Biden's Big COVID-19 Plan

 So now that Joe Biden was sworn in, it was inevitable he would come up with his own COVID-19 plan (PDF). It's not all terrible, but there are a number of troubling signs that he's about to adopt the kinds of stupid, bureaucratic responses that have hamstrung much of the local efforts, particularly with vaccination. An overview:

 The first order of business is to "[r]estore trust with the American people." To do this, he proposes the government "Establish a national COVID-19 response structure where decision-making is driven by science and equity." Okay, let's step back a minute: what the heck is "equity"? As Andrew Sullivan recently wrote in his Substack space,

...[E]quity means giving the the named identity groups a specific advantage in treatment by the federal government over other groups — in order to make up for historic injustice and “systemic” oppression. Without “equity”, the argument runs, there can be no real “equality of opportunity.” Equity therefore comes first. Until equity is reached, equality is postponed — perhaps for ever.

 Biden doesn't name his preferred groups, but I scarcely need to mention they're what the left refers to as People of Color. This was something the CDC tried and was forced to recant weeks ago in a draft vaccine rollout schedule. So once again, we're going to deal with more efforts to inject racialized everything at a time when vaccinations are ponderously slow.

The rest of that point is largely boilerplate and anodyne (although the continued use of "Biden-Harris administration" is a strong Tell that Joe doesn't intend to be around much longer). Perhaps more interesting is the plan to "Mount a safe, effective, comprehensive vaccination campaign."

Central to this effort will be additional support and funding for state, local, Tribal, and territorial governments improved line of ight into supply – to ensure that they are best prepared to mount local vaccination programs.

This legitimately will be a substantial improvement from the Trump administration's leave-the-vaccine-on-the-loading-dock-without-telling-the-hospitals approach. However, in the next graf on ensuring availability of vaccine, the piece once more raises the Defense Production Act as a means to increase vaccine manufacturing capacity. As with N95 masks, the problem isn't the will, but staffing and expertise necessary to build out specialized manufacturing capacity that doesn't yet exist. At best, it might help with simple things like stoppers, vials, or syringes, but the real bottleneck is on the vaccine supply side. With recent news stories of production difficulties with Pfizer (albeit in Europe), AstraZeneca, and newcomers Janssen (Johnson & Johnson) and Novavax, it's hard to imagine how anything else could be the case. (Michael Abramowicz gave a good background in Reason as to why the DPA is a non-solution to most production problems, and why it could actually exacerbate shortages if used incorrectly.)

As to the point to "[a]ccelerate getting shots into arms and get vaccines to communities that need them most", the "Administration will end the policy of holding back significant levels of doses." This is actually pretty funny, because the Trump administration drew significant criticism for doing exactly this over a week ago.

Skipping ahead to the next part, "Implement masking nationwide by working with governors, mayors, and the American people" is surprisingly good news coming from a Democratic president. It implicitly acknowledges, contrary to partisan fears of federal lockdowns and masking requirements, that the ultimate responsibility for such public health measures rests at the local level and not the CDC or FDA. Likewise, so is the emphasis on expanding testing — though the value of this depends heavily on whether the FDA persists in confusing diagnostic and surveillance testing.

As I've already covered the limitations of the Defense Production Act, I pass over Goal Four, "Immediately expand emergency relief and exercise the Defense Production Act". Goal Five, "Safely reopen schools, businesses, and travel, while protecting workers" seems oddly duplicative with prior efforts in this space. As with Biden's 100-day vaccination goal that was nearly met on the day he was inaugurated, his point here seems more expectations management than goal-setting. But Goal Six is a gallimaufry of "don't let a crisis go to waste" thinking, using the pandemic as an excuse to create a "COVID-19 Health Equity Task Force", followed by a call to "[s]trengthen the social service seafety net to address unmet basic needs", and "increasing data collection and reporting for high risk groups" (read: by race). "Ensure equitable access to critical COVID-19 PPE, tests, therapies, and vaccines" reads very like there will be a long list of rules for vaccine distribution of the sort that stalled vaccinations in New York.

The final section, Goal Seven, "Restore U.S. leadership globally and build better preparedness for future threats" is mostly about patching things up with the WHO, despite the latter's well-known failures. What's interesting about the "preparedness" part is that it doesn't even mention PPE stockpiles, a widely-remarked-upon failing early in the pandemic.

On whole, it's a political document more than it lays out a serious plan forward, with much derived from the Trump administration before it. There's some good parts (at least he didn't try to roll out a parallel federal health agency at the county level!), but there's serious risk of the Team Blue hidebound incompetence that has put California and New York near the bottom of arms vaccinated per capita statistics being nationalized. That must be resisted at all costs.

