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Saturday, August 28, 2021

Early Treatment with Fluvoxamine and Risk of Emergency Care and Hospitalization with COVID-19

 Gilmar Reis, Eduardo Augusto dos Santos Moreira Silva, Daniela Carla Medeiros Silva, Lehana Thabane, Aline Cruz Milagres, Thiago Santiago Ferreira, Castilho Vitor Quirino dos Santos, Adhemar Dias de Figueiredo Neto, Eduardo Diniz Callegari, Leonardo Cançado Monteiro Savassi, Vitoria Helena de Souza Campos, Maria Izabel Campos Simplicio, Luciene Barra Ribeiro, Rosemary Oliveira, Ofir Harari, Jamie I Forrest, Hinda Ruton, Sheila Sprague, Paula McKay, Alla V Glushchenko, Craig R. Rayner, Eric J. Lenze, Angela M. Reiersen, Gordon H. Guyatt, Edward J. Mills, the TOGETHER Investigators

SARS-CoV-2 Delta variant poised to acquire complete resistance to wild-type spike vaccines

 Yafei Liu, Noriko Arase, Jun-ichi Kishikawa, Mika Hirose, Songling Li, Asa Tada, Sumiko Matsuoka, Akemi Arakawa, Kanako Akamatsu, Chikako Ono, Hui Jin, Kazuki Kishida, Wataru Nakai, Masako Kohyama, Atsushi Nakagawa, Yoshiaki Yamagishi, Hironori Nakagami, Atsushi Kumanogoh, 

Yoshiharu MatsuuraDaron M. StandleyTakayuki KatoMasato OkadaManabu FujimotoHisashi Arase

A New Antibody-Dependent Enhancement Hypothesis

 By Derek Lowe

Here’s another post that I will regret writing, but a great many people have asked me about a new preprint that brings up the possibility of antibody-dependent enhancement with the current vaccines and the Delta variant. To be frank, some of the people promoting this seem to be rooting for the virus, just so long as it humiliates their enemies and proves their own positions to be correct, but there are a lot of honestly worried people out there who are wondering what this paper means. So let’s look at it, with an eye to lessons for evaluating such papers in general.

The authors are building on another recent paper (Li et al.) on neutralizing and non-neutralizing antibodies against the current coronvirus. The preprint version of that one came out in February, and the final version went online in June. That work appears to be very solid, and represents a great deal of effort, so let’s discuss it for a bit before returning to the preprint above. In it, the authors isolated antibodies from human patients that target the receptor-binding domain (RBD) and others that target the N-terminal domain (NTD). They found using in vitro assays that both neutralizing and (especially) non-neutralizing antibodies that bound to the NTD showed antibody-dependent enhancement in cell infection. This took place partly through a well-known ADE pathway involving the Fc-gamma receptor, which allows for infection of macrophages, and this was indeed the main mechanism seen with ADE of the earlier (2003) SARS virus. It should be noted, though, that these seem to use different subtypes of the Fc-gamma receptor, so they’re not completely identical. And there were other cellular ADE events that were Fc-receptor-independent, though a mechanism that has not yet been worked out.

But the Li et al. paper went on to demonstrate that this does not seem to happen in animal models for these SARS-CoV-2 antibodies. Indeed, antibodies that showed ADE in the cell culture models still protected primates from viral replication when they were challenged by the actual virus. Three of the 36 monkeys in the study had increased lung inflammation compared to controls, but still had decreased viral replication, which makes it likely not ADE (which depends on viral infection being worse) but some sort of effect of antibody treatment that is not mediated by virus. None of the animals that got the highest doses of antibodies, for example, showed any of these effects.

And the authors note that if antibody treatment led to ADE in humans, then it would have been seen in the convalescent serum trials and in its clinical usage. But it was not. Convalescent serum was not very beneficial in the end, but it was definitely not harmful. The paper also points out that the vaccine trials and the use of the vaccines in clinical practice have led to no signs of ADE, either. So ADE in cells for SARS-CoV-2 does not seem to translate to animal models of infection, and nothing of the sort has so far been observed in the (huge) human population.

