As reminders…

Alpha–Variant first identified in the UK

Beta–Variant first identified in South Africa

Gamma–Variant first identified in Brazil

Delta–Variant first identified in India

Omicron–Variant first identified in South Africa

Updating the chart above:

Ancestral: B.1.1.529 Omicron (and cousins)

Transmissibility: All the +

Immune Evasiveness: All the +

Vaccine Effectiveness: Check (for hospitalization)

Also as a reminder:

Monkeypox

–We mention this only because of the nature of the headlines about monkeypox in the last week. One was how the US “risks losing to monkeypox”, mostly over stoked concerns that we are not testing enough, and there are likely far more cases circulating right now than we currently know. One major Australian news outlet used this as its lede: “Killer virus spreads to new Aussie state as health officials urge calm.”

So this is here just to remind you that while there are definitely efforts to make monkeypox a thing, as a pandemic, monkeypox is not a thing. In the US, cases are still almost exclusively among middle aged men who have had sex with other men. Again, while I expect that to change, cases are few. The disease is NOT airborne, and thus remains difficult to catch (except in very close contact, like sexual activity), and is certainly not as transmissible as a damn coronavirus or flu. Nowhere are hospitals being threatened by overwhelming numbers of monkeypox cases needing treatment. In fact, most cases of monkeypox won’t need a hospital at all, other than for someone to say, “yep, that’s monkeypox you got there!” Out of ~6000 cases the WHO had registered as of last week, there have been a total of 3 deaths. Three. All in Africa. So this isn’t Ebola or the Black Death in terms of mortality risk either. In fact, 10 countries that previously reported a case as of last week have not had a new one in 21 days or more, which exceeds the known incubation period of monkeypox–their “epidemic” is already at an end.

Marburg

–Speaking of viruses with an actual, significant mortality risk, Ghana has two confirmed cases of Marburg virus. This is a cousin of Ebola, although generally not quite as deadly. That’s relative, though, as mortality is typically north of 40% with Marburg. Both of the confirmed cases in Ghana have already passed away. The WHO is mobilizing to help with testing. At press, there are no new reported cases, and I can’t find a good estimate of the number of possible close contacts they will need to trace and isolate to ring this, an actual, and significant infectious disease threat, off. Worth mentioning Ghana has had recent protests over inflation in food and fuel prices; how that may impact response is worth tracking too.

Coronavirus

–So to get back to the big pandemic, albeit still in late innings… We’ll be kind of bullet pointy this update, because this has been an exceptionally brisk work week.

–Around the horn, cases are still up in much of Europe. If monkeypox was not making fetch happen, at least in the US, the new hotness has been scare headlines over the impending wave of doom that is the BA.5 variant (apparently), and all its terrible features of terrible terribleness, and how your vaccines are useless against it (but you should still get vaccinated and boosted, because damn the mixed messaging).

The BA.5 variant, as we have been mentioning for several weeks now, is already well and truly active. While I agree again with reports suggesting that there are many more cases than being reported, most of these are mild, self-limited disease. Hospitals are not at risk; hospitalization has barely budged. And I would argue the official coronavirus case numbers are the best measure of that, since most of those will be reported from hospitals confirming an at home positive to hand out treatment for high risk patients, or the increasingly rare COVID case going in-patient. If BA.5 were going to kick off a new storm of cases in the US, it better get moving, because that should be happening already in the data. Otherwise, we are on target to dwindle off the BA.5 heavy portion by the end of the month.

In China, Macau has closed the casinos because of increasing positive cases there, and there is a very real risk that cases have already spread out of Macau. More “zero COVID” lockdowns seem likely there over the next couple weeks.

India has reported a new emerging variant, a more distant omicron cousin, BA.2.75. It has already been found in 6 US states, and is a solid bet to already be worldwide already. There are NO indications from India that there is any increased risk of disease severity. Most patients have 5 days of mild cold symptoms and that’s it. So while days are early, most signs again point to “more contagious, less severe.” And kudos to Indian health authorities for being as on top of it and transparent as South Africa has been.

–Been a couple weak sauce criticisms of vaccines and treatments this week. I ran into an article questioning the “Paxlovid flop” which is Pfizer’s acute COVID pill therapy and wondering why the US has spent billions on doses of the medication. The article correctly cites Pfizer’s data which lead to approval–90% reduction in unvaccinated and high risk patients. But then dings it for halting the study in patients with mild to moderate acute COVID disease, but normal risk–and this is why it is apparently a flop and a waste of money.

It’s not. While it’s true they did not show benefit in patients without risk factors for severe COVID, in the high risk patients we care most about, it absolutely DID show benefit. 90% reduction in hospitalization rate! And since this is the main pandemic threat, that’s still a pretty useful drug.

So while they criticize stockpiles of this drug, so far as I can tell from people who have gotten acutely ill with COVID recently who reached out to me, had risk factors for severe COVID, AND got paxlovid, they have been pretty happy. And I confirm from the complaints of the hoops they had to jump through that most, if not all places, are restricting it to high risk patients. As they should–based on the data the article itself cited!

I just don’t understand the thinking here. So because the drug doesn’t do much for patients already unlikely to be hospitalized, it’s a failure and a waste of taxpayer money–even though it clearly and significantly benefits at risk patients, of which there are MANY in the US? And we should what, pull it from shelves and demand money back from Pfizer? That’s nuts.

