Case Update: April 27th, 2021; Indoor Transmission, New CDC Guidance

This is a case update. I’ll also talk about a new paper discussing indoor transmission as well as new CDC guidance.

This US is recovering from the 4th wave.  Yes, the wave was much smaller than others, and if you don’t want to call it a wave, I won’t argue with you.  Michigan bore the brunt of new cases, but cases are going down.  Only Washington, Oregon, and Colorado are still experiencing higher case loads.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Endcoronavirus County Level Map, April 26th, 2021
Endcoronavirus State Level Map, April 27th, 2021

California and San Diego County continue to have fewer confirmed new cases.  In fact, California had just 661 new cases on Sunday.  The state hasn’t had fewer than 1000 new cases since almost exactly a year ago on April 28th. Yes, Sunday always has the fewest cases of the week, but it does indicate that cases are trending lower.

Graph is by me, from data collected from Johns Hopkins University COVID site. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Graph is presented in a logarithmic format to emphasize small numbers. Note that each number on the left is 10x higher than the one below it.

Internationally, a large peak is starting to improve. India has been particularly hard hit by the current wave of cases.  The higher cases are likely impacted by the more infectious new variants as well as slower vaccination rates.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus Country Page, April 27th, 2021

Indoor transmission: Several news outlets have been talking about a new paper on indoor transmission of SARS-2 published by a lab at MIT.  It makes several interesting points.  First, the paper points out that the Six Foot Rule was designed to mediate infection from large droplets like we see for the flu.  Large droplets usually only travel from a person to the ground in 6 feet or less.  SARS-2 on the other hand, appears to be transmitted as small droplets in an aerosol.  The micro-drops stay in the air much longer and can travel much further.  Transmission in indoor settings are a function of the number of people in a space, and the time of exposure.  Ventilation helps reduce transmission.

MZ Bazant and JWM Bush, PNAS2021 Vol. 118 No. 17
MZ Bazant and JWM Bush, PNAS2021 Vol. 118 No. 17

The authors also point out that the likelihood of transmission outdoors is very low.  One paper they reference has data from 7,324 transmission events, only 1 happening outdoors.  They also say that masks have much more effectiveness in preventing transmission than lockdowns or social distancing, adding more evidence that the virus spreads as an aerosol.

Are you surprised by the papers conclusions? If you’ve been reading my posts, then probably not. I’ve been writing similar things since May 27th of last year. So why are people talking about this now? I certainly have my opinions, and I’ll bet some of you can guess.  Meanwhile, several news outlets are saying that the CDC is about to release new guidance that vaccinated individuals can now go outdoors without masks.  At the risk of running counter the CDC, I’ll just mention that I’ve been going outdoors without a mask since March of last year, at my most concerned. I almost always wear a mask indoors, but almost never wear a mask outdoors.

Don’t fear, but be smart,
Erik

Case Update: April 20th, 2021, Vaccination in SD County, Herd Immunity

This is a case update. I’ll also discuss vaccination in San Diego County and herd immunity in general.

New cases may have plateaued in the US, but new outbreaks are apparent in some states. Michigan was the standout state for new cases, but endcoronavirus now suggests outbreaks across the Rust Belt, Northeast, Northwest, Colorado, and Florida. In most counties, actual numbers are small, but are obviously much larger in urban areas. If we are in a 4th wave, it appears to be much smaller than Wave 3, probably impacted by increased vaccination.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, April 19th, 2021
Endcoronavirus State Level Map, April 19th, 2021

New case loads remain low in California and San Diego, likely at least partially because cases were so high during Wave 3 in the Fall and Winter.

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

Internationally, new cases are very high worldwide. The new high cases numbers are likely impacted by the new variants such as B.1.1.7 (the UK variant) which is more infectious than the original Wuhan strain, and now dominates in many countries. Brazil and India are particularly hard hit. Canada’s current wave is as high as their Winter wave, but the numbers there are in general much lower than for the US.

Graph is by me, from data collected from Johns Hopkins University COVID site.