I tweeted about a couple (mostly better) alternative views here, and will eventually get a response to those out the door.

Maybe We're Not Helping? The Public Health Fiasco

An interesting piece in Medpage Today from a few weeks ago: "Op-Ed: Why Did Fauci Move the Herd Immunity Goal Posts?"

Late last week, Fauci told the New York Times that new science had changed his thinking on the herd immunity threshold -- but he also admitted that his statements were influenced in part by "his gut feeling that the country is finally ready to hear what he really thinks."

Specifically, the fraction of people who would need immunity to SARS-CoV-2 (either through vaccination or recovery from prior infection) to extinguish the spread of the virus was initially estimated to be 60% to 70%. In recent weeks, Fauci had raised the percentage: from 70% to 75%, and then to 75%, 80%, and 85%.

The problem with Fauci is his obvious moving of the goalposts and explicit admission that he's playing us:

"When polls said only about half of all Americans would take a vaccine, I was saying herd immunity would take 70 to 75 percent," Fauci said. "Then, when newer surveys said 60 percent or more would take it, I thought, 'I can nudge this up a bit,' so I went to 80, 85."

Similar sentiments in Bloomberg Opinion: "Pandemic Regrets? Experts Have a Few":

In the last couple of weeks, I’ve asked a number of experts what they know now that they wish they’d known in the spring, and where they think public health got things wrong. Two big trends emerged: lockdowns (too blunt) and testing (too slow). With months left to go before vaccination can curtail the pandemic, 2020’s regrets should be 2021’s lessons.

University of Minnesota epidemiologist Michael Osterholm, a member of Biden’s advisory board, said one March mistake was closing businesses in places in the middle of the country that had seen almost no cases. “Was it appropriate to shut down so many things back then when there was so little, if any transmission? I think you can argue now that probably was not the best use of resources … it clearly alienated the very populations that we needed to have work with us,” he says.

The time was squandered and so was public trust. He compares the situation to hurricane warnings. People take them seriously because they are usually right. In many Midwest states, people went into emergency mode at the wrong time.

 

The Wish For A Uniform Federal Vaccination Response Is Pure Narcissism

One of the most irritating things to come out of the COVID-19 pandemic is the repeated wish from epidemiological, scientific, and legal circles for a uniform, federal policy regarding vaccination distribution. If only such a policy were around, we are told, the problems of getting shots in arms would magically vanish. But why should this be so? Why should we not inspect the records of some of the allegedly virtuous blue states — like, say, New York, whose sclerotic vaccination policy led to many doses thrown away? Andrew Cuomo's all-stick, no-carrot approach led to this, and his "fix" may still result in wasted doses. So in California. Whether you believe Govex or the CDC (data updated mostly daily, so this may change by the time you read this), California is near the bottom of getting shots into arms on a population-adjusted basis. And then there was the whole fiasco of the CDC being forced to walk back its unscientific early trial balloons that would have prioritized people at least partly on race. Surely, this didn't help to protect the elderly, the group most at risk.

Why should we believe a larger, more hidebound entity would do a better job at this? The reason this belief gets so much traction is pretty simple: because the people making this assertion believe it would be themselves (or like-minded compatriots) running the show. The same thing fuels the endless demand for socialism, and is just as wrong. Instead, we need to look at places that are actually getting things done ­— like, improbably, West Virginia, which state eschewed the federal agreement with CVS and Walgreens, instead favoring local pharmacies with existing arrangements with long-term care facilities. This should be obvious based on outcomes alone, but much that should be obvious never is.

The Myth Of The "Mostly Peaceful Protests" And Unprovable Counterfactuals

Donald Trump, still pressing the narrative of a stolen election, met with protesters hoping to shut down the formal electoral vote count. These protests later turned into an absurd, theatrical farce, with dozens arrested and four dead. Very quickly, Joe Biden went straight into absurdities of his own, pretending that the kid-gloves treatment afforded the George Floyd protesters of last summer did not happen, and that they were instead somehow manhandled by the police:

Biden: "No one can tell me that if it had been a group of Black Lives Matter protesting yesterday, they wouldn't have been treated very, very differently than the mob of thugs that stormed the Capitol. We all know that's true, and it is unacceptable. Totally unacceptable." pic.twitter.com/TfWa25VzEt

— CBS News (@CBSNews) January 7, 2021

Kamala Harris and Michelle Obama made similar statements:

