Category: Current Affairs

This was emailed to me, but I am not doing a double indent…in any case I fear the person might be right…

“The prevailing sentiment is that the COVID pandemic is close to over. The vaccines are of course miraculous but we are not currently on a good trajectory.

• It is increasingly clear that two shots plus a booster of our current vaccines are the least one needs to have effective medium-term protection. Almost nowhere (least of all the US) is on track to reach this kind of coverage. The messaging in the US remains mistaken, where the CDC to this day recommends boosters only for those aged 50 and older. More broadly, the institutional confusion around boosters shows that the adults are not yet in charge.
• Even though Delta arose in the spring, we are still vaccinating (and boosting) people with the original Wuhan strain. This is insane, and probably meaningfully less effective, and yet nobody is up in arms about it.
• Severe outbreaks are manifestly possible even in exceptionally vaccinated populations, especially when booster uptake is low. See: Singapore, Gibraltar, Ireland. One should assume that almost every part of the US will see significant waves before COVID “ends”, whatever that turns out to mean. Note that just 60% of the US population is vaccinated today with two doses.
• There is early suggestive evidence from Israel that boosters may wane.
• Waning aside, it’s clear that breakthrough infections in boosted individuals are not uncommon. While the vast majority of those infections are not severe, this does mean that there will still be plenty of mutagenesis.
• It’s unclear that longitudinal cross-immunity is strong. Getting COVID is not enough to confer long-term protection. We probably can’t just “get this over with”, even if we are willing to tolerate a large number of one-time deaths.
• The currently-breaking news about the South African Nu strain shows that arguments about how the spike protein is running out of mutation search space are almost certainly wrong.
• While the fog of war is thick right now, the early data on Nu suggests that it may be a big deal. Even if it’s not, however, it has been obvious since we got the vaccines that vaccine escape is a concern. You can debate whether the probability of a vaccine escaping variant is 20% or 80%, but in any case we need effective contingency plans in place. If we fail to respond effectively to Nu, that will be a considerably greater institutional failure than anything that happened at the outset of the pandemic. We’ve had almost two years since the first COVID case and one year from the vaccine approvals to prepare. So I ask: what is the plan for the vaccine-escaping variant?

On current trends, it looks like we will probably need one of two things to effectively end the pandemic: (1) very effective COVID therapeutics (paxlovid, molnupiravir, and fluvoxamine all being candidates but my guess is that none is a silver bullet) or (2) pan-coronavirus vaccines (with broader protection than what is currently available).

It isn’t over yet.

P.S. Has any U.S. health body recommended the clinical use of fluvoxamine (an already-approved drug), or has the FDA given any guidance as to when it might approve paxlovid? If not, can they outline their reasoning? 1,600 Americans died of COVID on Nov 24.”

Here is the Eric Topol thread.  Do read it.  Here is the scary graph, based on preliminary data.  Here is Bloom Lab.  Here is a layperson’s take from the Times of London:

When was the variant first discovered?
South African authorities raised the alarm at 2pm on Tuesday of this week, when they found samples with a significant number of worrying mutations.

The samples dated from tests taken on November 14 and 16. On Wednesday, even as scientists were analysing the genome, other samples were found in Botswana and China, originating from travellers from South Africa.

Why were scientists initially concerned by this variant?
The spike protein is the tool a virus uses to enter cells, and the part of it our vaccines are trained to spot. This variant had 32 mutations in the spike — meaning it would look different to our immune system and behave differently when attacking a body. As a virologist at Imperial College put it, it was a “horrific spike profile”.

Why has worry increased over the course of the week?
When geneticists and virologists looked at the mutations they realised there was a high likelihood they could increase its transmissibility or help it evade immunity. But these concerns were still theoretical. However, today South African scientists spotted a quirk in the testing regimen. PCR tests look for three genes in the coronavirus and amplify them. If, however, the virus was this variant they were only able to amplify two.

In the province of Gauteng, where the proportion of tests coming back positive has rocketed to one in three, they found the proportion in which only two genes were amplified has also rocketed.

What does this mean?
There are three options. It is still possible — though unlikely — this is chance, with the variant’s apparently increased spread relating to an unusual cluster. If it does have a genuine advantage, then it is either better able to spread or better able to infect people who have prior immunity — either from vaccination or infection. Or, it is both.

This might come to nothing, but it is definitely a matter of concern.  One more general point is that even if Nu is a non-event, it seems to show that the space for possible significant mutations is largely than we had thought.

We are short a million health care workers. Today with extreme stress on the system there are 16 million health care workers, about five hundred thousand fewer than when the pandemic began in January of 2020 and about one million fewer than would be expected based on decades of growth. A loss of this many workers is unprecedented.

Ed Yong in the Atlantic discusses Why Health-Care Workers are Quitting in Droves:

Health-care workers, under any circumstances, live in the thick of death, stress, and trauma. “You go in knowing those are the things you’ll see,” Cassandra Werry, an ICU nurse currently working in Idaho, told me. “Not everyone pulls through, but at the end of the day, the point is to get people better. You strive for those wins.” COVID-19 has upset that balance, confronting even experienced people with the worst conditions they have ever faced and turning difficult jobs into unbearable ones.

In the spring of 2020, “I’d walk past an ice truck of dead bodies, and pictures on the wall of cleaning staff and nurses who’d died, into a room with more dead bodies,” Lindsay Fox, a former emergency-medicine doctor from Newark, New Jersey, told me. At the same time, Artec Durham, an ICU nurse from Flagstaff, Arizona, was watching his hospital fill with patients from the Navajo Nation. “Nearly every one of them died, and there was nothing we could do,” he said. “We ran out of body bags.”

…Many health-care workers imagined that such traumas were behind them once the vaccines arrived. But plateauing vaccination rates, premature lifts on masking, and the ascendant Delta variant undid those hopes. This summer, many hospitals clogged up again. As patients waited to be admitted into ICUs, they filled emergency rooms, and then waiting rooms and hallways. That unrealized promise of “some sort of normalcy has made the feelings of exhaustion and frustration worse,” Bettencourt told me.

Health-care workers want to help their patients, and their inability to do so properly is hollowing them out. “Especially now, with Delta, not many people get better and go home,” Werry told me. People have asked her if she would have gone to nursing school had she known the circumstances she would encounter, and for her, “it’s a resounding no,” she said. (Werry quit her job in an Arizona hospital last December and plans on leaving medicine once she pays off her student debts.)

…Many have told me that they’re bone-weary, depressed, irritable, and (unusually for them) unable to hide any of that. Nurses excel at “feeling their feelings in a supply closet or bathroom, and then putting their game face back on and jumping into the ring,” Werry said. But she and others are now constantly on the verge of tears, or prone to snapping at colleagues and patients. Some call this burnout, but Gerard Brogan, the director of nursing practice at National Nurses United, dislikes the term because “it implies a lack of character,” he told me. He prefers moral distress—the anguish of being unable to take the course of action that you know is right.

Health-care workers aren’t quitting because they can’t handle their jobs. They’re quitting because they can’t handle being unable to do their jobs.

Hat tip: Matt Yglesias.