Short Version Please

02/03/2021

Recently you heard the CDC director claim that cases were heading back up and that she was worried.

She appears right now to have been wrong.

What happened was two-fold:

1) A stabilization in the growth rate at about 0.25% for a period of about 4 days.

2) An apparent "spike" caused almost exclusively by southern and southeastern states where testing was interrupted by the winter storm.

The chart below displays this effect. Note that the overall slope of change is still negative and has been for over 30 days.

Hospitalizations continue to decline. Current prediction is to be below 40,000 in 5 days and below 30,000 in about 18 days at current deceleration rates.

New York and South Carolina are the only states in my data with higher-than-normal virus numbers based on a non-pandemic estimate of viral transmission.

Have a nice day :)

20/02/2021

Hello. I hope everyone is as well as possible after the Central Plains fiasco this week. Here is a data update for you.

Please note that my data site for hospitalizations will cease operation at the end of the month. Thus, starting in March, I will not have hospital data.

Things continue to slow. A lot of states are also showing signs of stabilizing at low counts, which we would expect as the virus will not be exterminated, only managed.

Have a good weekend.

17/02/2021

I know if you are in the South Central US, you could probably care less, but we are on pace right now to be below 45,000 hospitalized by the end of February and the doubling rate for new cases in the US is almost at ONE YEAR right now.

At least it's a little bit of good news.

14/02/2021

11/02/2021

By the way...anyone notice that there wasn't a "Christmas surge"?

Here are the latest data. Hospital census is falling by about 2% per day.

10/02/2021

Hey everyone.
I'm putting together a new series of podcasts on "faith". But it probably won't be like others you've heard. I'll let you know when the episodes are ready!

10/02/2021

Here is your case/hospital acceleration chart for 9 February 2021. At the current rates, IF THEY ARE MAINTAINED, we should see national hospitalizations at about 51,000 by the end of February and national new cases between 57,000 and 82,000 per day.

09/02/2021

Science thinking lesson time!

The recent headlines about the AZ-Oxford vaccine in South Africa being virtually powerless against the B.1.351 variant require some deeper thought. The first reaction of the media is to claim that the variants are smarter than the vaccines. Let's see why that's probably not true.

A larger study conducted by Johnson & Johnson recently showed that the protection rate was more than adequate, and a portion of that sample came from South Africa. It even included some people who were HIV-positive. Why is that important?

The J&J vaccine is the SAME TECHNOLOGY used by AZ-Oxford. Same adenovirus carrier, same everything, as far as I can tell. While they come from different manufacturers, the end product should work in the same way.

So why does J&J's vaccine work well, but AZ-Oxford's does not? I don't see anyone asking that question. What are the possibilities?

1) The recent South African study is flawed. This is entirely possible since it has not been peer-reviewed. It could be a statistical problem, but most likely if there is a flaw, it would be in the methodology, such as the selection of the sample or the administration of the vaccine.

2) The J&J data are flawed. This is possible, but since J&J's data are similar to what Moderna and Pfizer are showing in their work, it is less likely.

3) Something about the AZ-Oxford vaccine is flawed. The AZ-Oxford vaccine has been plagued with problems throughout its development, even having to stop operations in the UK for a bit. It also had to stop its clinical trials because it couldn't get the dosages right. Maybe the AZ-Oxford vaccine is just poorly made.

4) The two studies are asking different questions. Maybe the South Africa study and the J&J study were measuring the vaccine effects differently. Without reading the studies themselves, we don't know.

In short, something stinks here. If I had to guess, I would guess that the recent AZ-Oxford study probably means that the AZ-Oxford vaccine never really worked, not that the variants are winning. Let's see how it all plays out.

22/01/2021

Good Friday. We are nearing the end of January. I suspected that our virus numbers would be improving by now, and they are. Perhaps not as rapidly as I thought, but we're getting there.

Hospitalizations nationally are negatively accelerating (going down). While there are a couple of resistors (SC, GA, VA), most states are beginning to see decreases in actual counts as well.

The case growth data is much slower now. A month ago, the US was set to double at a rate of about 45 days. The doubling rate in the US is now 80 days and slowing. If cases decline, so will hospitalizations and deaths in turn.

Find your state in the charts below for more information. Have a good weekend.

21/01/2021

A friend of mine sent me a Yahoo News article on how the South African variant (N501Y.v2) is a poor match for the convalescent plasma generated by previously-infected persons. The article raises a false flag, implying that the vaccines will probably not work because of this.

Wrong. As usual for news about the biology of this virus, this is much ado about nothing.

Convalescent plasma is monoclonal; it is a match to the spike protein from the actual virus that created it, because that was the virus that those peoples' bodies were fighting. It is like a key that works only in a single lock; the key might fit a different lock, but it won't turn, right? Thus, it is unsurprising that the plasma does not work. If it did work, then we would not expect to see re-infections from this virus or any coronaviruses, ever. But the average adult gets 3 of them every year - they're called "colds".

So why is the vaccine different? The mRNA in the vaccines are polyclonal. A "skeleton key" metaphor would be a little too broad, but the point is that these keys can fit many different locks as long they are roughly similar in the right places. These "places" on the virus are the S1 and S2 regions, which contain the receptor binding protein. The rest of the virus' genome is largely irrelevant.

