Bubonic plague–  We’ll start with the one with basically no news.  No news is good news.  No reports of additional spread in China/Mongolia, and no reports of successful transmission by way of squirrels and other wildlife in Colorado.  Again, a few cases here and there in either region is to be suspected every year.  Barring some sudden resurgence with massive numbers of cases, we will consider the bubonic plague portion closed for the time being.

Ebola–Actual news here, and none of it is good, quite frankly.  We are up to 63 confirmed cases thus far.  More troubling, in the past two weeks, there have been over a thousand alerts for possible Ebola symptoms.  The way these alerts work is a local hospital/clinic says “Hey, this might be Ebola.”  A WHO or local Ebola worker then reviews the symptoms.  If the symptoms and history are still suspicious for Ebola after review, then it is logged as a “suspected” case, and now authorized for diagnostic testing and additional work up.  So, of those 1,015 alerts for possible Ebola in the last week, less than half had a WHO or local Ebola worker review to establish if they were a suspected case or not.  Of the alerts were symptoms were reviewed by a WHO or local Ebola worker, 18% were declared “suspected Ebola.”  Of the now official “suspected Ebola” cases, only 1/3rd were then followed up with diagnostic testing and additional work up.

That is not how you contain an outbreak, and why numeric and geographic spread continues and will continue.

More troubling, one of the new confirmed cases is in a known contact who had received the Ebola vaccine.  Now, this was reported to have happened a few times in other Ebola outbreaks.  There are no more details to know if this is a case of vaccine failure (where it did not successfully immunize–and then “why” becomes the question) or if the patient got the vaccine, but already was incubating Ebola by the time they were vaccinated, and thus too late to actually prevent disease.  That’s an important distinction.  Regardless, worth continuing to monitor, as some 16,493 people have been vaccinated in the latest outbreak.

The only good news is that the geographic spread is moving away from the Congo River.  But so far, 9 positive Ebola cases have been picked up at travel checkpoints, and likelihood of spread downstream along the Congo is rising.  As is “community resistance” to containment efforts.  Which, given community resistance to coronavirus measures in pretty much every part of the world to some degree, is now to be expected I guess.

Coronavirus–Speaking of, lots again.

–Hydroxychloroquine hits the news again, this time because of a viral video of several physicians describing their own personal experience treating COVID with it.  Here is my frustration with this entire situation.  It would be great if HCQ worked, either in early stage disease as the virus is actively replicating, or in late stage, where the immune system appears to be going Ah-nold.  HCQ is a cheap, generic medication with a long track record of safe use.  There is no more ideal solution for a drug that keeps patients out of the hospital, or out quicker, than that–a repurposed safe, cheap generic.  There have been clinical trials in both early and late settings.  The results have not been clear.

Let me be clear about that much:  the results of clinical studies on HCQ are, on the whole, very mixed–but that may be mostly a late phase/early phase of disease divide.

If HCQ works, it appears to be in the early phases of disease, where the virus is actively replicating.  The studies that Dr. Fauci touts, as demonstrating that HCQ does not work (as a blanket statement) are uniformly in late phase disease when the virus may not be the main driver of what is going on.  Dr. Fauci is, frankly, overstating the evidence against.  On the other hand, you have somebody sponsoring that viral video of doctors discussing their personal experience treating COVID with HCQ.  Much has been directed at the source of that funding, and one particular(ly crazy) pediatrician seen on the video.  Apparently, the other doctors who spoke are sane and typical physicians, because nothing is getting said attacking their credibility, except via association with our rather outlandish pediatrician. 