Vaccination in San Diego County: According to the County, about 37% of County residents are now fully vaccinated, with 60% having had at least 1 dose. Vaccination is now available to anyone 16 and up who wants to be vaccinated. If you want to be vaccinated, you can find a location on their website.

San Diego County Media Briefing, April 14, 2021

Herd Immunity: First, just a reminder that I am not an epidemiologist. Early in the pandemic, many recommended herd immunity as a way out of the pandemic. At the time, I argued that exposing a lot of people to a disease to protect people from a disease was counter productive. Now that we have a vaccine, herd immunity is a viable option for moving forward. For a population, herd immunity can be effective, although the percentage of people who need to have immunity to reach this is dependent on the disease and usually surprisingly high. On an individual basis, if you’re concerned about catching the virus, it’s far better to just get vaccinated at this point than to worry about if we’ve reached herd immunity.

Don’t fear, but be smart,
Erik

Case Update: April 13th, 2021; ADE and What You Should Do if there’s a SARS-3.

This is a case update. I’ll also talk briefly about ADE and it’s impact on the current pandemic and the potential impact on the next SARS virus, if one ever happens.

Cases in the US continue to rise slightly. Outbreaks continue in Michigan, with some new cases also in the Greater New York Metro area and the Texas panhandle. Why is Michigan having such a hard time? Frankly, I’m a little mystified, especially since Michigan has been in strict lock-down through much of the pandemic. It’s now well known that the viral load upon infection has a large impact on the severity of COVID symptoms. Those who get a low viral load upon exposure have lower symptoms. I will speculate and say that perhaps some states with very strict lock-downs caused people to interact in ways that encouraged larger viral loads upon infection, like being with groups of people in private homes. Again, I’m just speculating. This may also explain the large and sustained number of cases in LA county this Fall and Winter.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, April 13th, 2021

California and San Diego County both have come to an equilibrium, with approximately 3000 and 200 new cases a day respectively. Neither appears to have experienced an Easter related bump in cases. The new lower caseload in the US is likely related to vaccination and natural immunity, and is likely to become lower still as we head into Spring and Summer.

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 San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are reported by San Diego County. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.

Internationally, the caseload continues to increase, almost to Winter peak numbers.

Graph is by me, from data collected from Johns Hopkins University COVID site.

ADE and the next SARS virus: I wanted to explain a little more about my continued concerns about ADE. As the pandemic progresses and we have numerous variants circulating around the world and the US, ADE does not appear to have had an impact on the current situation. This is certainly good news. If it did have an impact, we would be seeing additional deaths from the new variants, which we do not.

My continued concern comes because ADE impacts our ability to fight the NEXT virus. SARS viruses (SARS, MERS, SARS-2) have the ability to easily infect the immune systems of those previously infected with closely related but different strain of the virus. If a future strain of SARS comes out, let’s call it SARS-3 for now, ADE may become a big deal. I stress that this is only theoretical at this point. SARS was moderately infectious, but also very pathogenic, giving all known patients severe symptoms and killing 10%. It was actually less dangerous globally, since outbreaks tended to be detected early and quickly snuffed out. SARS-2 is highly infectious, but much less pathogenic. It’s greater global impact came from it’s very high infectiousness and very long incubation time, being passed even from pre-symptomatic patients. The tendency of all viruses is to become more infectious and less pathogenic over time, a pattern followed by SARS and SARS-2. If we have a SARS-3 someday, it will likely be even more infectious than SARS-2, but less pathogenic. On the other hand, MERS is more pathogenic than SARS, so this pattern doesn’t always follow. The next time another SARS coronavirus breaks out, we will need to be very careful initially until we understand the parameters of the new virus.

So what do you do if you had COVID or had a COVID vaccine if a SARS-3 comes out? If that happens, vaccine production will likely be much faster than this time. Be very careful with the virus initially, and get the new vaccine as soon as it is available to you, because you may be at greater risk for severe symptoms. I know some of this is confusing and counter-intuitive! Feel free to ask questions below!

Don’t fear, but be smart!
Erik

Case Update, April 6, 2021; More on Vaccines, Auto-Immune Disease.

This is a case update. I’ll also add something to last week’s discussion of the South Africa variant and vaccines, and also talk briefly about autoimmune disease.

