Eyeing the Virus

One week ago, I wrote about my growing concern that one of the new SARS-CoV-2 variants (the 501Y.V2 variant, first identified in South Africa, in particular) might achieve immune escape. This morning, the New York Times reported on the same, in an article entitled, “Emerging Coronavirus Variants May Pose Challenges to Vaccines”; here’s what I see as the key line: “[S]cientists had hoped that the new vaccines would remain effective for years, on the theory that the coronavirus would be slow to develop new defenses against them. Now some researchers fear the unchecked spread has given the virus nearly unfettered opportunities to reinvent itself, and may have hastened the appearance of escape mutations.”

Public health failures may now be undermining remarkable techno-medical achievements, just as public health failures (and disregard for the health and well-being of the world’s poor) have created conditions conducive to the emergence of novel zoonoses like COVID-19. It’s important to note that the study (which can be found here) upon which this NYT reportage leans heavily examined the responses of antibodies found in convalescent plasma to the novel variant, and may not necessarily reflect in vivo immune responses. (The relatively rapid loss of neutralizing antibodies in convalescent individuals was – for a time, at least in the mass media – interpreted as a sign that infection with SARS-CoV-2 might not lead to lasting immunity, and yet both common sense (e.g., the fact that very few reinfections were occurring) and, subsequently, research findings both strongly suggest/ed that lasting immunity is conferred by infection.)

In the meantime, in other vaccine news, results drawn from Israel’s world-leading apartheid vaccine rollout suggest that two doses of the Pfizer vaccine really are necessary to achieve protection, while from the UK, evidence suggests that the same Pfizer vaccine is protective against the B.1.1.7 variant (which was never really in doubt).

Finally, I find it increasingly implausible that only rich, democratic countries (that happen to have disproportionately older populations, making it that much harder to hide the burden of mortality) are experiencing severe COVID-19 outbreaks. It is likely that subsequent epidemiological studies will uncover far more extensive spread of the disease across many poor and/or authoritarian countries than has yet come to light. Case in point, while there has certainly been coverage of the renewed outbreak in the vicinity of Beijing, and of the Chinese Government’s remarkable/aggressive attempts to contain it, Tweets like this one (captioned, by Bill Bishop, author of Sinocism [paywalled]: “You don’t build these unless you need to”) suggest that the extent of the latest outbreak is being dramatically under-reported.

I’m officially very worried about what potential immune escape will mean for the global path out of the pandemic, but withholding judgment until we have more definite information.

How Do We Fix Things That Also Require Defending?

Zeynep Tufecki has an excellent piece [maybe paywalled?] out entitled “The Crisis of Authority and the Crisis of Expertise: Age of Misinformation and Defending (Imperfect) Institutions Under (Often Bad Faith) Attack“; she was – and has continued to be – consistently out ahead of almost all of us on key issues with respect to the pandemic and our responses to it.

She emphasizes how frustrating it is that the remarkable achievement that is these safe, effective, approved vaccines is being widely discounted or even rejected. On a similar note, I continue to be frustrated that our national (and New York State and City) vaccine rollouts continue to exclusively be characterized as “troubled,” as if the US hadn’t administered ~1/3 of all COVID-19 vaccinations to date globally. The daily average for this week will likely exceed one million doses nationally, and NYS and NYC have both now vaccinated more than 5% of their populations. These are almost unimaginable success stories by any historical standard, or even just based on expectations (including my own) from as recently as the fall, and while we should absolutely be demanding rapid improvements in the rollout(s) – especially given that such public-pressure-driven iteration is a strength of our democracy – it would be nice to also maintain a certain sense of humility and gratitude.

In the meanwhile, there continue to be reasons for grave concern about the risk of immune escape by new SARS-CoV-2 variants, though nothing definite is known in this regard as yet so far as I can tell. If we avoid the grim escape scenario, the pandemic will be effectively over in a few months in the US, largely owing to the remarkable achievement that is these vaccines. This doesn’t mean that we might not subsequently discover that there are long-term health consequences associated with one or more of the vaccines (an eventuality that I see as pretty unlikely, based on the nature of these vaccine platforms), but we should at least strive to maintain perspective on just how incredible these scientific and technological accomplishments are.