Perhaps that’s why I haven’t been sent so many copies of the Li et al. manuscript, but rather this new one (Yahi et al.) I think it’s the title as well, which is an eye-catcher: “Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination?” The authors build on the earlier paper and make comparisons to the protein sequence of the Delta variant. They believe that the antibodies identified in the Li et al. paper as causing ADE in cell assays cause the Delta variant NTD to be more tightly bound to the membrane of human cells through an interaction with cell-surface lipid rafts, and they speculate that the balance between neutralization and infection enhancement, while favorable for earlier strains of the coronavirus, is tipped the other way for the Delta variant (thus the title of the paper, and this its rather bizarre Figure 2). About that title, while we’re on it – I’m not completely sure why they reference mass vaccination risks and not risks posed by previous infection by non-Delta strains, because I would have to think that the same concerns would apply.

This one is not a very long paper, and there’s a good reason for that – it contains no experimental data. The postulated binding enhancement via lipid rafts is completely a molecular modeling result, and has not been demonstrated in actual cells. Their computations are explained in more detail in another paper, where you can see that the authors believe that it’s the kinetics of the lipid-raft interaction that may drive transmissibility of various viral strains.

I have no comment on that per se, but I do have to note that modeling-only conclusions about large protein binding events have to be confirmed by experimental data before they can be taken seriously. There are a great number of things that look plausible in such simulations that do not translate to reality. To illustrate that, here is a paper from the same three authors, again completely based on molecular modeling, that goes into a detailed mechanistic explanation of how azithromycin and hydroxychloroquine work together as an effective therapy against the coronavirus. The azithromycin binds to the RBD, you see, while the HCQ is affecting the conformation down at the lipid-raft-binding part of the NTD (this one’s also lipid-raft-centric). That latter interaction is the subject of this earlier paper. The problem is, these two drugs together (or separately) are not actually an effective therapy for coronavirus infection, a fact that the earlier papers’ citations of the work of Didier Raoult cannot overcome. It is a detailed calculated hypothesis to explain something that does not, in fact, exist.

This is a constant danger with simulations. Readers who have not encountered much molecular modeling are often (and understandably) impressed by the graphics and tables that appear with such work, but if you’ve been involved with actual experimentation you’ve seen many, many examples of such hypotheses that turned out to be built on air. Confusing the graphics with reality is a constant danger for all of us.

And in my view, the Yahi et al. paper is not aligned with reality. They do work in a line about how “although the results obtained so far have been rather reassuring. . .” with a reference to the Li et al. paper, but they should also refer to the massive amount of real-world evidence now available. We have hundreds of millions of people who have been vaccinated to produce antibodies against the non-Delta coronavirus protein domains and are who are now being exposed to the Delta variant. To reiterate, there is (to the best of my knowledge) no evidence whatsoever of ADE in this situation. In fact, we see the opposite: people who have been vaccinated are far less likely to become infected with the Delta variant, and if they become infected, they are far less likely to experience severe disease. These trends have been seen over and over in different populations, and they are the exact opposite of what you would see if ADE were operating. If the mechanism proposed by Yahi et al. were happening in the real world, then we should see higher Delta infection rates among vaccinated people, with more severe disease. We are not. We are seeing the reverse. The vaccines simply to not appear to be causing ADE, no matter how many reasons one might be able to spin for them to do so.

In short, get real.

https://blogs.sciencemag.org/pipeline/archives/2021/08/16/a-new-antibody-dependent-enhancement-hypothesis

Having SARS-CoV-2 once gives much more immunity than jab—but no infection parties, please

 The natural immune protection that develops after a SARS-CoV-2 infection offers considerably more of a shield against the Delta variant of the pandemic coronavirus than two doses of the Pfizer-BioNTech vaccine, according to a large Israeli study that some scientists wish came with a “Don’t try this at home” label. The newly released data show people who once had a SARS-CoV-2 infection were much less likely than never-infected, vaccinated people to get Delta, develop symptoms from it, or become hospitalized with serious COVID-19.

The study demonstrates the power of the human immune system, but infectious disease experts emphasized that this vaccine and others for COVID-19 nonetheless remain highly protective against severe disease and death. And they caution that intentional infection among unvaccinated people would be extremely risky. “What we don’t want people to say is: ‘All right, I should go out and get infected, I should have an infection party.’” says Michel Nussenzweig, an immunologist at Rockefeller University who researches the immune response to SARS-CoV-2 and was not involved in the study. “Because somebody could die.”