.@KamalaHarris: "We witnessed two systems of justice when we saw one that let extremists storm the United States Capitol, and another that released tear gas on peaceful protesters last summer...We know this is unacceptable. We know we should be better than this." pic.twitter.com/Uc1FC8aZKg

— CSPAN (@cspan) January 7, 2021

Like all of you, I’ve been feeling so many emotions since yesterday. I tried to put my thoughts down here: pic.twitter.com/9xzRvrpk7y

— Michelle Obama (@MichelleObama) January 7, 2021

This is the purest of self-delusion. In fact, the summer protests are likely to go down as the most expensive in US history, with mayors in, at least, Seattle, Portland (especially), and Minneapolis all taking little effort and/or being slow to suppress the violence. Seattle only finally cracked down on October 3, but Minneapolis continues to have problems, and Portland Mayor Ted Wheeler actually said something mean about violent protesters. Yes, Trump famously (and stupidly) got unmarked federal police (some from the Bureau of Prisons) on the scene in D.C., and also to Seattle, but both dispersed relatively quickly. It's hard to look at this and conclude this is nothing but a narrative in search of its own facts — and that Democrats have no interest whatsoever in an honest accounting of any misdeeds from their side of the aisle.

A Necessarily Incomplete Overview Of COVID-19 Vaccines

Being a post I wanted to expose on a private Facebook group originally, only here I can add links when needed, and update as well. As ever, I Am Not A Virologist, etc. Info here is culled from This Week In Virology, assuming I understand them correctly, the Milken Institute's vaccine tracker, and the London School of Hygiene & Tropical Medicine vaccine tracker.

• The biggest gun out there right now is the mRNA approach used by Moderna and Pfizer/BioNTech. It consists of a nanoparticle container housing messenger RNA that eventually gets into your body’s cells. Once inside, the mRNA instructs your cells to manufacture a protein that looks like the “spike” protein from the disease — the protein SARS-CoV-2 uses to gain access to your body’s cells and eventually cause disease. Essentially, it tells your body to make a wanted poster, readying your immune system for real disease. 

  
  

  The super cool thing about mRNA is rapid turnaround. Once you have a virus sequenced, you can make a vaccine very quickly — Moderna had theirs two days after the Chinese published the genetic sequence. Everything else is safety/efficacy testing and approval. (You can read a very nice summary of how mRNA vaccines work here.)
• Next is the vectored vaccine approach used by AstraZeneca/Oxford, their  ChAdOx1. That name is a portmanteau of chimpanzee adenovirus Oxford (1). Originally developed for MERS, it was hoped it would readily translate to SARS-CoV-2 (COVID-19). Basically, they take a virus, in this case a chimpanzee adenovirus known not to infect humans, slice out the gene sequence for replication, and add genes to express the SARS-CoV-2 spike protein. Their testing is not going well — looks like a 62% overall efficacy, with a mistake group getting a half-dose first at 90% efficacy — and lately have started doing trials with other vaccines as a means to hopefully still be useful. My take on this is that such vaccines are functionally dead ends, because you can’t know whether the immune system is learning the vector proteins or the target protein(s), so a second injection might be useless. This in fact is why some vectored vaccines use a second viral backbone for the second shot. The Johnson & Johnson and Russian (Gamaleya's "Sputnik") vaccines are also vectored, and we shall see whether the former encounters the same problem.
• On to the inactivated vaccines. This is one of the oldest types of modern viral vaccines, including the polio, rabies, and annual influenza inoculations. Basically, you grow active virus in a medium (typically chicken eggs, but others are used) and then "inactivate" it. (Viruses aren't alive, but they can be made to fall apart by heat or chemical means.) This process leaves you (hopefully) with the outer proteins that the immune system needs to know about without all that infectious virus. These have a spotty record, which is part of the reason why, when you get one that does work, it becomes enormous news, as with the Salk polio vaccine (though there were other reasons for that). The inconsistent efficaciousness is also part of the reason we do extensive testing on vaccines. Sinopharm (the Chinese state entity) is using this approach and licensed theirs months ago. As you can imagine, I do not have a lot of faith in their trials or data.
• Protein subunit vaccines are by far the most popular approach with this disease, and is currently used in vaccines for shingles, hepatitis B, and human papilloma virus. Sanofi Pasteur is the most prominent name going to war with this approach, but a number of Chinese entities are also doing this. Basically, all this does is create the proteins of interest (here, the spike protein) and inject them straight into patients. It can produce a really strong immune reaction to the one protein in question, which is why it should in theory work well for SARS-CoV-2. (Coronaviruses tend to genetic stability because they have a proofreading ability most viruses lack.) The bad news for the US and Sanofi is that they had to pause their trials because the target population of people 65 and over did not respond well to the vaccination. 
  

