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.

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

Don’t fear, but be smart!
Erik

Case Update, February 24th, 2021

This is a brief case update. Case numbers continue to drop in the US, California, and San Diego County. There was a small outbreak in Iowa this week. Numbers are low enough generally right now that we can see outbreaks in particular places!

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, February 24th, 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.
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.

For those of you in the testing field, reported SARS-2 tests dropped below 1 million tests yesterday.

Graph is by me, from data collected from Johns Hopkins University COVID site. This graph shows reported tests. Laboratories are currently required to report both to the ordering physicians and also report positives (without identifying information) to the CDC as well as county and state public health. Some labs have been late reporting to public health, which is why you see some days which have either a very high or very low number of tests.

Don’t fear, but be smart,
Erik

Case Update: February 18, 2021

Here’s a short COVID update. New confirmed cases numbers continue to drop for the US, California, and San Diego County. Endcoronavirus show the central part of the country mostly under control, with just a few counties with increasing case numbers. And as a bonus, we didn’t have a Superbowl related bump in cases! Wave 3 is almost over! But we still have significant cases, so continue to be diligent!

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, February 18th, 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.
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.

On a short non-scientific note, support local businesses whenever possible! Lots of people, including me, have been shopping at the big boxes instead of small businesses which are really hurting, so shop at small businesses as your local regulations allow!

Don’t fear, but be smart!
Erik

Case Update: February 10th, 2021

This is a case update. New case numbers continue to plummet for the US, California, and San Diego County. New case numbers are now similar to those in early November. Obviously, the number are still not zero, so we still have work to do, but we have good news. As an interesting side note, the endcoronavirus map of new cases reveals a little pocket of new cases spreading out from Austin, Texas! Other parts of the country are generally improving, and the central part of the country is doing particularly well.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, February 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.
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.
Graph is by me, from data collected from Johns Hopkins University COVID site. This graph shows reported tests. Laboratories are currently required to report both to the ordering physicians and also report positives (without identifying information) to the CDC as well as county and state public health. Some labs have been late reporting to public health, which is why you see some days which have either a very high or very low number of tests.

Of course, we just had the Superbowl, which I count as an American cultural holiday. We may have had some new infections associated with gathering in peoples homes. If so, we may start to see numbers coming up starting on Friday or Saturday. After Thanksgiving and Christmas, new cases started to increase a little less than a week afterward.

During the year, we’ve seen testing capacity come up slowly but steadily from just a few hundred a day when the CDC was trying to do all the testing themselves in March, to around 1.5 to 2 million per day in December ’20 and January ’21. Now that new cases are starting to come down, testing is just starting to head down as well. If you are a medical professional, especially in testing, you may begin to find it easier to buy pipette tips in the next month! We can only hope!

Don’t fear, but be smart!
Erik

Case Update: February 2nd, 2021; New Variant CAL.20C

This is a case update, and I’ll also talk about a new SARS-2 Variant, CAL.20C. New confirmed cases continue to drop in the US, California, and San Diego County. New cases are now at about the same level as they were in late November or early December. This is great news of course, but there are still lots of actively infected people around, especially in Southern California. So continue to be diligent!

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, February 2nd, 2021
Endcoronavirus County Level Map, February 2nd, 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.
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.

CAL.20C: You may have heard of a new strain of SARS-2 circulating in the LA area. CAL.20C was first discovered in July, but then was undetected for many months until October. By December, it represented 25% of new cases in the LA area, and was spreading to other locations. Like most of the new variants, CAL.20C is more infectious than previous versions, but does not appear to be more pathogenic. All viruses have a tendency, over the course of years or decades, to become more infectious and less pathogenic, and SARS-2 seems to be following this pattern as well.

Don’t fear, but be smart!
Erik

Case Update, January 27th, 2021, Anaphylactic Shock in 0.0011% of Vaccine Recipients

This is a case update. I’ll also briefly discuss some cases of anaphylactic shock in some vaccine recipients. The US, California, and San Diego County are all experiencing a continuing decrease in new confirmed cases! The center of the country seems to mostly have recovered from the 3rd wave according to endcoronavirus, and the coasts are improving as well.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, January 25th, 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.
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.

Anaphylactic shock in some patients: According to Paul Offit, in a YouTube interview (at 2:30 in the linked video), a number of vaccine recipients have experienced anaphylactic shock after being vaccinated. All vaccines carry some risk of this phenomena, but the COVID vaccines appear to produce this at about 11x the rate of the flu vaccines. This is about 11 patients per 1 million vaccinations, about 0.0011%. Dr. Offit thinks this allergic reaction is likely caused by Poly Ethylene Glycol (PEG), a component of many vaccines, also used in many other products, including Dr. Pepper!

The good news is that anaphylaxis is easily treatable using an epi-pen. If you are prone to allergic reactions, let your provider know before getting the vaccine.

Don’t fear, but be smart!
Erik

Case Update: January 20, 2020; New UK Variant in San Diego

This is a case update, and I’ll also write briefly about cases of the UK variant, VOC 202012/01, arising in San Diego County.

Cases have plateaued and even appear to be falling in the US and San Diego, and perhaps even in California. Hopefully now with no major holidays pending, cases will go down in a significant way. This is just the beginning of a downward trend, and we still need to be diligent. Just because we’re past the middle of the woods, doesn’t mean we’re out of the woods! There are still a lot of new daily confirmed cases.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, January 18th, 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.
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.

New UK Variant confirmed in San Diego County: Several weeks ago, a patient in San Diego was confirmed to be carrying VOC 202012/01, the new UK variant discovered in December. The patient involved had not been traveling, so the new virus is suspected to already be circulating in the public.

This new variant appears to be more infectious that previous versions, but does not appear to be more virulent. It also appears that vaccine will still work against VOC 202012/01. Precautions taken against the original SARS-2 virus are still effective, so continue to take your normal precautions including:

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.
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.

Don’t fear, but be smart!
Erik

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. You can also see a flare up in new cases in January, right after Christmas.

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, 2020
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, 2021
January 10th
January 18th
January 25th
February 1st
February 10th
February 18th

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