The researchers also found that people who had SARS-CoV-2 previously and received one dose of the Pfizer-BioNTech messenger RNA (mRNA) vaccine were more highly protected against reinfection than those who once had the virus and were still unvaccinated. The new work could inform discussion of whether previously infected people need to receive both doses of the Pfizer-BioNTech vaccine or the similar mRNA vaccine from Moderna. Vaccine mandates don’t necessarily exempt those who had a SARS-CoV-2 infection already and the current U.S. recommendation is that they be fully vaccinated, which means two mRNA doses or one of the J&J adenovirus-based vaccine. Yet one mRNA dose might be enough, some scientists argue. And other countries including Germany, France, Italy, and Israel administer just one vaccine dose to previously infected people.

The study, conducted in one of the most highly COVID-19–vaccinated countries in the world, examined medical records of tens of thousands of Israelis, charting their infections, symptoms, and hospitalizations between 1 June and 14 August, when the Delta variant predominated in Israel. It’s the largest real-world observational study so far to compare natural and vaccine-induced immunity to SARS-CoV-2, according to its leaders.

The research impresses Nussenzweig and other scientists who have reviewed a preprint of the results, posted yesterday on medRxiv. “It’s a textbook example of how natural immunity is really better than vaccination,” says Charlotte ThĂ¥lin, a physician and immunology researcher at Danderyd Hospital and the Karolinska Institute who studies the immune responses to SARS-CoV-2. “To my knowledge, it’s the first time [this] has really been shown in the context of COVID-19.”

Still, ThĂ¥lin and other researchers stress that deliberate infection among unvaccinated people would put them at significant risk of severe disease and death, or the lingering, significant symptoms of what has been dubbed Long Covid. The study shows the benefits of natural immunity, but “doesn’t take into account what this virus does to the body to get to that point,” says Marion Pepper, an immunologist at the University of Washington, Seattle. COVID-19 has already killed more than 4 million people worldwide and there are concerns that Delta and other SARS-CoV-2 variants are deadlier than the original virus.

The new analysis relies on the database of Maccabi Healthcare Services, which enrolls about 2.5 million Israelis. The study, led by Tal Patalon and Sivan Gazit at KSM, the system’s research and innovation arm, found in two analyses that never-infected people who were vaccinated in January and February were, in June, July, and the first half of August, six to 13 times more likely to get infected than unvaccinated people who were previously infected with the coronavirus. In one analysis, comparing more than 32,000 people in the health system, the risk of developing symptomatic COVID-19 was 27 times higher among the vaccinated, and the risk of hospitalization eight times higher.

“The differences are huge,” says ThĂ¥lin, although she cautions that the numbers for infections and other events analyzed for the comparisons were “small.” For instance, the higher hospitalization rate in the 32,000-person analysis was based on just eight hospitalizations in a vaccinated group and one in a previously infected group. And the 13-fold increased risk of infection in the same analysis was based on just 238 infections in the vaccinated population, less than 1.5% of the more than 16,000 people, versus 19 reinfections among a similar number of people who once had SARS-CoV-2.

No one in the study who got a new SARS-CoV-2 infection died—which prevented a comparison of death rates but is a clear sign that vaccines still offer a formidable shield against serious disease, even if not as good as natural immunity. Moreover, natural immunity is far from perfect. Although reinfections with SARS-CoV-2 are rare, and often asymptomatic or mild, they can be severe.

In another analysis, the researchers compared more than 14,000 people who had a confirmed SARS-CoV-2 infection and were still unvaccinated with an equivalent number of previously infected people who received one dose of the Pfizer-BioNTech vaccine. The team found that the unvaccinated group was twice as likely to be reinfected as the singly vaccinated.

“We continue to underestimate the importance of natural infection immunity … especially when [infection] is recent,” says Eric Topol, a physician-scientist at Scripps Research. “And when you bolster that with one dose of vaccine, you take it to levels you can’t possibly match with any vaccine in the world right now.”

Nussenzweig says the results in previously infected, vaccinated people confirm laboratory findings from a series of papers in Nature and Immunity by his group, his Rockefeller University colleague Paul Bieniasz and others—and from a preprint posted this month by Bieniasz and his team. They show, Nussenzweig says, that the immune systems of people who develop natural immunity to SARS-CoV-2 and then get vaccinated produce exceptionally broad and potent antibodies against the coronavirus. The preprint, for example, reported that people who were previously infected and then vaccinated with an mRNA vaccine had antibodies in their blood that neutralized the infectivity of another virus, harmless to humans, that was engineered to express a version of the coronavirus spike protein that contains 20 concerning mutations. Sera from vaccinated and naturally infected people could not do so.

