virology blog

Heterologous Vaccine Regimens Might be Better

5 August 2021 by Gertrud U. Rey Leave a Comment

by Gertrud U. Rey

Have you ever wondered if you can “mix and match” SARS-CoV-2 vaccines? For example, would it be ok to boost a first dose of the vaccine produced by AstraZeneca with a dose of the vaccine produced by Pfizer/BioNTech? The latest science shows that such a vaccine regimen actually induces a stronger immune response than a regimen consisting of two doses of the same vaccine.

The occasional incidence of thrombosis in people under the age of 60 after receiving an adenovirus-vectored vaccine like the ones made by AstraZeneca and Johnson & Johnson has prompted several European governments to recommend the use of these vaccines only in people over 60. Because many people under 60 had already been vaccinated with a first dose of the AstraZeneca vaccine and still needed a second dose, they had to decide whether they should continue their regimen with another dose of the same vaccine (i.e., a homologous regimen), or receive an mRNA vaccine instead (i.e., a heterologous regimen).

In an effort to evaluate the efficacy of a heterologous SARS-CoV-2 vaccine regimen, the authors of this Brief Communication engaged the participants of an ongoing clinical trial, which aims to monitor the immune responses to SARS-CoV-2 in health care professionals and individuals with potential exposure to SARS-CoV-2. All study participants had already received a first dose of the AstraZeneca vaccine (referred to as “ChAd” in the study) and were given the option of receiving a second dose of the same vaccine or a dose of Pfizer/BioNTech’s mRNA vaccine (referred to as “BNT”). Although both of these vaccines encode the gene for the full-length SARS-CoV-2 spike protein, it is housed slightly differently. In the ChAd vaccine, the spike protein is encoded in an adenovirus vector of chimpanzee origin, while in the BNT vaccine it is surrounded by a lipid nanoparticle.

Out of the 87 individuals who participated in the study, 32 chose a second dose of ChAd and 55 chose to be vaccinated with BNT instead. Participants who chose a homologous ChAd/ChAd regimen received their second dose of ChAd on day 73 after the initial dose and donated a blood sample for analysis 16 days later. Participants who chose a heterologous ChAd/BNT regimen received their dose of BNT 74 days after their initial ChAd dose and donated a blood sample 17 days later. All results obtained from the analyses of the blood samples from these two groups were compared to results obtained from a group of 46 health care professionals who had been vaccinated with two doses of BNT (i.e., a homologous BNT/BNT regimen).

Briefly, the findings were as follows. Relative to the antibody levels induced by the first dose, homologous boosting with ChAd led to a 2.9-fold increase in IgG antibodies against the SARS-CoV-2 spike protein. IgG antibodies are mostly present in the blood and provide the majority of antibody-based immunity against invading pathogens. In contrast, heterologous boosting with BNT led to an 11.5-fold increase in anti-spike IgG, within the range observed in BNT/BNT-vaccinated individuals. A similar pattern was observed with anti-spike IgA antibodies, which are predominantly found in mucus membranes and their fluids. Boosting with BNT induced significantly higher increases in anti-spike IgA than did boosting with ChAd, suggesting that a heterologous boosting regimen induces better antibody responses. Interestingly, although the booster immunization induced an increase in neutralizing (i.e., virus-inactivating) antibodies in both vaccination groups, only heterologous ChAd/BNT vaccination induced antibodies that neutralized all three tested variants (Alpha, Beta, and Gamma), similar to what was observed in BNT/BNT vaccine recipients.

The authors also analyzed the effect of the two different boosting regimens on spike-specific memory B cells, which circulate quiescently in the blood stream and can quickly produce spike-specific antibodies upon a subsequent exposure to SARS-CoV-2. All vaccinees from both the ChAd/ChAd and ChAd/BNT groups produced increased levels of spike-specific memory B cells after receiving their booster shot, with no significant differences observed between the two groups. These results emphasize the importance of booster vaccination for full protection from SARS-CoV-2 infection.