Last week, cases in the US looked like they were rising, but this week, it’s more ambiguous. New cases in the US are the same or maybe even a little lower than last week, so I can’t point to a clear trend right now. A spike in new cases persists in the Eastern Michigan at the moment, as well as higher new cases in several other Eastern states.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, April 5th, 2021
Graph is by me, from data collected from Johns Hopkins University COVID site.

New confirmed cases are also slightly up from last week in California and San Diego County. If we have a bump in cases because of Easter, it will start to show up on Wednesday or Thursday.

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 San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are reported by San Diego County. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.

Update, Vaccines and the SA Variant: Last week I discussed the effectiveness of several vaccines on the South Africa variant (B.1.351). I said that the Astra-Zeneca vaccine works poorly against the vaccine and that the Pfizer and Moderna vaccine were still poorly understood. New data from a small study Pfizer released in early April suggests that their vaccine is effective against the SA variant, though the study is too small to say how much. The Moderna vaccine is not particularly effective against the SA variant, but they are testing a booster against the SA variant right now. The Johnson and Johnson vaccine is 75% effective in the US, and 57% effective in South African patients (as reported by J&J).

Auto-Immune Disease and COVID: It appears that those with auto-immune diseases, like me (celiac disease), may suffer more severe symptoms from COVID. There is some suggestion that this may be because of consistent use of NSAID medications to counteract inflammation. Most doctors will suggest remaining on anti-inflammatories unless COVID symptoms appear. Check with your doctor before changing any medications. I am continuing to take my NSAID medications. By the way, Ibuprofen (Advil) is an NSAID, so if you’re taking an NSAID regularly, take Tylenol instead of Advil for routine pain so as to not double up on NSAIDs.

Unfortunately, there aren’t really studies yet to determine if auto-immune sufferers are at greater risk from getting the vaccine. In my non-expert but informed opinion, the risk of SARS-2 infection for auto-immune sufferers is likely higher than the risk of a reaction from the vaccine. Since the COVID vaccines only present the Spike protein to the immune system, they’re likely no more risky than any other vaccination. If you tolerate other vaccinations well, you’ll likely tolerate this one too. My recommendation would be for auto-immune sufferers to get the vaccine. Of course, check with your doctor first. If you choose to get the vaccine, I strongly suggest getting it at a medical facility that can monitor you rather than in a mass vaccination center.

Don’t fear, but be smart,
Erik

PS. FB doesn’t like it when I discuss vaccines! They often add a note about vaccines when I discuss it, referencing info from the WHO. While comments FB has added recently are accurate, I generally don’t regard the WHO as a good source of information about COVID, since they are overly influenced by certain political entities and have occasionally been very wrong. The CDC is better, but it often very slow to present new information.

Case Update, March 29th, 2021; Dr. Shane Crotty on Vaccines and Variants

This is a COVID new case update.  I’ll also discuss new cases world wide, and discuss a new video from immunologist Shane Crotty with lots of important information on vaccines and variants.

In the US, we’re starting to see an increase in new case numbers in several states, Michigan and New York in particular.  This may be because of the relaxing of requirements by many municipalities, but may also be because of some of the new variants arriving in the US.  More on the new variants below. 

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, March 29th, 2021
Endcoronavirus US States, March 29th, 2021

New case numbers have stabilized in California and San Diego County with around 2000 new cases a day in California and 300 in San Diego. We have yet to see a clear uptick in cases in those 2 regions, but we may see this soon.

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 have been calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered. Recently, however, this would produce an active case number that is too low to make sense in comparison to San Diego. This graph estimates 17 to days to recover in January, but gradually moves to 22 days for mid-March. I’ve lost confidence that I can make an Active Case plot that is accurate, so this will probably be the last time I post this for California. Let me know if you think it’s still useful.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are reported by San Diego County. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.

