Ebola:

–The only major change from last week is the number of cases.  Now at 106 confirmed, may be closer to 112 by today.  Bright spots of fairly linear growth in known cases and no spread outside Equateur province remain.   Contact tracing percentages got worse, probably because they do not have enough trained boots on the ground and those that are appear to still be on strike.  They are starting to give more confirmed patients Ebola specific treatment, but not a lot of clarity as to what they are actually getting.  Mortality rate remains a shade under 40%, still on the low side for Ebola.  Expect this paragraph to look pretty similar next week too.

–In best of times, worst of times, a couple weeks ago the WHO declared that Africa was finally free of wild polio virus.  Last week, however, the WHO declared that the current polio outbreak in over a dozen African countries is all due to a polio vaccine used to eradicate the wild virus.  Polio vaccines come in two broad flavors, the Salk vaccine and the Sabin vaccine.  The Salk vaccine is dead polio virus, but must be injected.  The Sabin vaccine uses attenuated strains (weakened but still live polio virus), but can be given orally.  Three oral doses of the Sabin vaccine appears to lead to longer immunity to polio.  In the US, you are typically getting a Salk-style vaccine, with dead polio virus.  The Sabin vaccine, which is quite commonly used and a mainstay in the various polio eradication efforts in the world, has a rare but known possibility that the weakened virus will mutate and be weak no longer, causing some full blown polio.  This is what happened in Chad in late 2019, and is happening now with some of the more recent cases of polio virus in Africa.  While there are only a few cases of full blown, paralyzing polio, there are likely other cases that are not as severe–about 72% of people won’t even notice they had polio. 1 in 4 will have flu like symptoms and then a minority of people will get the central nervous system effects that polio is famous for. 

Symptom and severity breakdown sound familiar?

Anyways, if the mutant vaccine strain gets into places where there has still not been a lot of vaccine penetrence yet, it will find more hosts.  The concern now is that some of the populations with the mutated vaccine strain of polio are pretty mobile, and may spread it to places that are not at herd immunity from vaccination.  And then efforts at eradicating polio might have to begin anew.  We won’t monitor this terribly closely, because it should be a simmer and then dies out as polio as a whole has a lot more trouble finding susceptible hosts due to the success of polio vaccination campaigns.  But figured it was worth mentioning since the news hit the wires this past week.

Coronavirus:

–Aaaaaaannd it segues nicely into coronavirus updates this week, because vaccines and vaccine concerns have been prominent as well.

–First off, over the weekend, the Lancet published results of two open label phase 1/2 studies of ze Russians vaccine (“open label” just means everyone knows, researchers and patients, that they got the actual vaccine–no placebo control or randomization).  The strategy of the Russian steppes was to take adenovirus and hollow it out to carry SARS-CoV-2 proteins.  Adenoviruses are a different family of virus, but do also cause common cold, and have some unique features that make them a popular choice for this kind of “recombinant” strategy–they are easy to hollow out and get to carry other molecules of interest.  The common vaccine strategy in the West so far has been mRNA vaccines, as we discussed in a previous update.  There, the strategy is to provide the code for a SARS-CoV-2 protein to your cells, which make the protein, and your immune system learns to fight it.  In ex-Soviet Russia, virus carry protein to you.  Is different virus, sure, but is not capable of replicating, as SARS-CoV-2 part is incomplete, and adenovirus is different virus entirely. SARS cannot “run” its machinery. 

While the numbers of patients involved are small, the vaccine looks good based on these reports.  No significant adverse events (recall the published mRNA vaccines had a lot of fever, muscle pain, and body aches at the higher doses that they may not be going forward with), and the doses used got an antibody response at titers higher than known COVID patients with detectable antibodies.  Unlike some of the mRNA vaccines, T-cell response to the Russian vaccine peaked at day 28, while antibodies formed earlier.  At least one of the mRNA vaccines had SARS-CoV-2 specific T-cell response earlier than the antibodies, IIRC.

So, as hopeful as any of the mRNA vaccines at least.  Several of the mRNA vaccines are in Phase 3, including one we will get to shortly.  Of course, Putin is ready to roll on the Russian vaccine–some other countries have requested access as well.  Not sure if there is a Phase 3 of this on going in Russia or elsewhere, but more patients to assess safety at least would be nice.  No show stoppers so far, but these are not large studies published in the Lancet.

–Speaking of the mRNA vaccines, the Oxford/AstraZeneca mRNA vaccine announced a clinical hold on its Phase 3 result due to an undisclosed adverse event earlier this week.  That means they will not enroll any new patients until a determination is made on how likely the treatment caused the adverse event.  Since these coronavirus vaccines will be the first of the mRNA vaccines, depending on the nature of the event and if it was likely caused by the vaccine, the other mRNA vaccines may draw similar scrutiny in their clinical trials.  This will be something to watch going forward.  If the patient was merely spectacularly unlucky and the vaccine had nothing to do with it, the trial should resume shortly.

