Category Archives: All Articles

Case Update: January 10th, 2021

This is a case update. I’ll also briefly discuss some more new variants, and a testing equipment shortage. For the US, cases continue to increase. Day to day case rates have been very erratic for the past several weeks. This is partially because many testing facilities don’t report on holidays, so that there is an artificially low case number on holidays, and an artificially high case number the day after. The arrows in the case number graph for the US show Thanksgiving, Christmas, and New Years Day. Wave 3c, the wave starting after Christmas day, is still increasing in confirmed case numbers.

Graph is by me, from data collected from Johns Hopkins University COVID site. Arrows indicate Thanksgiving Day, Christmas Day, and New Years Day.
Graph is by me, from data collected from Johns Hopkins University COVID site.

New cases continue to be focused in the East and Southwest. In particular, new case numbers have plateaued in California, but numbers are still quite high, with 4 of the top 5 counties being in California.

Endcoronavirus County Level Map, January 9th, 2021
Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, January 9th, 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.

New confirmed cased numbers are continuing to increase in San Diego County, with no clear separation between Fall, Thanksgiving, and Christmas waves.

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.

More new variants? I mentioned the new UK variant a few weeks ago. Since then, I’ve heard reports of new variants also arising in South Africa and Colorado. I don’t have much information on those yet, but the more people who are infected, the more likely a new strain will arise.

Equipment shortage. For those outside the medical community, just a little inside knowledge. The crisis has revealed many of the items that are limiting in our efforts to combat the virus. For the medical testing industry, many common materials have been very difficult to obtain, leading to long wait times for testing. There is a short supply of testing instruments, detection kits, RNA extraction machines, extraction kits, plastic plates used to contain testing reactions, and even plastic tips used to move small volumes of liquid in the lab. If you place an order of tips today, they may not arrive until April or May! This is part of the reason testing has been so slow and new labs difficult to start. I’m told that part of the issue is that there are only a few factories in the world that make medical plastics, and they are all overwhelmed. As a country, we’ll have to rethink our supply chain now and in the future.

Don’t fear, but be smart!
Erik

Fall Wave “Animation”

Below is an “animation” of sorts, photos from endcoronavirus, about a week apart, with one photo from June, and then a series starting in September. I’ve said that the Fall wave started in the North and then moved to the South as the wave progressed. I think you can see this in this series of photos.

Counties are colored based the change in cases, not the number of cases. Red is increasing cases, orange is falling or constant cases, yellow is cases almost under control, dark green is cases under control, light green is no cases.

Erik

June 9th
September 15th
September 23rd
September 30th
October 13th
October 21st
November 1st
November 11th
November 19th
November 24th
November 28th
December 5th
December 10th
December 12th
December 21st
December 29th
January 5th
January 10th

Case Update: December 29th, 2020; New UK Variant

Friends,
This is a case update and I’ll also talk about the new UK variant, VOC 202012/01. Wave 3b, the Thanksgiving wave, is receding, with numbers going down for the US since around the 18th. However, if Thanksgiving is an indicator, we may see a Christmas wave start this week after Christmas gatherings last week. Wave 3b was higher than 3a, but there’s no way to predict right now if a wave 3c will be higher still. The wave of new cases that began in the North this Fall is now receding for much of the country according to endcoronavirus, and the bulk of new cases are concentrated in the Southwest, East coast, and a pocket of cases in Oklahoma. LA County is continuing to experience an explosion of new cases, with 194 thousand in the past 2 weeks.

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, December 29th, 2020

New confirmed case numbers are starting to decline for California and San Diego County as well, but again, we may see a new Christmas related wave start this 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 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.

As we are tentatively seeing some improvement, remember that an epidemic is like a wildfire. When “containment” is achieved, diligence and caution is still warranted, since a change in the winds can cause a new flare up. We certainly saw this after Thanksgiving.

New UK variant: A new variant has arisen in the UK, perhaps in September, but began to be noticed in December. It has been given the useful but very uninteresting name of VOC 202012/01. VOC stands for “Variant of Concern”. The variant appears to have multiple mutations including one in the spike protein (N501Y) that may make it more contagious than the original version. However, it is currently thought to perhaps be slightly less virulent, but it may be too early to be sure. I have to confess that I haven’t read much primary research on it yet, and most of my current knowledge comes from radio stories and Wikipedia! I will study it more as its impact warrants!

Don’t fear, but be smart!
Erik

Case Update: December 21st, 2020; Allergic Reactions to Vaccines in a Small Number of Patients

This is a case update and I’ll also discuss recent news about vaccines and allergic reactions.Cases continue to rise dramatically in parts of the United States, particularly, the Southwest, the East Coast, and South. The Northern states, where the third wave began, are continuing to improve, some counties are getting new cases under control.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, December 21st, 2020
Graph is by me, from data collected from Johns Hopkins University COVID site.

California is doing particularly badly, with the highest new case loads occurring in 5 California counties in the top 10 counties for the country. LA County alone has 170,000 active cases (new cases in the last 2 weeks), more than 3 times that of the next county, San Bernardino 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. “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 Johns Hopkins University COVID site.

