Ebola:

No new cases this week either, and the WHO has officially declared the outbreak over. That said, even they cautioned that with some tracing difficulties, there may still be transmission chains in some of the less accessible parts of Guinea that may be active. But with no new confirmed cases in a very generous overshoot of the usual incubation period for Ebola, chances of this are low. Not zero, but low.

Given the pace of Ebola outbreaks in the early portion of this century, though, we will probably be back to updating Ebola at some point down the road.

Coronavirus:

–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

–Around the horn, Indonesia is the next high population country with sharply rising cases. This has not made the news yet, but expect it to in the next couple of weeks given their current trajectory. This almost certainly going to be a combination of Delta variant and slow vaccine rollout given the population size (currently, only 4.67% of the population there is fully vaccinated).

As a reminder, Indonesia is the 4th most populous nation in the world, with a shade under 300 million people.

In the UK, new cases may be leveling a bit–check back next week to confirm the near term trend. New cases in Russia are definitely leveling off, and South Africa continues to see high levels of transmission with epiforecasts.io predicting a continued climb in new cases for the next several weeks. South American nations that had been flaring recently are also leveling off. In short, your local results will vary.

–In the US, cases overall continue to trend down. You are seeing rumblings of very localized case increases, as we expected. For example, saw an article today where hospitals near Branson, Missouri have seen an uptick in hospitalizations. They give an eye-popping 160%, but this is fortunately the percent change of a small number to a slightly less small number, and expressing as a percent change rather than absolute change looks more concerning. They are not expecting hospitals to be overwhelmed in Branson, right now. But they are worried that the increase might be sustained, especially in the local community, as travel continues to heat up and only 25% of the population in the region has been vaccinated.

The current risk in the US is the contagiousness of the delta variant. They have confirmed cases in Indiana, for example, but the numbers have not exponentially increased (either in total SARS-CoV-2 cases or those attributable to delta). The trend line over the next couple weeks will tell the tale. So far, though, vaccine and previous exposure resistance appears to be slowing the spread of delta through a decent portion of the US.

–China is anticipating extending border restrictions for another year. Given their advertised vaccination rate, and advertised success of Chinese manufactured SARS-CoV-2 vaccines, this seems unusually cautious. Caveat lector.

–Speaking of vaccines, the CDC formally linked myocarditis to the mRNA vaccines earlier this week, and FDA announced today they will be adding a warning to the label reflecting the increased risk of this side effect to the Moderna and Pfizer vaccines, particularly for males age 16-24. Again, all cases have responded to treatment, and the reaction, if it occurs, typically occurs after the second shot. However, there are a few where chest pain and shortness of breath have occurred after the first shot too. If you or others you know have this reaction with a few days of the mRNA vaccines, you should get evaluated by a physician.

The CDC estimates the risk of this complication at 19.8 cases per million doses of Moderna vaccine and 8 cases per million doses of Pfizer– so again, lottery level odds that this will happen to you or someone you know. That said, those statistics are based off of total shots out, and NOT total shots out in the most at risk cohort (males 16-24). Doing some back of the envelope, ~22 million males are age 16-24 in the US, and about 1/3rd of them have received both doses of the vaccine, or ~7 million. If we attribute all 1,226 myocarditis/pericarditis cases reported to CDC thus far to males age 16-24 (knowing that not all of them actually occurred in this demographic, but this gets our “at worst” estimate), that puts us, at worst, of 175 cases per million doses in males 16-24. Or a 0.017% chance of myocarditis/pericarditis for the most at risk group.

And before you ask, no, that’s not too far from the risk of death from COVID for that age cohort, assuming average height and weight and lack of significant medical history. But that is less than the chance of severe COVID in that group that would require ICU hospitalization–and again, we are assuming the worst possible case for rate of myocarditis and pericarditis in males 16-24. The actual rate of this side effect will be less than our calculation, making the benefit for damning the torpedoes and getting the vaccination higher.

–More optimistically on the vaccine front, word this week that Phase 2s will be starting soon, looking at mRNA versions of flu vaccines. If those are successful, the should result in a more flexible flu vaccine that can respond to an outbreak in progress–a quantum leap forward against what is still the most dangerous infectious threat to humankind (from a future pandemic perspective). Note my employer is NOT involved in these.