And this is the problem with HCQ right now.  The science has been totally politicized, to the point that I despair of ever getting a clean, definitive study in early phase COVID (which is where the best remaining evidence that HCQ is of any benefit resides).  This is the danger of politicizing science like this.  And it happened from the drop, when HCQ, after being touted as a possibly effective treatment before decent sized studies had been done, was suddenly getting lambasted in headlines as “potentially unsafe”–despite being taken chronically for malaria prophylaxis and some autoimmune disease for decades and being listed as an “essential medicine.”  
As I have said repeatedly, I know there are physicians, such as the apparently sane ones in the viral video, who are big believers and others who say they have not seen much success.  Even then, most of the latter have at least tried it on their patients.  Because of politics, though, all we are going to get is the current schizophrenia on HCQ, probably all the way through the rest of the pandemic.

Politics.

What a world.

–Speaking of the world, there is significant acceleration in new cases across the globe.  New travel restrictions were imposed on Spain by other countries, as cases in the Barecelona region in particular pick back up.  Reports of localized increased spread in the UK are hitting the rumor mill today.  Germany had another pop in cases.  Eastern Europe is still cruising through the first wave.  China acknowledged more new cases.  Japan is over a 1,000 per day, if I scanned that headline right.  Parts of Australia are seeing a very solid resurgence right now too.

So what’s going on?  Two things.  1)  As we have mentioned repeatedly, the virus is ubiquitous worldwide, and highly, highly contagious.  You are all going to get exposed to it, even if you haven’t been already.  Don’t delude yourself.  Hell, even the NYT today acknowledged that contact tracing in the US is a moot point (something that we have previously stated in these updates several times)–the virus is too contagious and spread too far already.  2)  Reintroduction into areas that disrupted the first wave before it crested are inevitable, and these will be the source of the more regional/city level “second waves” that you are seeing right now.  The hits will continue until herd immunity is met (or a safe vaccine is readily available to achieve herd immunity).  That will be significant only if there are enough susceptible, unexposed people around that if they all got SARS-CoV-2 at once could crash the local hospital system.  Effective treatment of the virus raises that threshold, and if one appeared right now would probably be enough in many, if not most, parts of the world to keep SARS-CoV-2 from being a realistic threat to crash the health care system.

The country to watch over the next month is Sweden.  Sweden is now world famous for not doing much in the way of restrictions.  They got a bunch of cases adjusted for population, cresting in June.  They have been mostly quiet since.  As first waves complete across the European Union right now, if Sweden does NOT significantly reignite, then my hypothesis that places which get their major first wave out of the way pretty much hit their herd immunity threshold gets a boost.  If Sweden does start to see another bump, especially if widespread across Sweden, we may be staring a much longer course of SARS-CoV-2 globally in the face, as the magic herd immunity number is more likely to be at the high end of estimates.

–Here is the situation in the US:

Much of the country is now light pink to green.  This is backed up by Rt calculations via rt.live  Cases in Arizona, Florida and Texas are starting to decline.  Deaths are nudging up (remember, they are a lagging indicator), but are still not close to March/April, especially as a percentage of new cases.  The overall % positive rate is trending slightly down in the US, and is definitely down in Arizona, Texas and Florida.  California appears to be hitting its peak–I suspect it will begin to tip to green before the end of next month.  Indiana seems awfully close to its peak, and I expect cases to trend back down again as well.  At least here, all through this interrupted first wave, new cases have been nominally higher than March/April, but ICU utilization has barely budged, % positive remains less than half of what it was in March/April, and hospitalizations have been flat for weeks even as new cases were trending up.  All of that is optimistic.

–Now, there are some corners of the internet suggesting that drops in places like Arizona may be accounted for by lower rates of testing.  While there are fewer tests right now in Arizona, the % positive reflects the current trends you see in Rt and on the map above, and are not so much lower that I am concerned that is driving the difference.  Instead, I think that reflects longer turnaround times at the big national reference laboratories, and more people being unwilling to wait that long for a test result, and simply foregoing getting tested.

–Which brings up the latest nonsense around COVID testing and restrictions.  Several states, including a few in New England, are demanding that out of state travelers either have a confirmed negative test within the previous 72 hours of arrival in the state, or mandatory quarantine for two weeks.  Enforcement of this is not clear.  Are they running road blocks?  To ALL roads crossing state lines, or just interstates?  When you get off the plane, do you need a printed result?  How are they verifying and how quickly?  How are they tracking and enforcing these quarantines?  None of this is particularly clear.