Internationally, the US and UK are doing better than average at the moment, but many countries scattered all over the world, with concentrations in Eastern Europe and South America, are seeing new surges in cases. The US and UK are both vaccinating heavily right now, with vaccine rollouts moving slowly in continental Europe, so vaccination may play heavily in this pattern.  Also several new variants of the SARS-2 virus are more infectious than the original strain and likely factor in these new surges.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus Countries, March 29th, 2021

Important new video with Dr. Shane Crotty:  MedCram has posted a new video interview with Dr. Shane Crotty, an immunologist in San Diego. His work looks into immune system responses to vaccination as well as native infection.  He has several very interesting points to make about SARS-2 immunity and vaccines. First, he says that those infected with SARS-2 do have significant lasting immunity for many months, although it does go down a bit over time.  Different people can respond very differently, however, and reinfection is possible in some.

Regarding vaccines, he said that those who have been infected have a good but not great immune response, but it is significantly boosted by a single vaccine dose, gaining an immune response higher than those vaccinated alone. So there is a good reason to be vaccinated if you have already been infected.  Of course, if you’ve been infected, you may choose to wait until at-risk people have been vaccinated before you get a vaccine booster.

As for variants, he says there are 2 broad categories of variants, those similar to the UK variant (now commonly called B.1.1.7), and those similar to the South Africa variant (B.1.351).  Both new strains are more infectious than the original Wuhan strain.  The big difference between them is that those who have had SAR-2 are immunized against the UK strain, but not the South Africa strain.  Also, the Astra-Zeneca vaccine does not protect well against the South African strain, and the Pfizer and Moderna vaccines appear to be less effective as well.  The good news is, the Johnson and Johnson and Novavax vaccines do appear to protect against the South Africa strain. This suggests that although the South Africa strain is different, it isn’t so radically different that we have nothing to fight it with. 

_____________________________
Update, April 6th
A new small study from Pfizer suggests that their vaccine does work on the South Africa variant. The patient number in this trial is small, so they still don’t know exactly how effective it is.
_____________________________

Soberingly, the South Africa strain has reached the US, so if we see a surge in the next few weeks, this strain may be at least partially responsible.

Impact on ADE?  If you’ve read my posts on ADE, then you know that the danger from ADE may come when a different strain arises.  With the South Africa strain arriving in the US, we may be able to see if ADE will have an impact with SARS-2 in the next few weeks and months.  So far, new death numbers have come down with Wave 3, and there is no apparent impact from ADE on case severity.  I will certainly be watching to see if this changes.

Graph is by me, from data collected from Johns Hopkins University COVID site.

Don’t fear, but be smart,
Erik

Case Update: March 24th, 2021

This is a COVID case update. New confirmed case numbers continue to decrease, although slowly. The endcoronavirus county level trend map shows a few small outbreaks in Michigan, but improvement everywhere else.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, March 23rd, 2021
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 have been calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered. Recently, however, this would produce an active case number that is too low to make sense in comparison to San Diego. This graph estimates 17 to days to recover in January, but gradually moves to 22 days for mid-March. Is this still useful information?
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are reported by San Diego County. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.

I’m going to get into the statistical weeds a little bit right now. Read on if you’re interested in that. I often post a graph of new cases along with active cases for California and San Diego County. San Diego actually publishes numbers of recovered patients, but California does not. My estimates for California have been based on the San Diego recovered numbers. San Diego’s recovered numbers have generally matched the new case numbers for 17 days previous, so I’ve been doing the same for California. Now, for whatever reason, San Diego’s recovered numbers have been matching new numbers for 22 days previous, which makes a big difference in “Active Confirmed Cases”. So now I’ve been making a bunch of modifications to my estimates for California numbers, and I’m not sure I feel comfortable showing you such adjusted numbers. So if you have an opinion, let me know in the comments if you want to continue seeing “Active Cases” for California, despite all the guesswork.

Don’t fear, but be smart,
Erik

What is Science?

This is a long post about the philosophy of science. I probably should have written this one a long time ago, but here it is. 

During the pandemic, we’ve often heard scientists and commentators say “I’m just following the science.”  Confusingly, we’ve heard people on all sides of the issues say this, pro-maskers, anti-maskers, vaccine fans, vaccine detractors, people who love Hydroxychloroquine, and those who think it kills people.  Very often, when people have used the word “science” in the last year, they’ve used it in a way that you DIDN’T learn in high school biology class (thanks, Mr. Walker!).  So what do people mean when they say this, and how can you evaluate what they are saying?