ChAd/BNT recipients also had significantly higher levels of spike-specific CD4⁺– and CD8⁺ T cells compared to ChAd/ChAd recipients. CD4⁺T cells are a central element of the adaptive immune response, because they activate both antibody-secreting B cells and CD8⁺ T cells that kill infected target cells. Compared to the ChAd/ChAd regimen, ChAd/BNT vaccination also induced significantly increased levels of T cells that produce spike-specific interferon gamma – a cytokine that inhibits viral replication and activates macrophages, which engulf and digest pathogens. Overall, these results suggest that a heterologous ChAd/BNT regimen induces significantly stronger immune responses than a homologous ChAd/ChAd regimen.

The study did have several limitations. First, it was not a randomized, placebo-controlled trial where each participant was randomly assigned to an experimental group or a control group. Randomizing trial participants eliminates unwanted effects that have nothing to do with the variables being analyzed, so that the only expected differences between the experimental and control groups are the outcome variable studied (efficacy in this case). Subjects in a control group receive a placebo – a substance that has no therapeutic effect, so that one can be sure that the effects observed in the experimental group are real and result from the experimental drug. Second, the authors were unable to test the antibodies for their ability to neutralize the Delta variant, which has recently become the predominantly circulating variant in many parts of the world. Third, the study mostly included young and healthy people, making it difficult to extrapolate the data to other specific patient groups outside of this category. Fourth, the data only show the results of assays performed in vitro, which may not necessarily manifest a clinical significance. Extended studies aimed at determining the practical importance of the observed immune responses are needed to validate the relevance of these responses.

Despite its limitations, the study provides information that could have some valuable practical implications. Most of the currently approved SARS-CoV-2 vaccine regimens involve two doses of the same vaccine. However, access to two doses of the same vaccine may be limited or absent under some circumstances, thus necessitating the use of a different type of vaccine to boost the first dose.

[For a more in-depth discussion of this study, I recommend TWiV 782.]

Trial By Error: Neurology Journal Fixes False Claim in MUS Paper–But Fails to Publish a Correction Notice (Ironically, I Have Added a Correction to the Post!)

31 July 2021 by David Tuller 5 Comments

By David Tuller, DrPH

UPDATE: August 4, 2021

Dr Villemarette-Pittman, the managing editor of Journal of the Neurological Sciences, has informed me that she has learned from Elsevier that a corrigendum has in fact been written and will be published in the near future. She also informed me that she plays no role in deciding on or setting policy about corrections and corregendi, and when or how they are published. I am very glad to hear about the corrigendum. Had I been informed earlier in the cycle of e-mail exchanges that the lack of a corrigendum did not mean that none was forthcoming and that a response from Elsevier was being sought, I would have written the blog post differently and/or updated it sooner. Dr Villemarette-Pittman had responded on behalf of the journal to my initial e-mail about the error, so I assumed she understood the practices and policies around corrections and corregendi. I apologize to Dr Villemarette-Pittman for having made that mistaken assumption.

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*Correction: I initially referred to Dr Villemarette-Pittman as a “neurologist.” I did not mean to indicate that she is a clinician but rather an academic specialist. She is an associate professor of research in neurology and oversees neurological research at her university. I apologize for any confusion.

*Note: Also, after reading this blog post, Dr Villemarette-Pittman noted that she is not the editor-in-chief nor the publisher of the journal, and clarified that she does not make decisions about corrigenda. (For the record, I have not referred to her as the editor-in-chief or the publisher, nor have I stated that she makes decisions about corrigenda.) I wrote to two editors initially about the error, and she responded. That is why we have been in correspondence over this issue.

I’ve recently bugged two separate journals to correct the same error—a mis-citation of a study concerning the estimated costs to the UK’s National Health Service of so-called “medically unexplained symptoms” (MUS). One of the journals, Psychological Medicine, has corrected the mistake and has also published a standard notice called a corrigendum that alerts readers to the fact that a change has been made.

In contrast, Journal of the Neurological Sciences has corrected the error in the text of the paper in question but has not published a corresponding corrigendum—or at least not one that I can find on the site of this Elsevier publication. Perhaps one is coming, although the offending sentence was fixed weeks ago, according to my communications with the journal. It is not acceptable for a journal to make a substantive correction and not indicate that this has happened.