Instead, what they are already doing, keeping it available for high risk patients only, because they clearly benefit, makes… a lot of medical sense! And probably cost savings sense to the healthcare system, by reducing the risk of “bed’s taken” and all cause mortality, by keeping high risk patients out of the hospital by treating their COVID effectively and early.

Guess they couldn’t find something else to get click-baity about? Have they not seen this week’s inflation numbers?

–Anyways, the other dubious one comes via a UK reader who sent along the link to the NHS’ data of COVID specific mortality in vaccinated and unvaccinated patients broken down by age and 1 dose/2 dose/2 dose plus booster/time from vaccine or booster etc. They did not send the article they ran into, but asked me to take a look at that data because whatever they found was claiming that it showed the vaccines were not as efficacious as claimed. I will admit that due to time constraints, I did not take a long look, but my guess is that whomever our UK reader found was looking at raw numbers of vaccinated versus unvaccinated only. When you look at the 80 year olds, for example, the number of deaths due to COVID totaled in all the vaccinated groups are about the same as deaths due to COVID in the unvaccinated groups.

“Aha! Clear proof the vaccines are not working! There should be LESS deaths in the vaccinated group!” I hear you say, Hypothetical Reader Who Clearly Wrote Whatever Article My UK Reader Found.

Yeah, not so fast homie. The problem with looking at the raw numbers there is that there are about 6 times as many vaccinated 80+ people in the NHS data than those without vaccination. So if the vaccines were really doing nothing, deaths from COVID specifically in the vaccinated group should be 6x higher than the unvaccinated. That they are ~the same means that there is an about 6-fold reduction in COVID specific deaths from the vaccines. And that’s before confounders, like patients with high risk co-morbidities probably being the ones more likely to be vaccinated.

So my guess is whatever rumor was flying in the UK, it was someone who looked at the raw without adjusting for the number of patients at risk in the time period vaccinated/unvaccinated, and drawing an inappropriate conclusion. FWIW, below about 40 in that data, it’s not even close on the raw numbers. Nearly all COVID deaths are in the unvaccinated, even before adjusting for population size differences. Vaccines a CLEAR winner.

At best, it means my ~10 fold reduction from the published scientific studies in terms of risk of death/hospitalization with the vaccines is a little rosy, and may be somewhere between 5x and 10x. But it’s still a lot, and clearly in favor of vaccines.

–Will the vaccine stop your mild cold/flu from an omicron or its cousins? Probably not. Nearly worthless in stopping breakthrough infections at this point.

–And anecdotally, I know of no first line responder (pulmonary, infectious disease doc, ER doc), who doubts the efficacy of the vaccines in reducing the risk of death among high risk patients especially. At least none I have spoken to, anyways.

–In other news, pre-print data out of Qatar (available here) is important for the following observation:

“Effectiveness of primary infection against severe, critical, or fatal COVID-19 reinfection was 97.3% (95% CI: 94.9- 98.6%), irrespective of the variant of primary infection or reinfection, and with no evidence for waning. Similar results were found in sub-group analyses for those ≥50 years of age.”

cited from Chemaitelly et al., pre-print of “Duration of immune protection of SARS-CoV-2 natural infection against reinfection in Qatar” last accessed 13 Jul 2022 at link above.

That’s a long way of saying that after you have caught COVID, no matter the variant, there was ~97.3% prevention of severe COVID in subsequent reinfection. Or if you have had your omicron breakthrough, chances just got much, much, much lower that COVID will ever hospitalize you, even on reinfection. That they also found no evidence of waning in this protection from the main pandemic threat is consistent with the “more contagious, less severe” trend as well as arguing that we are at, if not very, very close, to a level of herd immunity to the pandemic threat of hospitalization rate.

Will COVID still cause annoying cold and flus into the future? Probably. New omicron-ish cousins will keep coming until the virus really and truly runs out of ways to shift its spike protein and still infect human cells. But with durable protection from severe COVID, there is not much of a pandemic threat from those.

Before you ask me, Hypothetical Reader, if that means I am close to calling it, let me remind you of this:

Socioeconomic

–Super brief this week, but you can track headlines like me. Protestors in Sri Lanka invaded the president’s home, and the president ultimately fled the country to the Maldives in a military transport. He named the Prime Minister the new head of government, and that guy is getting the same treatment from protestors already.

Sri Lanka will not be the only country with these kinds of challenges.

–Germany has seen limits on hot water use, some energy restrictions on residents by large apartment complex owners, and is quietly building warming shelters for the winter. It is unclear if the LNG from Russia will flow to Germany again once the Nordstream pipeline supplying it is back “operational” from maintenance in about a week. Gazprom in Russia is already making excuses for why that might not happen.

–Dutch farmers were joined by firefighters in on going protests blockading streets over the agricultural legislation changes we mentioned before. Germany farmers have also met with Dutch farmers in solidarity.

–Going to continue to be an interesting year in a run of them, lately…

Chances are:  

–Finally, your chances of catching monkeypox depend greatly on your sex life. The closer that is to something Prince or Rick James would sing about, or something that begins with “Dear Penthouse…” the better your chances. Calculate amongst yourselves, and fergodsake, DON’T send me details and ask me to calculate for you.

You know you who are.

–Your chances of catching Marburg are equivalent to the chances Russia turns the gas back on while war continues with the Ukraine, and sanctions are still applied to them.

–Your chances of catching coronavirus are equivalent to the chances you will watch this and, as I did, wonder what the hell happened to your fully detachable, clear, and intelligently stored door panels for your fruits and vegetables… among other features of this fridge from the future, in the past…

<Paladin>