When you hear the word “science” on the news or in discussions on the pandemic, other definitions are often smuggled in. I’ll give you a few different ways people use the word “science”, and then I’ll talk about how you can evaluate science related discussions.

1) In actuality, science is a method for measuring things in the natural world, and using reasoning and the scientific method to make, falsify, and confirm hypotheses about natural things.  Science has been phenomenally successful about describing aspects of the natural world, as well as producing useful applications for communication, travel, health, manufacturing, the arts, and nearly every conceivable human endeavor.  The incredible success of science has given it enormous cultural power as well, and many ascribe to it powers that it does not have. By definition, science measures and describes the natural world, but cannot describe many common aspects of reality, questions like “what is justice?” or “what is the meaning of life?”. 

While many contributed to the Scientific Method, the steps were formalized by Francis Bacon.  The steps include 1) the formulation of a question, 2) the development of a hypothesis, or a guess about what actually happening, 3) a prediction about what impact the hypothesis may have on a system, 4) doing experiments to test the hypothesis, and last 5) analyzing results, to include falsifying or confirming the hypothesis and forming a new question.

The scientific process is not a slow gradual accumulation of truth.  It’s often ugly, with long searches down the wrong path before finding the right one. Fields can experience sudden, jerky changes in direction.

2) The collection of facts currently believed by the majority of scientists.  When many in our current culture use the word “science”, this is what they mean. The phrase “settled science” often refers to this.  But scientific truth is not decided by a vote.  Yes, if a “fact” is believed by most scientists, it’s more likely to be true, but science history is full of people who had “weird” ideas that later turned out to be right.  By definition, topics under current study are not well understood, and there can be widely varying opinions about what’s going on. 

It’s always OK for a scientist to question current thought.  Trust me when I say that having a PhD does not mean that other scientists have to believe you.  I’ve heard shouting matches at conferences over what to believe about seemingly simple things.  

Real “Truth” transcends opinion.  Things are true whether you believe them or not. Science is the search for the truth about the natural world, not the search for ways to force your view on others.

Which leads to…

3) The collection of facts currently believed by scientists who agree with me.  When things are murky and not well understood, which is quite often in active fields, there can be 2 or more models of how a system is working. Sometimes the evidence that is out in the world can appear to be contradictory. This may be because some of the evidence is wrong, or because conclusions based on the evidence is wrong, or because a crucial piece of evidence is still missing, or because the system is just more complicated than anyone is aware of. At this point, a good scientist will try and rethink the available evidence or perhaps design a new experiment to try and get at something still unknown.  Instead, some people, even good scientists in a moment of weakness, will simply declare that their view is correct prematurely.  Scientists must always seek to be more persuasive, and not just shout louder.

4) The collection of facts currently believed by me, right now.  This definition is common for those who believe an outlier view.  It’s not bad to have a view that is outside the current orthodoxy, this is how scientific breakthroughs happen, but a person in this position must seek even more to persuade with evidence, not just be dogmatic.  Do more internet work, read more literature, or design another experiment.

5) An atheistic worldview, as in “I believe science”. Science is great at discovering information about the natural world, but it can’t answer the big questions. What some call “science” in this way is really “naturalism”, the belief that only matter and energy exists. It rejects any worldview that includes a transcendent or supernatural component. Science alone does not support this worldview, because by definition, science can’t “prove” the non-existence of things outside the known universe. Other philosophical structures are necessary to support this view.