And this is becoming something of a catch 22.  If you can’t get a test result from someplace like a CVS (shipping to one of the national reference labs) for 14 days right now, how do you travel to these states without avoiding quarantine?  I have also heard of some universities requiring their students to have a negative test result obtained in the previous 10 days to return to campus.  Again, if it’s taking 14 days to get a result (as is being quoted by some labs), how does the student get back to campus?  Even if you do get tested, the various state health departments have no way of communicating the results between each other to verify the test result.  And how, by whom, and how quickly does that get called back to the police officer pulling you over to check your most recent test status?

Worth mentioning that Florida was running travel checkpoints on I-95 as recently as the fourth of July weekend, and I have heard even before that.  How did that go for them in avoiding a resurgence in SARS-CoV-2 cases?

–Speaking of testing, really interesting pre-publication paper looking at PCR testing for SARS-CoV-2 over time in large cohort of nursing home patients and staff here:  https://www.medrxiv.org/content/10.1101/2020.07.20.20157792v1?%3Fcollection=

The main takeaways? 
1)  The nursing home staff median age was in the 40s; the residents median age was in the 80s.

2)  Unsurprisingly then, 15.5% of the residents (older) vs 4.1% of the staff tested positive during the study.

3)  This is higher than the percentage of confirmed cases in Massachusetts as a function of the total population of Massachusetts overall, and is further evidence that there has been MUCH broader spread in the community writ large than the number of confirmed cases suggest.

4)  Of those WITHOUT symptoms, few tested positive (shocker I know).

5)  This compared to a positive result in 53.1% of the residents who had COVID like symptoms and 18.2% of the staff with COVID like symptoms.  Now, we don’t know exactly how many of the asymptomatic people were actually exposed to SARS-CoV-2–the few who tested positive were just the ones caught at the “magic time” when their exposure to the virus was present to be detected at all.  But it’s safe to say asymptomatic people are MUCH less likely to test positive for SARS-CoV-2

6)  Interestingly, the amount of virus detected was not statistically significantly different between patients with symptoms or without.

7)  BUT the overwhelming majority of people who had symptoms were tested after the symptoms were largely gone (which may also explain the surprisingly low % positive in patients with symptoms).  Another caveat is that this assay may not accurately quantify the amount of virus present, and does not differentiate between active and inactive virus.  The assay only says if the virus is there or not.

8)  Recently, in the last two weeks of the study period (and thus out of the March/April peak), the amount of virus detected by this PCR assay has been less than during the March/April peak on average.  This difference is statistically significant, and also fits with the “higher numeric cases, but less severe disease” trend we have been tracking nationwide lately.

–Lastly, social impacts.  Those of you stateside may want to hold on to that 1 month of food.  There may be some shenanigans around the election in November the way politics have gone this year, and again, you’re safest to protect your downside.  Worst case is you just eat it later.

And this.  I suspect I will wind up linking to all the parts of this series: https://www.epsilontheory.com/the-grifters-chapter-1-kodak/

–Your chances of catching bubonic plague are your baseline risks of catching bubonic plague.  Do not touch dead marmots.

–Your chances of catching coronavirus remain excellent in nearly all parts of the world, and improving in some of them.

–Your chances of catching Ebola are equivalent to the chances that Lou Williams was just there to pick up an order of chicken wings.

Yes, Lou Williams really played No. 5 off the Top Ten list.

In fairness, the wings at that particular establishment are literally named after him.  Although, that…..  that doesn’t entirely help either, does it? 

How does one get the wings –at a strip club– named after you? 

“Honey, I know you’re upset…but they didn’t name the lap dances after me.  It’s just sauce.  Chicken wing sauce.  For wings.  Baby, I love you.  Please don’t divorce me….”

–Lou Williams, probably, if he were actually married

<Paladin>