part of the country.  I might speculate that this might be related to the coming Fall weather, but of course it’s too early to say for now.  The US also crossed a threshold of 200,000 total COVID deaths, outpacing a prediction I made several weeks ago that we would have 100 – 200 thousand deaths.  California is back down to pre-2nd wave new case numbers, but is not sinking below that.  In San Diego County, we had a small wave of cases related to a series of outbreaks at SDSU, but we’re back to a lower persistent new case rate.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, September 23rd, 2020
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.

Internationally, India now has the second most cases in the world, with 5.6 million cases as of this posting.  Of course India’s very high population and densely packed cities are likely a contributing factor. Brazil and Mexico have managed to slow the rate of new confirmed cases, having peaked in late July.  While things are improving in the US, many countries are experiencing first or second waves right now, including France, the UK, Israel, and Austria. 

Existing Immunity: I’ve resisted talking a lot about existing immunity because the information is complicated and may have phenomena with overlapping and opposing impacts.  Also, I’m not an immunologist! Be aware that what I say next may change.  There is data suggesting that the reason many, especially children, are asymptomatic is that there may be some existing immunity to Coronavirus in those individuals.  Coronaviruses is a large family of viruses which includes the SARS and MERS viruses, but also several viruses that cause the common cold.  As such, many may already have some kind of immunity to Coronaviruses as a group.  This is good news of course.

Reinfection:  On the other hand, I listened to a story on the September 2nd episode of the Nature Podcast about several cases of SARS-2 reinfection.  These cases appear to be rare, and most are not well studied.  In one case in Hong Kong, however, both the 1st and 2nd strains which infected a patient were sequenced and were found to be different strains.  This has several implications.  It suggests that immunity to a single strain may persist at least for a few months, but also that several strains are circulating, and immunity may not apply to other stains. 

If you’ve followed my page for long, you know that I’m concerned about Antibody Dependent Enhancement (ADE). In some cases of reinfection, symptoms were worse the second time, but in others, they were less severe. So unfortunately, these don’t necessarily provide clarity on whether ADE will be an issue, although if this is ambiguous now, it may be the issue will at least not be as serious as I feared.  We’ll have to see more of these cases to know for sure.

Strains and Vaccines: I’ve written about the D614G strain that arose in April and May. When I first heard about it, scientists were saying it may be several times more infectious than the already very infectious SARS-2.  I suspect that the 2nd wave we saw in the US may have been so large partially because of this strain.  All of this, as well as the reinfection story above, highlights that we have several strains moving around at once, and will likely have more.  Like HIV and Flu, Coronaviruses are RNA viruses.  RNA viruses use a RNA dependent polymerases to copy their genomes, and these enzyme tend to be VERY error prone as compared to DNA dependent polymerases.  Because of this, RNA viruses mutate quickly, and are resistant to the use of vaccines.  This is why we need a few Flu vaccine every year, and part of why we still don’t have a vaccine against HIV.  This of course also complicates the prospect of a vaccine against SARS, along with concerns about ADE. I’ll keep you posted as I learn more.

Don’t fear, but be smart,
Erik

Piracy and Mask Wearin’

Avast! This be Talk Like a Pirate Day! So if you be havin’ a question below, use your favorite dialect of the high seas!

The New England Journal of Medicine foisted a flag regardin’ mask wearin’. It appears masks reduce scurvy and COVID symptoms even in infected seafarers. This may be explainin’ why even with the large number of cases during the second wave, fatalities were low.

Have ye no fear, but keep a wary eye,
Erik

Case Update: September 15, 2020; Bob Woodward and Communicating in a Crisis.

Friends,
This is a virus update. I’ll also have a few comments regarding the recent Bob Woodward book. New confirmed cases continue to drop for the US, California, and San Diego. California new case numbers are back down to what they were before the 2nd Wave hit in mid June.

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

San Diego had a moderate sized outbreak at SDSU in the last few weeks which created a spike in new confirmed cases for the County, but those numbers are coming down 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.

Endcoronavirus.org’s county view map now shows mostly yellow across much of the South, including California, Arizona, Texas, Louisiana, and Florida, which was perhaps hardest hit by the 2nd Wave. It looks like that region is now recovering, and the Mid-West is now the region of greatest concern, with increasing numbers in many Mid-Western states.

Endcoronavirus County View Map

Bob Woodward comments: If you’ve been reading my posts for long, you know that I try to keep these posts as politics free as possible, referring to policies, but not to people. You also know that my recommendations sometimes support those commonly from the “left” and sometimes from the “right”. I do my best to pass along the science as I see it, since I believe politics and science are terrible together.

If you’ve read my July 7th post, you know that a major concern of mine is Antibody Dependent Enhancement. This phenomena is still not discussed openly in the media, and the only other commentator I hear discussing it is Chris Martenson of the Peak Prosperity YouTube channel. Tony Fauci has mentioned it only in passing. I have been concerned about this phenomena since February when I started studying the SARS-2 virus.