I’ve got a real thing about this particular error because it has been repeatedly committed in multiple articles since the paper containing the original finding, Bermingham et al, was published in 2010. Bermingham et al estimated that the cost of treating working-age people with MUS accounted for 10% of the NHS budget for that demographic group. (The study involved England only.) That statistic has routinely been mis-rendered as 10% of total NHS costs—that is, for all ages. In fact, the study estimated that the total spent on working-age people with MUS accounted for around 3% of the NHS budget, not 10%. (In making this point, I am not endorsing Bermingham et al’s methodology or its estimates.)

The same time period has also witnessed a forceful push to expand NHS mental health care for patients diagnosed as experiencing MUS—an expansion implemented through a program called Improving Access to Psychological Therapies (IAPT). Medical experts in the MUS field have been among those advising the government on this IAPT expansion. They have also been among those mis-citing Bermingham et al in a way that dramatically increases the apparent health care burden of MUS. It is self-evident that demonstrating the high cost of MUS to the NHS would be likely to generate or bolster support for expanding services for these patients—as advocated by some of those doing the mis-citing.

I’m not suggesting that these mis-citations have been intentional. In fact, I assume they were all unintentional. This episode demonstrates how a false data point or meme takes hold and gains currency because it fits the preconceptions and the interests of those perpetuating it. Some of those mis-citing the claim likely picked it up from a previous mistaken reference without actually checking the original source themselves. After all, it made sense to them that MUS was such an enormous problem that it could account for 10% of the total NHS budget.

Some investigators have been repeat mis-citers of Bermingham et al. That is the case with Professor Anthony David, a neurologist at University College London and the senior author of the article published by Journal of the Neurological Sciences, called “Medically unexplained visual loss in a specialist clinic: a retrospective case-control comparison.” He also was senior author of the paper in Psychological Medicine that was corrected due to my intervention. And he is a co-author of the published protocol for a major clinical trial, which included the same mistake and was corrected in 2019 after I alerted the journal.

This was the sentence in the first version of the paper published by Journal of the Neurological Sciences (with the original misspelling of the first author of the cited study retained): “In estimation of the associated health costs of medically unexplained symptoms, Birmingham [sic] & colleagues propose that healthcare utilisation amounts to £3billion per annum, or 10% of total NHS expenditure.” In the current version of the paper, the sentence now reads: “In estimation of the associated health costs of medically unexplained symptoms, Bermingham & colleagues propose that healthcare utilisation amounted to £3billion in the year 2008-2009, or approximately 10% of total NHS expenditure on these services for the working-age population during this period.” (I’m glad they also corrected the spelling of Bermingham et al.)

Professor David* [I initially wrote Professor Anthony here–I apologize for the error], his co-authors and Journal of the Neurological Sciences have an obligation to make corrections in a transparent manner. Fixing sentences but giving the appearance that nothing has been done does not meet this basic academic standard and cannot be justified. Interestingly, the same journal published a formal corrigendum last summer when a misspelt name was corrected. Certainly a mistake that has the effect of more than tripling the apparent costs of MUS to the NHS is of sufficient gravitas that the journal should be willing to accord it the same treatment.

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Letter to editor of Journal of the Neurological Sciences

I have sent the following letter to Dr Nicole Villemarette-Pittman, an assistant professor of research in neurology* [this sentence has been corrected] at Louisiana State University and the journal editor with whom I had been corresponding about the error:

[After reading this blog post, Dr Villemarette-Pittman sent an e-mail noting that she is not the editor-in-chief nor the publisher of the journal, and does not make decision about corrigenda. I have not called her the editor-in-chief or the publisher, nor have I claimed she makes decisions abou corrigenda. I wrote to two editors initially about the correction, and she responded. That’s why I have been in correspondence with her.]

Dear Dr Villemarette-Pitman–

I am writing a post for Virology Blog about the apparent decision by the Journal of the Neurological Sciences not to indicate or flag the correction of O’Leary et al with an actual corrigendum. (If there is a corrigendum and I can’t find it for some reason, please advise!) Do you want to comment on why the journal has chosen not to issue a corrigendum for this correction? It does seem rather unusual to correct a substantive factual error and not alert readers that anything has been changed.

