BY ERIC J. TOPOL
JAN. 4, 2024
The pandemic is far from over, as evidenced by the rapid rise to global dominance of the JN.1 variant of SARS-CoV-2. This variant is a derivative of BA.2.86, the only other strain that has carried more than 30 new mutations in the spike protein since Omicron first came on the scene more than two years ago. This should have warranted designation by the World Health Organization as a variant of concern with a Greek letter, such as Pi.
By wastewater levels, JN.1 is now associated with the second-biggest wave of infections in the United States in the pandemic, after Omicron. We have lost the ability to track the actual number of infections since most people either test at home or don’t even test at all, but the very high wastewater levels of the virus indicate about 2 million Americans are getting infected each day.
In several countries in Europe, wastewater levels reached unprecedented levels, exceeding Omicron. Clearly this virus variant, with its plethora of new mutations, has continued its evolution with mutations adapted for infecting or reinfecting us.
There is, however, some good news about this big wave of infections. It has not resulted in the surge of hospital admissions seen with Omicron. The “updated” booster (based on the XBB.1.5 variant that rose to dominance in the U.S. in February), available here since September, has some cross-reactivity with JN.1 in lab studies for inducing neutralizing antibodies to the virus, and a recent Kaiser Permanente report showed the booster provided protection from hospitalization in the range of about 60% against JN.1 and other recently circulating variants.
With the marked differences in the spike protein between XBB.1.5 and JN.1, we are very lucky to see this level of vaccine-induced immune response. Nevertheless, only 19% of eligible Americans have gotten the updated booster. The Kaiser study also showed low levels of protection against hospitalization and emergency room visits for people who had received only prior versions of the vaccine, without the updated booster. That aligns with even more striking differences in the virus sequence of early strains compared with JN.1, and the problem we have with waning immunity four to six months after vaccination.
All of this is occurring on top of the flu and RSV waves, both of which are at very high levels, not clearly having peaked yet, with some people experiencing two of these infections at once.
With all three respiratory viruses circulating at full force, you would think we’d be seeing people wearing masks everywhere in public. That couldn’t be further from the truth. The state of denialism and general refusal to take simple steps to reduce the risk of infection can be seen everywhere.
It has taken healthcare systems many weeks after JN.1 showed up in October to recognize the threat. Only very recently have some reinstated mask mandates for healthcare workers and patients. Little has been done across the country to improve indoor air quality, upgrading filtration and ventilation.
Now in its fifth year, SARS-CoV-2 has once again proved to be highly resilient, capable of reinventing itself to infect us. Yet we continue to make-believe that the pandemic is over, that infections have been transformed to common cold status by prior exposure(s), and that life has returned to normal. Sadly, none of this is true.
The massive number of infections in the current wave will undoubtedly lead to more people suffering from long COVID. For a high proportion of people, especially those of advanced age, immunocompromised or with coexisting conditions, getting COVID is nothing close to a straightforward respiratory infection.
What is the exit strategy that could get us to “return to normal”? It certainly can’t happen with the current complacency and false belief that the virus will burn out and go away. Inevitably, there will be another strain in the future that we are not at all prepared for and will lead to yet another very big wave across the planet.
Still, there has been exciting new data on oral, inhaled vaccines that achieve high levels of mucosal immunity and protection against infections, which would be variant proof. The U.S. has invested hundreds of millions of dollars to rev up clinical trials for two different nasal vaccines with promising early clinical trial data, and for improved, variant-proof shots with better protection and durability. But most of these efforts started only recently and are not getting urgent priority for completion during 2024, nothing like what we saw with Operation Warp Speed in 2020.
It’s crickets from the White House on COVID now, with no messaging on getting the updated booster or masking. The Biden administration has done far too little to accelerate research on effective treatments for long COVID.
This passivity reinforces the illusion that the pandemic is behind us when it’s actually raging. And this season will be followed by a more quiescent period, which will, once again, lull us into thinking the pandemic is over. But there is no getting over it until we recognize reality and double down on the research that will allow us to block infections and virus spread, and achieve lasting, variant-proof immunity.
Eric J. Topol is a professor of molecular medicine at Scripps Research and author of the Substack newsletter Ground Truths.
Sadly I don't see us addressing Covid proactively again until we're adequately past the GOP threat...and that may not happen in my lifetime. We've been seeing a resurgence here but the only doctor's offices requesting masking are my PCPs and they don't enforce it with patients. Half the people I know who traveled for the holidays are now down with Covid and it's been pretty bad for a few of them, but not hospital-level.
