virology blog
About viruses and viral disease
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.
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.
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.
[Read more…] about Trial By Error: Some Lightning Process Updates
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.
By David Tuller, DrPH
My friend and colleague Steven Lubet is a professor of law at Northwestern University. He and I have collaborated on a number of articles, including a response to Professor Michael Sharpe’s views on so-called “medically unexplained symptoms” in the journal Medical Humanities and a piece on links between ME/CFS and Long COVID for STAT. This spring, along with Professor Brian Hughes, a psychologist at the National University of Ireland, Galway, we wrote an essay for Health Affairs, a public health journal, about the ongoing paradigm shift in this medical domain.
By David Tuller, DrPH
Last week, I wrote about the correction made to the “Highlights” section of the paper reporting the long-term follow-up results for the GETSET trial. (The trial was conducted by Professor Peter White, one of the three lead PACE investigators, and colleagues.) I noted that this correction was not indicated or identified—a fact I attributed to the ambiguous status of “Highlights” sections, which could be viewed as more like news headlines than part of a paper’s core text.
By David Tuller, DrPH
A year ago, I wrote a post about how the biopsychosocial ideological brigades had completed a trifecta of major studies that investigated cognitive behavior therapy for a variety of so-called “medically unexplained symptoms” (MUS). As a group, the studies demonstrated the overall ineffectiveness of CBT as a treatment for this category of disorders—despite herculean efforts to spin the results the other way. MUS is usually defined to include chronic fatigue syndrome, irritable bowel syndrome, fibromyalgia, functional neurological disorders, and other conditions for which pathophysiological mechanisms have not been identified.
Gertrud U. Rey
Vaccination against the vaccine-preventable diseases is preferable to natural infection because it prevents illness and the long-term effects associated with many infections; and in most cases, it also leads to better immunity. In the case of immunity induced by SARS-CoV-2 vaccination, it is slowly becoming clear that the immunity is of overall better quality than that induced by COVID-19.
Vaccination leads to production of polyclonal antibodies, which are derived from many different types of B cells and may target many different portions of an antigen (i.e., “epitopes”). Isolation of B cells from a blood sample allows one to artificially produce monoclonal antibodies, which are derived from a single type of B cell and target a single epitope. Using blood samples from 6 SARS-CoV-2 mRNA vaccine recipients and 30 COVID-19 survivors, the authors of a recent publication compared the dynamics of vaccine-induced antibody immunity to those resulting from natural infection. A comparison of total antibodies between the two groups of people revealed that polyclonal antibody levels in vaccinees were generally higher than those in COVID-19 survivors. However, when the authors tested the antibodies from vaccinees for SARS-CoV-2 neutralizing activity, only a minority were neutralizing, including antibodies that target the receptor-binding domain (RBD) on the SARS-CoV-2 spike protein.
To see whether any of the neutralizing antibodies from vaccinees were capable of binding to the RBD, the authors performed competition experiments, where they exposed the antibodies to the SARS-CoV-2 RBD alone, or to RBD pre-mixed with its binding target – the human ACE2 receptor. This experiment revealed that increasing concentrations of ACE2 led to decreased antibody binding, suggesting that the antibodies compete with the ACE2 receptor for binding to the RBD, and that they neutralize the virus by inhibiting its binding to ACE2.
A plasmablast is a type of B cell that differentiates from an immature B cell into a mature plasma cell, which can produce large amounts of a specific antibody. Although they are short-lived, plasmablasts also make antibodies, and are typically abundant and easy to isolate from peripheral blood. Analysis of monoclonal antibodies produced from the plasmablasts of vaccinated individuals showed that a substantial number of these antibodies also bound the N-terminal domain of the SARS-CoV-2 spike protein in addition to the RBD, suggesting that these two epitopes co-dominate as antibody targets.
“Original antigenic sin” is a phenomenon initially discovered with influenza viruses, where the immune system mounts the strongest response to the first version of one particular antigen encountered (i.e., the first virus variant with which one is infected in life). Similar observations have been made in the context of COVID-19, with natural SARS-CoV-2 infection purportedly also substantially boosting antibodies against seasonal β-coronaviruses OC43 and HKU1. To see if SARS-CoV-2 vaccination produces a similar effect, the authors analyzed the specificity of antibodies isolated from vaccine recipients before and after vaccination against the spike protein of α-coronaviruses 229E and NL63 and β-coronaviruses OC43 and HKU1. Although vaccination did not increase titers of pre-existing antibodies against 229E and NL63 viruses, it did increase titers against OC43 and HKU1, consistent with what happens during natural SARS-CoV-2 infection. These results suggest that some of the vaccine-induced antibody responses may be biased by pre-existing immunity to other circulating human β-coronaviruses.
The authors also determined whether plasmablast-derived monoclonal antibodies and polyclonal antibodies from the sera of COVID-19 survivors and vaccinated individuals could bind to the RBDs of different SARS-CoV-2 variants. Although complete loss of binding was rare, antibodies from COVID-19 survivors varied widely in their ability to bind to different variants. Antibodies isolated from vaccinees varied less, depending on the variant. However, for most plasmablast-derived monoclonal antibodies from vaccinees, there was no impact on binding to RBDs in the binding assay used, regardless of the variant.
This study raises several interesting points. First, the ability of SARS-CoV-2 vaccination to boost pre-existing antibodies against HKU1 and OC43 supports the premise for a universal β-coronavirus vaccine, several of which are already in development. Second, the ability of the RBD and N-terminal domain to co-dominate in eliciting spike-specific antibodies justifies the use of vaccines containing the entire spike protein, rather than just the RBD. Third, although it is surprising that vaccination induced so few neutralizing antibodies, the role of non-neutralizing antibodies in protection against disease and infection is currently unknown. Considering that vaccination is obviously so protective against disease and asymptomatic infection, the authors speculate that the antibodies induced by vaccination could have protective functions outside of neutralization. Lastly, the fact that vaccination-induced antibodies fluctuate little, if at all, in their ability to bind the RBDs of different variants compared to antibodies induced by natural infection, suggests that vaccination is more likely to protect from different variants than natural infection. Collectively, these findings further highlight the importance of vaccination for ending this pandemic.
By David Tuller, DrPH
I have pressed the Journal of Psychosomatic Research to correct a recent paper—”Guided graded exercise self-help for chronic fatigue syndrome: Long term follow up and cost-effectiveness following the GETSET trial.” The senior author is Professor Peter White. Now the journal has published a revised “Highlights” section of the paper that accurately presents the study’s null results for the intervention rather than claiming success on an illegitimate basis. But the fact that this laudable change has been made is not indicated.
By David Tuller, DrPH
The Guardian has published a lot of nonsense about Long COVID and has provided a platform for people who argue that robust manly thoughts are the path to recovery. Of course, it also published George Monbiot’s powerful columns on the topic, including his rebuttal of silly accusations that he was triggering more Long COVID cases by writing about it.
So it can be a mixed bag over there.