Why did I wait until July to post about it? In any crisis, there are people who are anxious about it, they are the first to react, and some overreact. There are others who are unconcerned, and react slowly if at all. Many are somewhere in between. Anyone who communicates to the public has to aim somewhere in the middle of these perspectives. My goal from the beginning has been to communicate adequate concern while being as positive as possible and not cause the anxious to over-react. As I’m sure you’ve heard, there have been many mental health issues attached to recent events, and I have friends in the mental health field for whom this is a great concern. I struggled for a long time before my July 7th post. I wanted people to be adequately concerned, but I didn’t want to cause needless anxiety. The ADE phenomena is still poorly understood, and it’s not certain if it will play a roll in this crisis. I finally decided to discuss it because I had a lot of friends who I felt were not taking the virus seriously enough, and I began to feel it was wrong of me to not inform them. To this day, I wonder if I waited too long, or maybe shouldn’t have mentioned it when I did.

All this to say, Bob Woodward’s discussion with the President was in February, if my understanding is correct. In February, the virus had still not come to the US, except for a few small clusters. Little was still known about how it would behave in the US, and the opinion of medical professionals regarding how to deal with it has changed many times since then. If President Trump was wrong to downplay the virus in February, then I was wrong too. I hope you will have some understanding for the difficult decisions to be made.

The CDC continued to treat the virus like it has always treated epidemics somewhere else, deep into March. Only in Mid-March did they allow other entities to do SARS-2 testing in the US, responding to the President’s request. Large scale testing did not start until early April. In my opinion, the CDC is most responsible for reacting too slowly to the virus.

Don’t fear, but be smart,
Erik

Case Update: September 9th, 2020

Friends,
This is a case update from the last week. For the US and California, confirmed case numbers continue to improve. In San Diego, we seem to be having a small bump in cases right now, after a consistent fall since late July. My friend Brit Colanter who works at San Diego County Public Health tells me that there was an outbreak at SDSU in the last few weeks. 444 cases so far and 1 hospitalization.

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

I just got back from a trip to a hospital lab in Rochester, New York, helping them expand their COVID testing. As much as we can grumble about conditions here in California, they are even more strict in New York. New York has a quarantine program going for residents of some states, including California! I was required to check in with Contact Tracing every day, and stay in my hotel room when I wasn’t at the lab. So I was kind of under house arrest!

I have a new appreciation for Door Dash and other delivery people working out there today. So thanks to all of you who are working hard to bring needed items to those who can’t leave their house! You have important work right now!

Don’t fear, but be smart!
Erik

PS. I’ve heard a rumor that many African nations are having official events to pray for the US. Many thanks to my African readers for your prayers. We certainly need them!

Co-morbidities, vaccines

People have been asking me about a story that came out in the last few days about 94% of deaths having co-morbidities. The implication many have made is that most don’t really die from COVID, they die from something else, and they also happen to have COVID.It’s certainly true that contributing factors can make symptoms worse, and many of those with symptoms have another underlying issue. But I think it would be a mistake to think that this means COVID can be dismissed as no big deal. The fact is, the list of contributing factors is long, and includes the following:

age
asthma or COPD
heart conditions
kidney conditions
liver disease
high blood pressure
diabetes
obesity
auto-immune disease
use of NSAID anti-inflammatory medications
being immunocompromised (HIV infected, undergoing cancer treatment, under medication for a transplant)
vitamin-D deficiency
type A blood (Type O appears to be protective)

A lot of people are on this list, including me, since I have Celiac Disease, an auto-immune disease. Think of it this way. If someone dies because they got pushed in front of a train, did they die because of the train, or because someone pushed them? Well, both. Getting shoved generally doesn’t kill you, but it does if you get shoved into a train.COVID on it’s own may not be very deadly on it’s own, but it is in combination with a lot of other conditions.

The good news is, COVID is getting more survivable as treatment gets better, and also perhaps since people are getting exposed to lower viral loads because of mask wearing. We should be concerned, but not fearful, and we can also be optimistic that things are getting better!

I’ve also been asked by several people recently about a vaccine. You may remember my post about ADE, Antibody Dependent Enchancement. It’s a rare phenomena in which a virus can use an antibody against a previous infection to infect the immune system (link to my original post below). This can make a second infection much worse than the first. This only occurs with a small handful of viruses, but SARS, MERS, and likely SARS-2 are some of them. Because of this phenomena, I am suspicious of vaccines against SARS-2, and will wait to see what happens before I get one for myself, or recommend others do. I am not an anti-vaccine person in general! I have gotten the annual flu shot many times! But SARS-2 is different. If someone involved with the vaccine creation process can convince me it’s safe, I will certainly let you know.

Don’t fear, but be smart!
Erik

Links:
June 22nd Summary
Antibody Dependent Enhancement

Update: September 1st, 2020

Just got home from some traveling, setting up a new COVID lab. Just a quick update.

New cases continue to drop in the US, California, and San Diego, as do probable active cases. Endcoronavirus.org counties map shows most of California recovering.

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.
Endcoronavirus’ Counties Map.
From Rt Live.

Good news! Let’s keep it up!

Don’t fear, but be smart!
Erik

Case Update: August 23rd, 2020; New study on transmission from masks.

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.

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

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.

Fischer EP, et al., Low-cost measurement of facemask efficacy for filtering expelled droplets during speech, Science Advances, pre-released August 7, 2020
Fischer EP, et al., Low-cost measurement of facemask efficacy for filtering expelled droplets during speech, Science Advances, pre-released August 7, 2020

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!

Don’t fear, but be smart,
Erik