–In other COVID news, Ivermectin keeps getting more traction in the popular press, both for Twitter censorship of those advocating its possible use, as well as claims about its effectiveness. I thank you for your understanding that I will be circumspect in choosing my language here, and stress that this is my opinion only, and has not been reviewed by anyone, work or elsewhere. All treatment decisions should be based on a discussion between you and your healthcare provider for your individual needs, and all medications used should be done under the supervision of a licensed healthcare provider and in accordance with labeled indications whenever possible.

So, in my humble opinion, some of the claims around ivermectin exceed the available clinical evidence. That said, there are computer generated reasons to believe, as computer simulation suggests that Ivermectin should be able to fit itself essentially in between the ACE2 receptor and the SARS-CoV-2 spike protein. Studies in petri dishes show that ivermectin can reduce replication of SARS-CoV-2. Clinical studies have been a mixed bag. The trend has been in favor of ivermectin, but none of the studies done so far have, in my opinion, been large enough or rigorous enough to be definitive.

You can find a summary of the key ones, according to the NIH anyways, here–all in one handy table.

Here is a recent interview with a Canadian scientist working on a large study re-purposing many different possible, approved drugs for treatment of COVID, including Ivermectin. This is the definitive study, in progress. The long story short is that ivermectin has not failed, but they are still accumulating patients and data to know if it works, and how well it works. 

However, the entire interview is worth a read, because Dr. Mills does not need to be quite as circumspect as I do.

–Finally, on the conspiracy front… This one is finally getting some mainstream headline coverage today, which is good.

The long detailed story made short is that a Fred Hutch researcher found the ghosts of SARS-CoV-2 sequences obtained from Chinese patients early in the Wuhan outbreak which had been inexplicably deleted from online international databases of SARS-CoV-2 sequences. The deletion of this important epidemiologic data occurred despite these specific sequences being mentioned in published reports from China around that time, and, coincidentally (we’re sure), shortly after an order from the CCP requiring central review of all statements made on SARS-CoV-2 and its epidemiology in China. Thus, our intrepid Fred Hutch researcher knew these particular data existed at one point. He found the raw files again anyways–solely because those databases had backed up to the Google cloud, and he could get the backups off the Google cloud server.  He asked the curators of the repository (based in the US) about the deletion and got no response. UK media organizations also asked and were told that data submitted to the repository can be pulled at the depositors request, although there is still no comment if the Chinese researchers who uploaded it made such a request. That’s usually if there is a problem with the data or consent for the data–since they had been published previously, those problems are unlikely, to paraphrase our Fred Hutch author.

He has now also copied them to the Wayback Machine–just in case they get should happen to get lost again.

Analysis of those samples by our hero shows that the Wuhan Seafood Market was most likely NOT the origin of the outbreak.  However, I would argue that his evidence shows that Wuhan may not be the source of the outbreak either, as multiple strains were clearly circulating in the city already by the time the Seafood Market exposure event flared.  Yes, Virginia, that is a strike against a lab accident hypothesis too. Instead, Wuhan may just be the place where the outbreak concentrated in enough patients to finally get noticed as something serious and “not flu”.  Alternatively, SARS-CoV-2 originated in Wuhan earlier than thought, and was circulating more heavily within Wuhan (and then spreading to other regions of China) before the superspreader event in the Seafood Market flooded the hospital with symptomatic cases.

The pre-peer review print is here in full: 2021.06.18.449051v1.full.pdf (biorxiv.org)

Those of you with a medical/scientific background are encouraged to read, not only for the solid analysis, but the truly artful way the strident criticism of the “sus AF” (as the kids say) removal of these sequences from the curated databases is handled in polite scientific literature form.

Or for those less fluent in science-publishing-ese:

–Speaking of not seeing bullshit, your chances of catching Ebola this week are equivalent to the chances that the “invisible sculpture” sold by an Italian artist for, and I am not making this up, $18 grand, this week is an actual invisible sculpture that one might trip over, despite the Italian artist’s certificate of authenticity.

–Your chances of catching coronavirus are equivalent to the chances that I am something of a sculptor myself, and quite skilled with an oeuvre that is also invisible to the naked eye. My masterpiece is not only larger than the Italian work that recently sold, but the culmination of fevered inspiration and craftsmanship as I channeled all the existential angst, all the hope, all the sorrow, all the small moments of cheer and connection this past year into its creation. I call it “Breathtaking Naivete“, and it is available for sale, complete with a NFT of the only panoramic picture of the sculpture in its fullest expression, and, of course, a certificate of authenticity.

Serious offers only. No lowballs. I know what I have here.

And that’s your chances of catching coronavirus this week in most places in the world.

<Paladin>