San Diego County is in 7th place for new cases in the country with 33,000 new cases. Cases continue to increase despite new restrictions on outdoor dining.

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.

I never go indoors without a mask on, but still frequently eat at restaurants outdoors and do a lot of hiking. I almost never wear a mask outdoors. I get tested nearly every week, and am always negative. Here in SD County, I’m noticing a lot of people wearing masks outside, and often get the stink eye from them when I’m not wearing a mask outside. Especially if there’s a breeze, I believe it is unnecessary to wear a mask on a hike! Data shows very few outbreaks occurring outside, at least in non-crowded environments. One Japanese article claimed a 19 fold smaller likelihood of becoming infected outside, and other articles saw no transmissions outdoors, according to an article in Science Magazine.

Allergic Reactions to Vaccines: As of this writing, 6 people have been reported to have suffered from severe allergic reactions after receiving a vaccine against the SARS-2 virus. This is out of 272,000 vaccinations given so far, or about 0.002% of vaccinations. The CDC has issued a guidance that those with known allergies to vaccines or injectable medications should not get vaccinated. Those with allergies to food, pets, venom, or latex are still safe to receive the SARS-2 vaccine. For those with latex allergies, know that most medical facilities have changed to non-latex gloves because of allergies to latex.

Mild allergic reactions such as site redness or pain are more common, but will resolve on there own within a day or 2.

I am currently encouraging the elderly or those with significant risk factors to get vaccinated when you can, and to inform your health care provider of your risk status so you can “get in line” for your vaccine.

Don’t fear, but be smart!
Erik

Case Update: December 12, 2020; Important news on Vaccines and ADE!

Here’s an overdue case update. Cases continue to rise for the US, California, and San Diego County. The timing of the current US peak makes it clear that the bump is directly related to the Thanksgiving holiday, starting less than a week after Thanksgiving, and after cases had started to come down. LA County currently has more that 100,000 active cases, more than twice the number than the next highest county, Cook County, the home of Chicago.

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.

New case peaks have left the Northern states and are now centered in the Southwest and Northeast.

Endcoronavirus County Level Map, December 12th, 2020

San Diego County now has 24,000 active cases, far higher that the 4,000 we had at the low point between peaks 2 and 3.

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.

More on ADE and Vaccines: Some potential very good news for me on the vaccine front. For months I’ve been warning about ADE, the phenomena that some viruses can be even more dangerous in a second infection than the first. Karen Parrott, a former colleague at Quest Diagnostics, often provides me with interesting COVID related stuff. This week she sent me a podcast featuring Paul Offit, the developer of the first Rotavirus vaccine and an author of many books on immunology and vaccine production. I am not an immunologist but he is. More importantly, he’s the first authoritative person that I’ve heard in the media speak at length on the ADE issue and how it relates to COVID. He claims in the attached clip (time stamped at 14:40) that the current vaccines do not appear to trigger the ADE pathway in animal models, and human trial subject never displayed the signs that ADE was involved in secondary exposures. This difference from SARS-1 and MERS may be related to the fact the SARS-2 is much less virulent than these other 2 viruses.

This makes me more optimistic that the vaccine will be safe from an ADE perspective. I won’t be able to get the vaccine for some time, but I am more willing to get it now than ever before. Several physicians I know are eager to get it as soon as it is available. This is great news!

In the interest of full disclosure, I will point out the some patients receiving the vaccine the UK have experienced some injection site irritation, especially in those with allergies. This is actually somewhat normal for vaccines, and appears to pass within a few days.

In addition, now that mRNA vaccines have been produced for the first time, future development of this new kind of vaccine should be even faster than this time!

Don’t fear, but be smart,
Erik

Case Update: December 4, 2020

Well folks, I’m disappointed to report that after a dip in cases, the confirmed case numbers are rising fast again. The timing clearly suggests that the rise in cases is related to the Thanksgiving holiday. The numbers really seem to have peaked a few weeks ago, but are back on the rise again in the US, California, and San Diego. The situation is still developing of course, so we don’t yet know how much of a rise we will see. I’m reporting this early to give you a heads up that this is happening.

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.

Don’t fear, but be smart,
Erik

Case Update, December 1st, 2020

Friends,
This is a case update. As I suggested last week, it appears we may be past the peak of wave 3 for now. New confirmed case numbers for the US continue to trend downward, and California and San Diego County numbers appear to perhaps have peaked as well. Tammy Stevenson was right last week to point out that holiday gatherings may produce some new outbreaks. New cases don’t appear for between 5 and 20 days, so we may still see some Thanksgiving related increases, but for now, the numbers look very encouraging.

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. “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.

The Northern states, where the 3rd wave started, are recovering, except perhaps for Michigan and Minnesota, and the peak of the wave is moving southward. Los Angeles County now has the most new cases in the country, surpassing Cook County (Chicago). Gallatin, Madison, and Carbon counties in Montana are all past their 3rd wave peak.

