This will be on the shorter side too. Been attending an e-conference through the weekend and early part of this week.

Still no symptoms for the Most Popular 1st Grader Ever, and COVID contact jail wraps up mid next week.

–Ebola news: Not much, really. There has been no update on case numbers, which I am going to assume means no new cases, but give that another week or two to catch up. 11,000 or so doses of vaccine arrived in country this past week, and ring vaccination was started immediately. Given the small number of cases, known exposure event, and early and active tracing by Guinea, that strategy is a good one to start. Hopefully the lesson learned is to have smaller patience for cases that pop up outside the known rings to switch to a more geographic approach to vaccination. They are still sequencing samples from the known cases to determine which variant is responsible. Odds on favorite remains Ebola Zaire. If it’s not, that may actually get a little dicey, as the vaccines were designed against Zaire and have not been formally clinically tested against the other strains. In theory, there is enough overlap that there should be some protection though.

Coronavirus–

–Gradually thawing continues. Case numbers in most places are still well off the holiday highs, and falling still in most places as well. Variants of concern remain of, well, concern. Up to 46 cases of the variant first identified in South Africa in the US now. South Carolina has gone from 2 to 21 these past couple weeks. Since they are likely not sequencing every case, the true number is probably higher. Yet, South Carolina, like most of the nation, has total case numbers falling.

Again, give it about 4-6 weeks to see if any of these variants can build a critical mass.

–We have reinfection data out of South Africa, speaking of the variant first identified there! Sort of. South Africa reported this week that it has 4,000 cases (at least) of known reinfection. “Most of that” was attributed to the variant first identified there. The news outlets reporting this result from the South African health authorities claimed that a more formal report on the B.1.351 variant would be out today, with data on transmission, reinfection and severity. I have not seen that report anywhere yet, and it is closing in on tomorrow in South Africa as I write this. But I am sure it will hit the wires at some point.

–At any rate, 4,000 reinfections tells us something, but not enough. We can do some back of the envelope calculations in the meantime though. We know the variant was dominate by December and through January in South Africa, and we will ballpark 510,000 cases in that period by estimating the AUC of the Johns Hopkins daily case tracker for South Africa in that period.

South Africa has also had ~1,510,000 cases of COVID total, per Johns Hopkins numbers.

South Africa tests pretty vigorously, so that approximates the level of activity there (although again, you probably have some number of mildly symptomatic or asymptomatic patients not getting tested at all).

We will make the following assumptions (thus ensuring this model is -wrong-, but it may be useful for estimation):

1. We will -assume- that the 4,000 reinfections all happened in that early Dec-late Jan period.
2. We will -also- assume that -all- 4,000 reinfections were reinfected by SARS-CoV-2 variant B.1.351–although that may not be the case. Again, I doubt those were all sequenced (just because of time and cost to do that), but about 90% of the cases during that period were the South Africa variant, so we’ll just give the other 10% to the variant.
3. We will -assume- that the -other- 506,000 cases (510,000 Dec-Jan minus the 4,000 reinfections) were all new cases, and not reinfections.
4. We will -assume- that all South Africa’s 1,510,000 cases happened by the end of Jan period.
5. We will also assume that -all- of the patients previously infected with COVID were exposed to this new variant as it circulated in South Africa at high levels during this time.

So, we have 1,510,000 total COVID cases – 506,000 new cases in the Dec-Jan period. Thus, there were 1,004,000 previously infected patients who were exposed and potentially reinfected in the Dec-Jan period with this variant.

Yet, there are only 4,000 confirmed reinfections. That implies a reinfection rate of ~0.4%–on the lowest possible end. (much depends on how many of our 1,004,000 actually ran into the new variant during that period for your -true- denominator)

I cannot stress enough that our back of envelope is likely a -low- estimate. But it suggests that a sizeable portion, if not a sizeable majority of previously infected patients, may still be resistant to the strain first identified in South Africa.

For example, let’s assume only 1 in 10 of the previously infected were actually exposed to the new variant. That leaves us with 4,000 reinfections divided by 100,400 exposures, or a reinfection rate of ~4%.

That certainly does not doom the vaccine, or herd immunity, to failure.

These numbers, if they hold up in the actual report of South Africa’s data, suggest the variant they first identified may dominate new cases–it may be a higher, but still infrequent to rare, chance of reinfection. But that is not a reinfection rate that will move the current vaccination/herd immunity trajectory.

–I remain cautiously optimistic we are on pace to be largely medically contained by July. We will -still- be watching for the South Africa transmission and reinfection hard data (this time done by actual epidemiologists and not back of the envelope like me) and will -still- watch case velocity over the month.

–Speaking of vaccines, JNJ’s single shot vaccine is on pace, clearing an FDA review board. The JNJ vaccine is DNA for the spike protein in an empty adenovirus shell–only the spike protein gene is present, so the adenovirus that “infects” the cell cannot actually replicate. Since only the spike protein gene is present, and not the entire SARS-CoV-2 genome, the SARS-CoV-2 virus is not replicating either. Efficacy is not quite the same as the mRNA vaccines (which has been a trend for these adenovirus vaccines). That said, it is approximately equivalent to the single dose efficacy that Pfizer has been reporting with their vaccine (skipping the booster 2nd dose). The vaccine is easier to store, and again, is single dose, so would improve access to at least -some- protection in places where storage or getting back for a booster is difficult.

–Pfizer is also presenting data to the FDA showing their vaccine can be stored without the need for as deep a freeze, which would improve access as well, as the kind of freezer needed now is neither common nor cheap.

–210 million completed doses worldwide of vaccines this week and rising…

–Sick of coronavirus? Ready for it to be over?

No you’re not.

Not nearly as much as the flu is:

And that, ladies and gentlemen, is your -peak- flu season this year…

–Yes, I saw the report that showed that Florida (little restrictions, and little adherence to them anyways) had no significant difference in COVID cases or deaths per capita compared to California (heavy restrictions, much more strictly enforced). No, I’m not commenting on it, because we have gone over why you should ignore retrospective exercises in “finding data to fit your preferred political opinion on lockdowns.”

–Just remember that when it’s pandemic time, the lesson of the Black Death “Choose Your Own Adventure” is that your choice affects your outcome a LOT less than you think it does. Once the first case is confirmed in your town, you have already been exposed. Vaccine/herd immunity/highly effective treatment or bust from that point on.

–We’ll be back to societal pontificating that you’re probably not reading at some point, possibly as early as next week.

–Until then, your chances of catching Ebola are equivalent to the chances I would pass on an opportunity to dunk on Ohio State for losing a critical Big Ten game, at home, to Michigan this past Sunday.

–Your chances of catching coronavirus are equivalent to the chance that Hunter Dickinson already dunked on Ohio State though.

And yes, it counts for football this year too.

#BasketballSchool

<Paladin>