As for the Israel medical records study, Topol and others point out several limitations, such as the inherent weakness of a retrospective analysis compared with a prospective study that regularly tests all participants as it tracks new infections, symptomatic infections, hospitalizations, and deaths going forward in time. “It will be important to see these findings replicated or refuted,” says Natalie Dean, a biostatistician at Emory University.

She adds: “The biggest limitation in the study is that testing [for SARS-CoV-2 infection] is still a voluntary thing—it’s not part of the study design.” That means, she says, that comparisons could be confounded if, for example, previously infected people who developed mild symptoms were less likely to get tested than vaccinated people, perhaps because they think they are immune.

Nussenzweig’s group has published data showing people who recover from a SARS-CoV-2 infection continue to develop increasing numbers and types of coronavirus-targeting antibodies for up to 1 year. By contrast, he says, twice-vaccinated people stop seeing increases “in the potency or breadth of the overall memory antibody compartment” a few months after their second dose.

For many infectious diseases, naturally acquired immunity is known to be more powerful than vaccine-induced immunity and it often lasts a lifetime. Other coronaviruses that cause the serious human diseases severe acute respiratory syndrome and Middle East respiratory syndrome trigger robust and persistent immune responses. At the same time, several other human coronaviruses, which usually cause little more than colds, are known to reinfect people regularly.

https://www.sciencemag.org/news/2021/08/having-sars-cov-2-once-confers-much-greater-immunity-vaccine-no-infection-parties

Largest Study of Long COVID Points to an Alarming Prognosis

 The body of real-world evidence around COVID-19 continues to build, and a study released Thursday in The Lancet points to concerning long-term effects for hospital survivors at the one-year mark. 

The study, which was led by Dr. Bin Cao from the China-Japan Friendship Hospital in Beijing, is a head-to-head comparison of 1,276 people discharged from Jin Yin-Tan Hospital in Wuhan between January and May 2020 and comparable Wuhan residents who were not infected with COVID-19. In what is the largest paper of its kind yet to be published, the former patients were assessed at both six and 12 months following the onset of their first symptoms.

Common long-term effects suffered by COVID-19 survivors include fatigue, muscle weakness, sleep disturbances, changes in taste and smell, dizziness, headache and shortness of breath. At the six-month mark, 68% of participants reported at least one persistent symptom, which fell to 49% after one year. In all, the former patients self-reported experiencing a lower quality of life than their counterparts, and the most common maladies were fatigue and muscle weakness.

Reflective of the enigma that is COVID-19, the number of patients reporting breathing problems actually increased between the six and 12-month check-ins from 26% to 30%, while the percentage of people who felt anxious or depressed rose from 23% at six months to 30% at one year. Both mental and physical health challenges were especially prevalent among those who had experienced the most serious disease.

That people would still be in a rehabilitation period after 12 months is outside of the norm for David Putrino, director of rehabilitation innovation at Mount Sinai Health Systems in New York. Putrino told TIME that this is not an example of a glass-half-full story.

“After most hospital stays, including for, say, walking pneumonia, I would not be expecting people at 12 months to still be reporting symptoms to me,” said Putrino, who oversees the network’s Long COVID rehabilitation program.

According to Putrino, being fortunate enough to escape hospitalization may not guarantee a full immediate recovery.

“This virus doesn’t end once you get discharged from the hospital or once you get over the initial acute symptoms,” he said, referencing smaller studies showing that symptoms may linger in around 20% of these patients.

These studies could spell bad news for a lot of survivors. According to a collection of four international studies published in late July, there are more than 200 possible Long COVID symptoms. In one paper, researchers assessed responses from 3,762 patients from 56 countries with either confirmed or suspected COVID-19 and found an average of 56 reported symptoms across 9 different organ systems. More than 91% of these patients required at least 35 weeks to recover. The most commonly reported symptoms after six months were fatigue, post-exertional malaise, and cognitive disfunction. 

It appears that even vaccination is not a complete get out of jail free card in every case when it comes to preventing Long COVID. In an Israeli study of 1,497 vaccinated health care workers, 39 became infected regardless, and 7 of those individuals experienced symptoms that lasted at least six weeks.   

"We had hoped that when you get vaccinated and even if you did have a breakthrough infection you would have enough of an immune response that would block this protracted symptom complex now known as long COVID,” said Dr. Eric Topol, a professor of molecular medicine at Scripps Research. “This study is the really first to give us an indicator that there's some long-haulers among that small group of people that had breakthrough infections.”

https://www.biospace.com/article/largest-study-of-long-covid-points-to-an-alarming-prognosis-/