Stay tuned, kids.

Don't Panic About The New UK Coronavirus Strain

 As ever, I use the word "strain" in the title here with some hesitation, because it hasn't been shown (yet) conclusively to affect pathogenicity or transmissibility, but some very good stuff in yesterday's This Week In Virology Episode 697. This doesn't cover all of it, but it hits the big points I think people are most interested in:

• Increased transmissibility has not been conclusively shown but the genomic data is suggestive. The mathematical models can be tweaked to show any result, and don’t take into account founder effects or population-level changes that might be affecting transmission.
• Spike protein changes are sufficient to require new primers for PCR tests, so they have had to rely on other genes for diagnosis.
  
• The spike protein change is NOT enough to alter antibody response. This has been verified in animal models. Existing vaccines will most likely work fine on the new variant.
• Underdiscussed: the ORF8 deletion may make a less-virulent disease course. (SARS-CoV-1 had one midway through that outbreak with that consequence.) It’s not that the disease is intrinsically more transmissible, but if you don’t feel sick you’re more likely to be out and shedding virus. We do not definitively know this to be the case at this point, however. 

Update 2020-12-29: I wanted to address a point that @politicalmath raised on his recent Substack post on COVID-19 strains; the consensus on TWiV seems to be that the US does much less viral sequencing than they do in the UK, although it’s unknown if what we do is enough to adequately assess spread by particular isolate. In any case, he links to a useful new (to me) site that tracks viral spread, Nextstrain.org. Bookmarked.

 

Update 2020-12-30: It was pointed out to me on Twitter that the strain is actually called B.1.1.7, which "has an unusually large number of genetic changes, particularly in the spike protein". I'm still not terribly worried about antibody response to this variant, for several reasons:

1. It's not clear that this has enough difference from other isolates to prevent existing vaccines from mounting an effective immune response.
2. We have known for months that other (possibly zoonotic) coronaviruses leave antibodies capable of reacting with SARS-CoV-2. It doesn't have to be perfect to work.
3. If B.1.1.7 is really a major shift, changing the mRNA vaccine to include the new spike protein should be a simple thing that could be turned around rapidly. (Of course, that assumes the FDA will allow an altered vaccine to be delivered without widespread testing first.)
   

Some Thoughts On The COVID-19 Mid-Term

 

 Cut-and-paste from a comment elsewhere on a news story about Dr. Fauci's remarks on the timetable for a return to "normal", and expanded on here. Particularly, this graf:

"I mean, if normal means you can get people into theater without worrying about what we call a 'congregate setting.' Superinfections. If you can get restaurants to open at almost full capacity, if you could have sporting events to be able to be played with spectators, either in the stands or in the arena, then I think that's going to be well, well into 2021 and perhaps beyond. I think one of the things that will be clear that our sensitivity to the potential devastating effects of a pandemic will be extraordinarily heightened. And I don't think that we will have the normal way of interacting with each other, particularly in the sense of wearing masks, which I think will become very commonplace as it is in many countries in Asia, even outside of the context of a pandemic outbreak. Again, I think it's many months."

We’re probably looking at a widely-deployed vaccine in the mid-2021 timeframe. Do not be surprised to see this pushed back as failures occur among the front-running vaccine candidates.

 

We will not know the durability of the immunity it confers. In that regard, it will be a phase III test (the actual term used by vaccinologists is phase IV). We may need to get revaccinated as often as twice yearly, forever. I am modestly hopeful on that front, because SARS-CoV-1 reactive T-cells have been documented as long as 17 years after infection. If T-cell immunity is the primary response, we could be golden.

 

We know that B-cell (antibody) immunity declines rapidly. A recent large-scale UK study showed antibody prevalence dropping from 6% to 4.4% in three months. This is strongly suggestive that we should not expect sterilizing immunity from a vaccine, but only protection from disease. This is not an uncommon outcome. The injected Salk (inactivated virus) polio vaccine has this effect also.

 

Because we will not get sterilizing immunity, we cannot rule out disease transmission even among the vaccinated. And because a vaccine will only confer protection on a (large) fraction of individuals, viral transmission will continue. The hope is that viral loads among the infected-but-vaccinated will be sufficiently low so as to reduce or eliminate transmission, but we cannot count on it.

 

So I can see what Fauci’s saying as not improbable. Masks, occasional lockdowns (hopefully becoming more infrequent as we find out how effective the vaccine(s) is/are) and other measures will probably continue to be necessary for a while.