Endcoronavirus County Level Map, December 1st, 2020
New confirmed cases in Gallatin County, Endcoronavirus County Level Map, December 1st, 2020

Note: Since writing the above, several of my friends in the medical community have told me that they are not as optimistic as I am! While their info doesn’t contradict mine per se, they are expecting a spike in cases due to holiday gatherings. Just posting this in the interest of completeness.

Don’t fear, but be smart,
Erik

Case Update: November 24, 2020

This is a case update. We are continuing to see a rise in cases for the US, California, and San Diego County. However, there is a glimmer of hope. If you look carefully at the graph for the US (or just look at the red arrows), you’ll see that this Sunday’s new confirmed case number is very close to last week’s.

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.

With numbers varying so much every day, it can be hard to see trends. But I noticed some time ago the Sunday consistently had the lowest new case numbers of the week. If a Sunday’s number was higher than the previous Sunday’s number, we would have a bad week, but if it was lower, things were getting a little better. After several weeks of steadily increasing case numbers, Sunday number suggests that we may have reached the peak of the 3rd wave. Of course, this may not pan out, and I may be apologizing later for misleading you, but it looks good right now. Also, lots of extra people are getting tested right now before Thanksgiving, which will also add to the numbers for this week.

Also notice a few more orange counties in the northern states on the map of US counties. These are likely counties where things are improving. Peaks of new cases are moving south however.

Endcoronavirus County Level Map, November 24th, 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.
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.

So we can be optimistic while still working toward the end of the 3rd wave!

Don’t fear, but be smart!
Erik

Case Update: November 19th, 2020

This is a case update. The US continues to see a large spike in new cases during a 3rd wave. New cases appear to be centered in the northern states and around the Great Lakes, but more southern states are now experiencing new cases as well. The county with the highest new cases right now is Cook County, the home of Chicago. New confirmed cases in the US are now double what they were during the second wave. This is all likely being driven by colder weather causing people to gather indoors.

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, November 19th, 2020

California and is also experiencing a 3rd wave, just slightly higher in numbers than the 2nd 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.
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 County’s 3rd appears substantially higher than the 2nd wave. County Health reports that most known outbreaks are occurring in restaurants, especially those with bars, with the second most being businesses. The County is not reporting to the public what kind of businesses are experiencing outbreaks.

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.

Don’t fear, but be smart,
Erik

New Vaccines and ADE

Vaccines – Because of this week’s announcement about vaccines, lots of folks are asking me about it.  I’ll give you my thoughts.  I am not an immunologist, I’m a molecular biologist specializing in infectious disease testing, so my thoughts on vaccines are informed, but not expert.

As I’ve discussed before, I’ve been pessimistic about COVID vaccines, mostly because of the phenomena of Antibody Dependent Enhancement, or ADE (link below).  This is the phenomena in which some virus can use antibodies against a similar but not identical virus to infect the immune system and cause more severe disease.  As this relates to a vaccine, a person given a vaccine could gain immunity against virus very similar to the vaccine given, but less similar strains may still infect and cause more severe illness.  This has been my concern about both vaccines and the herd immunity approach. 

In the past few months, however, a trickle of known cases have come out about people who have been reinfected with SARS-2. Some of these patients have had worse symptoms, and some more mild.  It’s also evident that they are not being infected with the same strain they had before, but by a different strain.  If all this is true, then the ADE experiment is already being done.  And it looks like while some experience more severe illness, not all do, and reinfection appears to be rare, despite several circulating strains.

This week Pfizer announced that studies with their vaccine show 90% effectiveness in preventing COVID infection.  My hesitation with vaccines has always been about ADE.  It’s still not well known if ADE will play a significant role, but if it doesn’t, then perhaps there is reason for hope.

All medications and vaccines carry the risk of side-effects and harm.  However, I’m actually becoming cautiously optimistic about a COVID vaccine.

Some technical info about vaccines.  There are actually several kinds of vaccines.  Various developers tried different pathways to a COVID vaccine, and several kinds are in trials right now.

Killed vaccines – These are vaccines that have been deactivated or broken down into various parts and then injected into the body.  They cannot replicate and degrade in the body, so parts are attached to molecules called adjuvants that serve to boost their visibility to the immune system. 

Attenuated vaccines – These are live viruses that have been engineered to cause infection, but with no or mild symptoms.  Some are other viruses like Adenovirus which are symptom free, but produce viral proteins that your body can recognize and raise a response against.

RNA vaccine – This a brand new kind of vaccine that has been in testing for years.  Several SARS-2 vaccines are of this kind, and are the first potential viable candidates ever.  The patient is injected with a piece of RNA that codes for a viral protein. The RNA enters a cell and temporarily causes the cell to make the viral protein. RNA naturally degrades rapidly in the body and does not persist or permanently change the patient’s genetic material. This promising technique has the potential to generate new and more effective vaccines in the future.

Personally, I’m still taking a wait and see approach.  Vaccines will probably not be available to the general public for few months.  By then we may know more about how people are responding.

Don’t fear, but be smart!
Erik