So it would take a significant number of mutations in the S1 and S2 regions of the virus genome to render the mRNA useless. BUT - evolution will reject mass mutations in these areas because many of them will reduce viral fitness; this is called "conservation". If these regions mutate too much, those regions won't work and the virus cannot infect at all, and so evolution would not select for that.

I have conferred with a couple of virologists on this that work in veterinary medicine (cows get CVs all the time), and they are certain that the odds of the virus changing to the point of outmaneuvering the vaccines are very low due to evolutionary conservation of key parts of the genome. And even if that unlikely scenario were to happen, the mRNA could be revised and new vaccine rolled out in a matter of weeks.

The bottom line is this - now that the mRNA vaccines are in manufacture, the virus will lose. It simply cannot mutate fast enough or in the right places enough to win this race.

18/01/2021

Good morning. I want to share some good news with you.

This is a chart of growth in hospitalizations and cases for the US. For the first time in quite a while, hospital growth in the US is flat and on the way to a negative trend.

This week is critical. Hope and/or pray that the trend continues.

18/01/2021

Episodes of my walk through Acts 17 are posting on my podcast every 3-4 days. Please give them a listen! Thanks.

16/01/2021

Welcome to the weekend!
I see promising trends in the data right now. It's still early but I'm encouraged.

These states are sorted by: 1) overall growth rate right now, and then 2) doubling index (rate of increase/decrease). Doubling is now expressed as a percentage of days rather than raw days so that all states can be compared.

The first thing to note is that among the high-growth states, the trends are mostly flat. Texas has the strongest upward acceleration right now in this group, and it is not that strong. That's a good sign.

Second, note that no state is above 1.6% growth. That compares to several states being greater than 3% just 60 days ago.

Third, these data include Thursday/Friday data from this week, typically the strongest count days.

Finally, hospital census continues to slightly decline, even in states like CA and TX. There is still a LONG way to go, but any improvement is worth a note. Remember - census will decline if the number of admits does not equal the number of discharges/deaths. So while we like to see the number go down, don't forget that death is a part of that.

I hope you have a great weekend. Let's hope next week continues these trends in the data.

15/01/2021

Hello all - I wanted to offer a glimmer of light in this virus tunnel. There is a pattern in the national data now that I've seen before.

The chart below tracks the growth of cases against the hospital growth data. We ideally want the orange line and the blue area to be below the "zero line", but we also want to see a negative trend (top left to bottom right).

With the exception of the last few days (which is probably the result of data equalization after the Xmas holidays), note the general direction of the orange line. While there are waves, the peaks are getting smaller and the troughs are getting deeper. Also notice that the hospital data is moving in the same direction, albeit slowly. The time frame of the trend I'm pointing out here is about 60 days.

I last saw this pattern when the "summer burst" hit in Texas, Florida and elsewhere. It marked the beginning of a continued downturn in growth. So let's cross our fingers that it means the same thing now.

13/01/2021

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13/01/2021

Hello Kids!
Time for the latest edition of Coronavirus Variant Theater!

OK, so it's starting to get a little confusing now, because we are sequencing so many samples now after B.1.1.7 made the news in the UK that we are discovering new variants that may not actually be all that new. So let's try to get things sorted.

The mutations that have gotten everyone's attention are located on the part of the virus that attaches to host cells. This is one of the spots that antibodies will attach to on the virus - not to block it, but to mark it for immune response. And of course, it is the link between the virus and us. Here are the ones you might hear about:

N501Y - Asparagine has been replaced at site 501 with tyrosine.
This substitution occurs in both the UK and South Africa variants. Preliminary data suggests that N501Y slightly increases the strength of the bond between the virus and our cells, which would increase its replication rate. As of now, it does not appear that N501Y has any impact on severity of illness, and early data suggest that it will not reduce vaccine effectiveness.

K417N - Lysine has been replaced at site 417 with asparagine. This substitution occurs in multiple variants, including the B.1.1.28 clade in Brazil which has been connected with re-infections. This mutation also may increase receptor bond, but it is unknown right now. No data suggest that the mutation increases severity of illness or reduce vaccine effectiveness.

E484K - Glutamate has been replaced at site 484 with lysine.
This is the one that is currently generating the most concern among scientists. E484K is also suspected of helping to increase bonding strength and replication rate, but there is one study that also suggests that E484K "MIGHT" reduce vaccine effectiveness IN A MINORITY OF PEOPLE.

It is VERY IMPORTANT to note that the vaccines are polyclonal; they aren't manufactured to attach to JUST the spike protein or only at the sites where these mutations have occurred. Even if the virus mutated to the point where the vaccine begins to diminish significantly in effectiveness (which is VERY unlikely), vaccine scientists have said that "re-tooling the vaccine" to the new receptor site structure would take less than 6 weeks. Now that the vaccine formulation is complete, tweaking the mRNA payload is really not a big deal.

These random mutations have been selected for by evolution because virus copies with them have been more successful at replicating compared to viruses without them. That is all that is happening. The vaccines generate strong immune response to all variants so far AND these mutations will have no impact on T-cell or innate immune response.

So to sum up, these variants are worth watching and studying, but they are NOT worth becoming panicked about.

Questions? Let me know.