I'm current with all my boosters including RSV and will continue to be. I have autoimmune issues and have had pneumonia three times so everything seems to attack my lungs. As @Julie808 pointed out, I only have so much time left and don't want to waste it fighting Covid. Interestingly, when I do mask, I think people presume I'm sick so they tend to don their masks. We are a very strange species indeed.
As always, thanks for the update.
Sadly this administration really does not need to give the far right nutters any more ammo than they already have for attacking every damn thing this ad min does. An extremely sad situation,
especially with the on going hearings, Fauci is set to testify. I think the health care profession needs to be held to some sort of account also, the people in the office have to do a better job of masking themselves and promoting the vaccine. Here in redneck stupid country it is not an easy thing and many in the profession are just gob smacked at the level of stupid they have seen.
That said I have not had my booster nor any of the other vaccines for RSV or the flu. I just have not been indoors for any length of time and wear my NK95 mask when I do go indoors.
Recently had a round with a member in this site over masks, what a fucking idiot. His claim is masks do not work at stopping the virus. No one ever claimed they did, the idea is to limit the viral load that flows from an infected person mouth and nose. AHHHH don't get me started.
Thanks for sanity posting!!!
Ah yes Topol. He’s been pushing nasal vaccines for a while now. Eventually we may see them.
I got my XBB shot in September, so hopefully my antibody levels are still sufficient to respond quickly. There are memory B cells though. And T-cell immunity is important. It’s just that the time involved in staging a response means people might feel lousy for a few days or more.
Maintaining high levels of neutralizing antibodies circulating may be an unusual situation. Plus at this point with people having different vaccination and infection histories I wonder how important original sin (or imprinting) will become. There may be an offset between imprinting and B-cells being able to mutate toward matching newer spike antigens (epitopes). If imprinting is at play our immune systems may get stuck on a previous adaptive peak. If not mutation will allow our B-cells to migrate to peaks represented by newer vaccines or infections. With vaccines the issue is prediction and how close the match might be toward unforeseeable variant looks. Hopefully SARS-CoV-2 tames into a common cold in coming years.
I’ve pretty much thrown in the towel on masking. I think people are burnt out on this stuff and fatalistic. I’ll keep getting whatever shots come out…hopefully nasal at some point as allegedly those will result in greater mucosal immunity instead of the systemic immunity the current shots bring.
Sadly the proportion of people getting the updated shots is lower than with the first series. If there were like 80% or more people currently updated things might look a little different. The infections will update many of them.
In a way, we've got to admire viruses...they're clever, flexible and tough.
Many retroviral fossils litter our genomes so we are too. Oddly there’s a connection between retroviral infections long ago and evolution of placentation in mammals. Rarely viruses might change our DNA for the better.
In short
Covid has not gone away, and like Spanish flu it will never go away, we've just learned to live with the inevitability of it for the sake of so called normality.
I still wear an KN95 mask on the plane, but that's about the only place nowadays that I wear a mask, simply because most everywhere I go is either open air or a large space where I am not very close to anyone.
Upon my flight home from Seattle to Kauai yesterday, I had my mask on as I took my window seat. The elderly couple in the seats next to me noticed my mask and promptly took out their own masks to put on, joking that I've shamed them into wearing their masks.
I said, oh, I'm just super careful. Personal preference. I'm actually a very safe person to be around. I want to be sure I stay healthy so I can work this week.
They said they each had had covid in 2020 and have had 5 shots, and I said me too! But they still wore their mask the whole 6 hours, except when the snack/drink cart came around, then their masks were back on. They were likely on the fence about whether they should wear their masks and were waiting to see what was the norm. They had their masks handy, so I think that was the case.
They were older than me, and traveling with friends seated in the row behind us. I think they didn't mind, and were perhaps relieved to feel okay wearing a mask on the plane, since it's right after holiday gatherings, when colds, covid and flu always seem to have an uptick.
It's just a personal preference for each individual, with no real guidance. I see the numbers and I hear the coughing. With being around travelers as much as I am, I just like to be careful for myself now. It used to be that I was careful for others.
At my age, I just don't really ever want to be as sick as I was in 2020, but with that immunity plus all my vaccinations, I'm pretty sure I won't ever get covid again, but I still want to be careful. I still have a lot of life to live. I don't want to waste any of it with even a common cold.
I wore a mask during the days leading in to my cataract surgery, because I did not want that procedure delayed. I don’t fly, but if I did I would probably mask. I don’t want to go back to the misery of masking every day. Been there, done that.