This was not a typo or a grammatical error. The mistake had the effect of more than tripling the presumed impact of so-called “medically unexplained symptoms” on the National Health Service’s budget. According to the corrections policies of Elsevier, your publisher, a corrigendum is appropriate when “a small portion of an otherwise reliable publication proves to be misleading (especially because of honest error).” That certainly seems to be the appropriate approach here–or should have been. The claim in the paper was highly misleading and presumably unintentional.

The International Committee of Medical Journal Editors has also highlighted the importance of identifying a correction. When a correction is made, according to the ICMJE guidelines (as cited in Elsevier’s website), “the journal should publish a correction notice as soon as possible detailing changes from and citing the original publication.”

In other words, simply correcting a sentence that includes a factual error–as you have done in this instance–is insufficient. By any standard, transparency requires the publication of an explanatory corrigendum as well.

I will likely post this comment on the journal’s actions tomorrow (Friday). If I receive a response from you after I have already posted, I will be happy to update the blog.

Best–David

David Tuller, DrPH
Senior Fellow in Public Health and Journalism
Center for Global Public Health
School of Public Health
University of California, Berkeley

Paul and the Mosquitos

30 July 2021 by Vincent Racaniello 2 Comments

From the authors of Paul Has Measles and Paul Stays Home comes Paul and the Mosquitos, an illustrated book for children about mosquito-borne diseases.

In his camp, Paul and his friends discuss which is the most dangerous animal of all. They would never have imagined it would be the mosquito. Why are they dangerous and what can we do to prevent the diseases transmitted by them?

Paul and the Mosquitoes is written by Susana López, Selene Zárate, and Martha Yocupicio, with illustrations by Eva Lobatón.

A pdf of Paul and the Mosquitos can be downloaded free of charge here.

T cells will save us from COVID-19, part 3

29 July 2021 by Vincent Racaniello 6 Comments

In the two previous installments (one, two) of what has now become my praise of T cells, I explained that the SARS-CoV-2 protein sequences recognized by T cells do not change, likely explaining why vaccines prevent serious disease and death caused by any variant. Today I will explain that virus-specific T cells appear a week after mRNA vaccination when neutralizing antibodies are weakly detectable. Their presence is likely responsible for vaccine-mediated protection against severe disease.

Since the first COVID-19 vaccines were tested in clinical trials, much has been made of their ability to block infection. At ten days after the first vaccine dose, clear protection against severe disease is observed. But at this early time, neutralizing antibodies can barely be detected. That job is likely being done by T cells, the other arm of the adaptive immune response.

T lymphocytes come in two broad types: CD8+ and CD4+. The former, also known as cytotoxic T lymphocytes (CTLs) can recognize a virus infected cell and kill it (pictured). The latter T cells produce cytokines that are important for maturation of both CTLs and B cells, the antibody-producing cells. The importance of antibody versus T cells in controlling infection depends on the virus. For many viruses, antibody can block infection, but T cells are important for recovery. In COVID-19, antibodies rise late in the course of infection, when virus titers are already declining. This observation is in line with the resolution of infection by T cells.

People with agammaglobulinemia, who cannot make antibodies, or who have been depleted of B cells do not have a serious course of COVID-19, further supporting a role for T cells in preventing severe disease.

During the trials of mRNA vaccines it was observed that protection against severe COVID-19 arose at 10 days after the first inoculation, a time when neutralizing antibodies are barely detectable in serum. The logical candidate for this effect is the T cells.

To address this question, a group of mRNA vaccine recipients were sampled at different times after the first and second doses. CD8+ T cells in blood were examined for the ability to recognize a few spike-specific epitopes. A rapid and substantial induction of CD8+ T cells in these individuals was observed beginning at 6-8 days after the first vaccine dose. At this time, neutralizing antibodies in sera of these subjects were barely detectable. CD8+ T cell numbers are substantially increased by the second vaccine dose, which also leads to much higher levels of neutralizing antibodies. CD4+ T cells are also detected after the first vaccine dose and likely coordinate the expansion of CD8+ T cells and B cells.

mRNA vaccination also induces spike-specific memory B and T cells which circulate for at least several months. Their exact longevity remains to be determined by longer term studies.