Finally, speaking of science, here are two sobering articles on what we lose, collectively, when corporations/unfettered greed/capitalism/extractivism destroy biodiversity. The world and other beings around us are unimaginably beautiful in their own rights, but it turns out that they are also fundamental sources of knowledge (including about potential treatments for disease).

The Risk of Immune Escape

Last week, I pointed, for the first time, to my concern about the risk of immune (or immunological, or antigenic) escape by one of the new SARS-CoV-2 variants. My concern was triggered by this podcast episode from the NEJM, and in response to my inquiry, one of the NEJM editors who has been kind enough to correspond with me via email from time to time wrote: “I think that it’s just too early [to know about the risk of immune escape]. […] But we should know fairly soon, particularly if we see cases in vaccinated individuals. There will also be in vitro data about antibody binding (some of which is already in the media) but we don’t know the significance of this yet.”

To the point about antibody binding, this Nature article from January 7th of this year concludes, “There is emerging evidence that the E484K mutation can enable the virus to escape some people’s immune responses. […] But […] scientists are hopeful that the mutations in the variants won’t substantially weaken the performance of vaccines.” The article also points, however, to a recent pre-print [that is, an as-yet-un-peer-reviewed publication] that suggests: “The evolution of SARS-CoV-2 could impair recognition of the virus by human antibody-mediated immunity.” If both the former hope and the latter possibility prove true, it would mean that new variants with this mutation (chief among them, for now, the 501Y.V2 variant that was first identified in South Africa) might prove resistant to immunity inferred by infection with older SARS-CoV-2 variants, but still subject to immunity conferred by vaccines. This would be good news, in a measured sense, but would militate against my bull case for the pandemic ending in the spring in the US, given that it could mean that many of us who already had COVID-19 might not enjoy any naturally conferred protection against the new variant(s).

This piece from the 15th (from Science, but journalistic in tone) quotes a researcher as follows: “Several vaccines could be easily changed to reflect the latest changes, but regulators might balk at authorizing them without seeing updated safety and efficacy data,” while this pre-print [again, not yet peer reviewed] from the 13th offers the most alarming assessment: “Rapidly spreading SARS-CoV-2 variants present not only an increased threat to human health due to the confirmed greater transmissibility of several of these new strains but, due to conformational changes induced by the mutations, may render first-wave SARS-CoV-2 convalescent sera, vaccine-induced antibodies, or recombinant neutralizing antibodies […] ineffective.”

Finally, this BMJ piece from today offers a helpful summary of the three most worrying variants (B.1.1.7, first identified in the UK; 501Y.V2, first identified in South Africa; and P.1, first identified in Brazil), and, among other things, quotes a researcher as follows: “[T]he variants may be arising in Brazil and South Africa because of high transmission (as many as 40-50% of people being infected) in populations living in crowded conditions.” It would be the height of brutal irony if failures to take public health seriously globally – failures epitomized by vaccine nationalism and the collapse of many multilateral programs once spearheaded by the US, and characterized by a lack of concern about the lives and well-being of the poor, especially across the Global South – undermined the efficacy of vaccines just at the moment when the US and other rich countries across the Global North – having mostly failed to control COVID-19 through well-understood non-pharmaceutical interventions – are rushing headlong towards what they hoped would be the techno-medical denouement of the(ir) pandemic.

We should care about public health globally because people’s lives matter, but I fear that even the hard-hearted (who so often see themselves as cold-blooded pragmatists) may be on the verge of learning a painful lesson about the consequences of embracing parochial (and inhumane) solutions to complex problems.

Reading Recommendation #2: The New Climate War

Occasionally, I find it necessary to write a post about some things I clearly got wrong. It’s also been a while since I made a book recommendation. To pull these two threads together, I can happily recommend that any reader interested in an accessible, thorough, action-oriented primer on the history and current state of climate science, policy, and action pick up Michael Mann‘s new book, The New Climate War, from which I quote:

[The climate-denial complex] has promoted the narrative that climate-change impacts will be mild, innocuous, and easily adapted to, undermining any sense of urgency, while at the same time promoting the inevitability of climate change to dampen any sense of agency. This effort has been aided and abetted by individuals who are ostensible climate champions but have portrayed catastrophe as a fait accompli, either by overstating the damage to which we are already committed, by dismissing the possibility of mobilizing the action necessary to avert disaster, or by setting the standard so high (say, the very overthrow of market economics itself, that old chestnut) that any action seems doomed to failure. The enemy has been more than happy to amplify such notions.