So how do you figure out what’s really true about a scientific opinion being presented.  This can be difficult, but it can be a little easier to figure out if someone is abusing “science.” Here are some clues that science might be being misused.  You’ll have to dig deeper to be sure:

  1. A real scientific argument includes a conclusion supported by evidence.  Does the person talking give any evidence for their position? Often, people just make an assertion, a claim without evidence.  This is OK if they can back it up, but very often they can’t.  Ask “can you clarify that?” or “how did you come to that conclusion?”
  2. When questioned, a person should have evidence for their claim. If instead they call you anti-science, or *phobic or *ist, then they are abusing science.
  3. If a story or comment starts with “X person is brilliant and has been in the business for years”, this is often a red flag for me.  While a person’s qualifications are important, they must still present evidence.  A title or degree is not enough for them to be automatically believed.  The more glowing the terms used to describe a source, the more I’m suspicious that they are about to spout nonsense.
    Yes, these even applies to me.  If you tell someone “This Facebook friend of mine is a real scientist and he says <something really smart>”, you should rightfully expect your friend to ask what evidence I had for my claim. If you don’t know, then re-read my post, or just message me!  I’m happy to work through it with you, and I’ll tell you outright if I’m just speculating.
  4. News articles are OK, but they are only a starting place.  If a person references a news article, they still have homework. What news outlet? What evidence did the author use? Journalists often misunderstand or misrepresent information from scientific sources.
  5. Real evidence can be a scientific paper, a study learned about on the radio (who presented it?), or a comment by an authoritative source (who is the source?).  Each of these can in principle still be wrong, but they have more weight than other sources.
  6. Often, we gain knowledge about the world from someone we trust, an authority on the matter.  This is a fine way to learn things. Your parents were the first authority that you used for learning much of what you needed to know.  But authorities, even good ones, are not always right.  You learned this about your parents when you were a teenager. It’s OK to pick someone you trust as an authority on scientific matters, but still don’t believe everything you hear.  The CDC, the WHO, Dr. Fauci, the President (either one), yes even me, have been right about some things and wrong about some things during COVID. During an evolving situation, expect opinions and “facts” to change as more information is gathered.  Your favorite authority doesn’t know everything.

Of course, the debate on several COVID related topics have become politicized, which can make it difficult for scientists to do good work, and often VERY difficult for lay people to know the truth. I feel for you. It can be really difficult for folks to figure out what’s true about something that’s not in their field.  I feel the same way about climate change, an important topic of frequent debate that’s not in my field.  Don’t feel dumb if you have trouble figuring out what’s going on.  Lots of folks are abusing science, trying to make you agree with them.  Hopefully I’ve given you a few tips on how to discover the truth.  Here’s an article on how to communicate scientific things!

Don’t fear, but be smart,
Erik

Case Update, March 17th, 2021; Still higher new case numbers than Wave 1?

This is a case update. New cases continue to fall for the US, California, and San Diego. There was a spike in cases for the US on March 8th. At the same time, there is a spike in cases in most counties in Missouri. The spike was so consistent across the state, and stops on every nearby state line, that my suspicion is that this represents a reporting problem rather than actual new cases in every county in the state. Sometimes labs or public health departments don’t report on time and allow new case reports to stack up. When they finally report the results, it looks like a big outbreak. I can’t prove that this happened in Missouri, but it’s my suspicion. I couldn’t find any news about this phenomena, and the Missouri state health department shows no spike in cases during this time.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, March 16th, 2021
Endcoronavirus State Level Data, March 17th, 2021.

My total case number graph for California assumes that patients recover after 17 days. But today’s number gives a unbelievably low 6500 active cases in California. California doesn’t report recovered cases, so I’ve been using San Diego Counties numbers and extrapolating an estimate for California. Right now, San Diego’s reported recovered numbers suggests a 22 day recovery time instead of 17. If you use 22 days for California, current active cases for California is 28,000. This is why I tell you exactly how I get my information, so if it’s wrong or suspicious, you can decide for yourself if you believe my source.

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. Given this criteria, the active cases are crazy low right now, probably too low to be real.
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. If I change this assumption to 22 days for the last few weeks, matching the estimate from San Diego County, active cases in California is 28,000.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are reported by San Diego County. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.

Still more than in Wave 1? For the last few weeks, I’ve been saying that while our numbers are getting really low, the numbers are still higher than in Wave 1 from last April. A friend pointed out that last Spring we weren’t really testing much, so maybe the cases were higher. That’s an excellent point and absolutely true. In fact I have several friends that were really sick during the Winter of 19/20, some after spending time with friends or family from Asia. So yes, there may have been far more cases last Spring than we know.