The gradual escape of multiple variants of concern from neutralization by sera from vaccinated individuals has been met with alarm by public health officials. At least one prominent leader has suggested that the virus might even mutate so as to escape vaccine protection. An even cursory examination of the facts reveals otherwise. Despite reduced neutralization by vaccine-induced antibodies, vaccine recipients are still protected from severe disease and death by all variants. In contrast to changing B cell epitopes, T cell epitopes do not change in any variant. Furthermore, virus-specific T cells are induced early after the first mRNA vaccine dose, and confer protection against severe COVID-19 at a time when neutralizing antibodies are barely detectable. These observations indicate that T cells will save us from COVID-19.

In vaccinology, the correlate of protection refers to what is needed – antibodies or T cells – to protect from infection or disease. High levels of antibodies appear to correlate with protection against infection by SARS-CoV-2. However, when antibody levels decline, as they always do after infection or vaccination, infection can no longer be prevented. In this case, protection against severe disease and death is accomplished by T cells.

Trial By Error: Tack and I Write to Psych Medicine; Struthers Writes to Medical Research Council

24 July 2021 by David Tuller 4 Comments

By David Tuller, DrPH

A recent study of cognitive behavior therapy (CBT) for patients with “persistent physical symptoms” (PPS), a category alsocalled “medically unexplained symptoms,” reported null results for its primary outcome. These null results were not mentioned in the conclusion of the abstract, which instead focused on minimal reported benefits for a minority of secondary outcomes. This is not cool! The study was published in Psychological Medicine—a journal with close ties to the PACE investigators and other members of the CBT ideological brigades.

Trial By Error: CBT Model of Medically Unexplained Symptoms, Explained; CBT Trial for Q-Fever Fatigue

22 July 2021 by David Tuller 5 Comments

By David Tuller, DrPH

As I have recently written, four major clinical trials of CBT for so-called MUS have documented the opposite of what the investigators hoped to prove. In fact, the evidence from this research suggests that CBT is not an effective treatment for these conditions. That hasn’t stopped these investigators from claiming otherwise, of course. As my earlier post indicated, they have deployed a range of methodological, statistical and rhetorical strategies to obfuscate or downplay their poor results. Three of these studies were based at King’s College London, and one—the now-discredited PACE trial—at Queen Mary University of London.

Trial By Error: Medical Societies and new Komaroff-Lipkin Paper Highlight Long COVID and ME/CFS Links

20 July 2021 by David Tuller 2 Comments

By David Tuller, DrPH

While some medical professionals argue that prolonged non-specific symptoms after acute COVID-19 are psychogenic and that “Long COVID” as a presumed clinical entity was concocted by a cabal of queers and feminists, others are getting on with efforts to disseminate more appropriate information to their colleagues. These efforts often involve drawing parallels with the pathophysiology of ME/CFS.

A whale of a virus story

15 July 2021 by Vincent Racaniello 4 Comments

The ancestors of cetaceans (whales, dolphins, and porpoises) moved from land to the sea over 50 million years ago. Many viruses infect cetaceans, but how they evolved during the shift from land to sea is unknown. Fossilized retroviral genomes integrated into cetacean DNA provide insight into this question.

The retroviral reproduction cycle involves the conversion of viral RNA into DNA followed by integration in host chromosomes, leading to what is know as proviral DNA. If this integration event occurs in germ cells, the provirus may be transmitted to offspring for many generations. Analysis of cetacean endogenous retroviral DNA (ERV) provides insight into when in evolution these viruses were acquired.

Cetacean retroviruses may have arisen in two ways. In the land-to-water scenario (pictured), the terrestrial ancestor of cetaceans was infected, and then carried the retrovirus into the oceans. In the secondary host switching scenario, only after cetaceans were in the oceans were they infected by cross-species transmission from other non-cetacean mammals.

Analysis of cetacean ERVs provides support for both scenarios. A search of the sequenced genomes of mysticetes (baleen whales) and odontocetes (toothed whales) revealed 8,724 ERVs. Phylogenetic analysis of these ERVs places them into 315 distinct lineages. Of these, 298 are found in both mysticetes and odontocetes, implying that they were present before these lineages diverged. The copy numbers of these ERVs are very low, suggesting that they did not proliferate after their hosts entered the waters. Some are related to ERVs found in hippopotamuses, which share a common ancestor with cetaceans, and are even found the the same location in the genomes.