–In terms of spread and new cases, Europe has passed the United States this week for most reported new cases.  The US is again largely back to a sea of green on the Johns Hopkins “Did States Flatten the Curve” tracker, although Idaho is getting a little frisky.  Despite the green, Rt calculations at rt.live are not particularly shifted from last week, with most states hovering right around an Rt of 1.  That is a flat curve, at least.  In the US overall, daily new cases continue to fall.  The CDC’s COVID-NET weekly summary of hospitalizations shows that hospitalization rates continue to fall as well.  Deaths continue to fall.

Again, very different situation from March/April here in the States.

Around the world, India and Argentina continue to climb through their first waves.  China has reported another of the rare re-infections with COVID.  Sweden has a slight blip that we will watch, but is still pretty much low on the deck in terms of new cases.  That said, Sweden does have one of the lowest rates of testing in all of Europe–but one of the highest positivity rates.  They limit the test to the symptomatic or those very likely to have SARS-CoV-2, and I would say their numbers are an accurate measure of clinically significant SARS-CoV-2 cases.  And those are still much lower than their first big peak.

–Also again, you will be able to vote safely in person in November with the way the numbers in the States are right now.  Not even counting sports teams have announced opening their stadiums to be polling stations to give the cities polling stations with greater social distancing.  If you still have concerns about social distancing in lines on election day, you have options that don’t involve the US mail.

Given that California discovered a ton of USPS mail just dumped and abandoned this week, a non-USPS dependent option may be preferable.  I know you want your vote to count this year!

Many states offer options for early in person voting.  For some of those, you do still need to get an absentee ballot and bring it in.  Early, in person voting may save you line exposure if you are worried about that for yourself or others in the time of coronavirus, and be a safer option.  One that ensures your vote is counted, on election day, safely and securely.  You can find a bunch of useful links here on all of this:  https://www.usa.gov/absentee-voting

Those of you living abroad, yeah, you’re still going to have to use Colt Crockett.  Tough to do the whole in person thing across the oceans.

–No, nothing on the Woodward/Fauci/Trump he said she said they said about who knew what when from whom and why from earlier this week.  SARS-CoV-2 doesn’t care, and neither do I.  Besides, I’m old enough to remember when popular media opinion was Trump was being too serious about coronavirus, if not discriminatory, by banning flights from China.  And then was not taking coronavirus seriously enough without ever harsher lockdowns.  Regardless, you can go back to updates  in the archives for my take on what was done right and what was done wrong at the time–just realize that’s all my personal opinion.

Besides, every country, no matter their strategy, has been hit. 

The Black Death got to England.  The Black Death will always get to England.  Or put another way, pandemics are going to pandemic.  That’s one of my takeaways from this.  The moral of the Choose Your Own Black Death Adventure rings true from the pages of history–once it’s out, you’ve already been exposed, and what you do or don’t may not change that much.
The better question is not what persons, but what systems, and what institutions, were wanting in a time of crisis.  People come and go.  Those are what need to be fixed.

–Updating other stories, remember wayyyyyyy back when (like, SEVERAL months ago, or in 2020 time, ~37 years ago), the CDC was doing mass antibody testing to see how many total exposures there have been at key hotspot cities (at the time)?  That data is rolling in.  Seroprevalence unsurprisingly shot up in hard hit places like NYC after March/April.  A key takeaway from this data is that antibody positive versus confirmed positive cases consistently suggest 7-12x more infections out there than were captured with positive tests.  Further, recall from previous updates that the less symptomatic you are, the less likely antibodies are to be detectable.  The 7-12x higher based on the discrepancy between PCR and serology is likely the low estimate.

With 6.39 million confirmed cases, seroprevalence data thus suggests somewhere between 44.73 to 76.68 million Americans have already been exposed to SARS-CoV-2.  On the low end.  That is anywhere between 13.4-23.4% already exposed, and thus, presumably, now immune.  Again, and I stress, on the low end.  The actual number is higher, considering how many asymptomatic people do not develop detectable antibodies.  How much higher you want to fudge factor will put your personal estimate closer to the herd immunity ball park of 50-70% from previous updates.
Coupled with the state and national trends, I would say that’s all consistent.  Herd immunity in the US seems tantalizingly close. 

–Your chances of catching Ebola are equivalent to the chances that Africa can ever have nice things from an infectious disease standpoint, apparently.

–Your chances you will catch coronavirus in the future are slowly, but surely, becoming lower than the chances you have already caught SARS-CoV-2 in many places in the world. 

Yes, that’s right–absent a vaccine or treatment, there is a point those probabilities cross!

<Paladin>