Don’t fear, but be smart,
Erik

Case Update: March 10th, 2021

This is a brief case update. New confirmed case numbers are continuing to drop for the US, California, and San Diego County. After a pause, numbers for the US are improving again. For all three regions, numbers are at or near the pre-wave 3 levels, but these are still higher than wave 1, so we still need significant improvement. Notice that the active cases for California are now below the trough between waves 2 and 3.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, March 10th, 2021
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. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered. Because our new active case numbers are getting low, I’ve switched to a logarithmic view. This emphasizes small values and makes them easier to see. Notice that the case number on the left now go up 10 fold with each higher line on the graph.

Don’t fear, but be smart!
Erik

Case Update, March 3rd, 2021; When will the Pandemic be Over, New Variants and Vaccines

This is a case update.  I’ll also talk about when the pandemic may be considered “over”, and briefly discuss the new SARS-2 variants.

For the US, the downward trend in new cases has paused.  New cases have been steady for the past 2 weeks.  The daily new cases continue to be higher than the first wave, and almost as high as for the second wave this summer.  The new case map from endcoronavirus shows recovery, but this particular map only shows changing trends.  The small number of counties in red may be misleading, because many of these counties are rural, so represent very few actual cases.  If you look at the top 10 counties for new cases in the country, there is still a significant number of new cases in several counties.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, March 3rd, 2021
Endcoronavirus County Level Map, March 3rd, 2021

We continue to see a downward trend in California and San Diego County. However, the new case numbers remain higher than they were during the 1st wave.  

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. “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.

When will this be over?  The 3rd wave this Fall and Winter is winding to a close, which makes many speculate on when the pandemic will be over.  I’m going to speculate on this, and what criteria we may use to determine this, but remember that I am not a physician or epidemiologist.  This is my informed but not expert opinion.  I am a molecular biologist specializing in infectious disease testing.

The most significant event happening right now that will impact the progress of the pandemic is the ongoing vaccination program going on in the US. We are currently into Phase 1B, vaccination of all individuals over 65. If you are over 65, I encourage you to consider vaccination.  Check in with your local health department to find out how you can be vaccinated.  You know I have some concerns about the ADE issue, but on balance, those over 65 will almost certainly benefit from the vaccination despite these concerns. As more vulnerable people are vaccinated, we will continue to see a drop in new cases, as well as a further drop in severe symptoms and mortality. Soon, we will enter Phase 1C, in which anyone over 16 with COVID risk factors will be able to receive the vaccine. 

Once everyone who is vulnerable has been vaccinated, this may rightfully be considered the “end” of the pandemic in the minds of many.  We should also pay attention to the number of COVID deaths. In order for the pandemic to be considered truly over, the number of deaths must be very low as well. I’m not willing to speculate yet on exactly what “very low” means.  Keep in mind also that many other countries do not yet have the vaccine, so vaccination in the US alone will not end a global pandemic!  Even after the epidemic in the US is over, travel to and from other countries may still be restricted.

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.

Variants: We have seen several SARS-2 variants arise over the last few months.  Most of these variants have made the virus more infectious but not more pathogenic.  This is because they alter the Spike protein, the viral protein that is used to infect our cells.  This is also the protein that the immune system, and the vaccines, target to neutralize the virus.  However, the vaccines currently in use appear to still work on most variants.  The exception to this is the South African variant (501.V2) which some suggest may evade the current vaccines.  Concerns about this are strong enough that Moderna is currently working on a vaccine against 501.V2.  This variant is already present in many countries, including the US.

The Second Shot: I haven’t been vaccinated yet, but I’ve heard several accounts of people feeling significant flu like symptoms after their second COVID vaccination. It’s actually not unusual to have flu like symptoms after a vaccination. Flu like symptoms are your body’s normal response to an invasion and many of the symptoms we experience are designed to help you fight an infection. That’s why so many infectious diseases produce “flu-like symptoms”. So unless your symptoms are severe, or your fever is over 102°, you don’t need to get medical attention. If you are prone to allergic reactions after a vaccine, inform your healthcare provider before you get one.

So we have lots of good news, but we need to continue to be diligent!

Don’t fear, but be smart!
Erik