While I don’t love Mann’s use of the language of war, contrary to the employment of militarized pandemic-response metaphors, in this instance, I at least feel there is sound justification for all the martial imagery, for there is, indeed, an enemy, in the form of the climate-denial complex. I pull this quote, in particular, from Mann’s book, though, because I myself have been guilty of at least two of these three mis-steps at different times in the past. In fact, my choice to start this blog, now almost three years ago (with an inaugural post title honoring the late Martin Luther King, Jr., no less) was predicated largely on my desire to shift away from the raw (and no doubt, at times, indulgent) anger that had often characterized my posts on Medium, in the direction of a more constructive and generous tone.

Incidentally, Mann has also been among the most outspoken popularizers of an important shift in climate science consensus – namely, to oversimplify, that: “If we stop burning carbon now, we stop the warming of the planet [within a few decades, rather than – as many of us had previously believed and stated – only after centuries of locked-in warming].”

As I’ve addressed elsewhere recently, the ~10% decrease in US GHG emissions in 2020 stands to have little to no lasting impact, alone, on the trajectory of global heating, but were the US and other heavily-polluting nations to move aggressively in the coming years and decades to reduce emissions and transform their economies, it could dramatically reduce the global mean temperature increase by 2050. Couple this with the revelation now being popularized by Mann, and there are real reasons for hope, that, not only is it possible to limit heating this century, but that the prospects for averting catastrophic long-term heating may be much better than had been previously understood.

This framing only redoubles my conviction that climate crisis is the defining issue of our time and that those of us who enjoy the luxury of agency in these matters have a moral imperative (an obligation, but also an opportunity) to commit ourselves to preventing global catastrophe while also shaping a more sane, just, and equitable future.

From Climate Central, in case you need any additional motivation to throw yourself into climate action.

Postscript: Full disclosure, I’m passingly acquainted with Michael Mann through a mutual friend, and he was kind enough to gift me a copy of his new book; however, he is not aware that I write this blog, and – even were he to have been – I can’t imagine he would have been moved by anything other than the goodness of his heart to share his work with me, as I don’t think he needs my help in reaching an exceedingly broad audience.

Immunological Escape

Yesterday, I reaffirmed my conviction that the pandemic will be effectively over in the US by early this spring. Today, I’ll share the one caveat about which I remain deeply worried.

First, it is tragic what has been unfolding in the UK as the B.1.1.7 variant has spread there; however, I’ve yet to hear any argument that that variant is either more deadly, or that it has evolved such that existing vaccines (or infection-acquired immunity) would not be effective against it. (That is, immunological escape by this, or other variants, of SARS-CoV-2 has thus far appeared an unlikely eventuality.) It is wreaking havoc because it is just as deadly as other strands, but far more infectious, so spreading more rapidly, and thus killing and hospitalizing a larger number of people than less infectious strains would have in the same amount of time.

Shortly after sending out yesterday’s newsletter, though, I listened to this podcast episode from the New England Journal of Medicine featuring “South African infectious disease physician Salim Abdool Karim”; long-short, Dr. Karim explains that, while until recently, evolutions of SARS-CoV-2 observed by his team had been modest and gradual, the recently-emerged variant that has been spreading rapidly in South Africa appears to have undergone a large number of mutations at once, including some which bear on the structure of key viral proteins, and that there is some risk that this could lead to immunological escape. He further speculates that these mutations could have been the result of the virus passing from humans into a non-human species and then back again. Be the case as it may, were a new and highly-infectious variant to actually undergo escape, all bets would be off, and it would put us back where we started (or almost, as I have to imagine that all the vaccine progress to date would further speed the creation of still newer vaccines to address new mutant viral strains), confronted with the necessity of controlling a novel pathogen for which no cure or vaccine exists.

Here’s hoping that it never comes to that. That this risk highlights the need to vaccinate rapidly, and otherwise control the spread of COVID-19, not just in rich countries, but all over the world, should go without saying.