Another 17 lineages were not common to mysticetes and odontocetes, but are found in specific sub-lineages of cetaceans. This observation suggests that they were acquired from other non-cetacean mammals. In support of this hypothesis, it was found that these ERVs are closely to ERVs in a variety of land mammals including bats and cows. These ERVs are more numerous in the cetacean genome, implying that they entered recently and might still be infecting these mammals. Whether or not the infections have pathogenic consequences is unknown.

The reader might be asking how a whale might acquire a virus from terrestrial and semi-aquatic mammals. Apparently there is more interaction of cetaceans with these animals than we think: killer whales have been observed feeding on terrestrial mammals and seals.

Given the difficulty in sampling cetaceans, it will be difficult to determine how other viruses originated in these animals. This question can be readily addressed for endogenous retroviruses because they are integrated into germline DNA, often for millions of years.

Trial By Error: Some Lightning Process Updates

13 July 2021 by David Tuller 15 Comments

By David Tuller, DrPH

A Final Round in Norway

Lightning Process supporters got some bad news recently when a Norwegian national research ethics panel rejected a proposed study because it was poorly designed and fraught with conflicts of interest, as I wrote about here. But that wasn’t the end of the drama.

Although the ethics panel’s decision was meant to be final and not subject to appeal, the study team appealed anyway, sending a long letter to the ethics panel defending the trial’s methodology and disputing the charges of conflicts of interest. The ethics panel agreed to take up the issue one more time. After another review, the panel reinforced its initial action by firmly rejecting the proposed study a second time. The ethics panel has made clear that it is not categorically against research into the Lightning Process—just this inadequate effort.

Evolution of a bacterial protein into a virus-like, RNA binding capsid

8 July 2021 by Vincent Racaniello 1 Comment

Starting with a bacterial protein, directed evolution in the laboratory has been used to produce a virus-like capsid that binds and protects RNA. This finding has implications for the origins of viruses.

One view of the evolution of life is that viruses were present even before the first cells in the form of self-replicating molecules. These were technically not viruses, because they did not need cells for their replication. The idea is that when cells did arise, the replicators invaded them and then recruited host proteins for the formation of capsids.

The starting point for experiments intended to provide insight into how a protein might become a viral capsid is a bacterial protein, lumazine synthase, that forms 60-subunit particles that have no affinity for nucleic acids. The protein was redesigned and linked to a peptide that binds to an RNA stem-loop called BoxB. It was then further modified for the ability to package an mRNA that encodes the synthase. Packaging was stimulated by adding BoxB tags to the ends of the mRNA. However, only one of 8 particles packaged the mRNA.

To improve the capsid, the bacterial gene was mutagenized and capsids were selected by rounds of incubation with ribonuclease of smaller and smaller size. The idea was that this strategy would select for capsids that not only packaged the mRNA but would protect it from RNAse digestion. The result was a protein that could form a capsid called NC-4 (pictured) which encapsidated mainly the mRNA and protected it from digestion.

The changes that occurred during this evolution process led to the production of what looks very much like a viral capsid. It is composed of 240 protein subunits arranged in pentamers and hexamers with t=4 icosahedral symmetry*. The amino acid changes that led to the formation of this capsid can be readily discerned. The pores on the capsid are very small, explaining its relative nuclease resistance compared with earlier versions. In addition, the RNA appears to play a role in assembly of the capsid. Finally, changes in the mRNA appear to have led to formation of a stem-loop which facilitates packaging of the nucleic acid into the particle.

These results are amazing: we know that arranging proteins with icosahedral symmetry is an efficient way to build a stable virus particle with the least number of subunits, confirmed by the directed evolution of an icosahedrally ordered and stable capsid.

These observations have multiple implications. They show how ancient self-replicating RNA molecules, the precursors of viruses, might have recruited a host protein and driven its evolution into a protective capsid that specifically packages only the viral RNA. They also indicate how stable particles might be designed as alternatives (dare I say improvements?) to viruses for therapeutic purposes, such as gene therapy and vaccination.

*If you do not understand what icosahedral symmetry is or what t=4 means, please watch my lecture on virus structure.