The Evidence which Suggests that This Is No Naturally Evolved Virus A Reconstructed Historical Aetiology of the SARS-CoV-2 Spike Birger Sørensen, Angus Dalgleish & Andres Susrud Immunor & St Georges University of London
ABSTRACT To discover exactly how to attack SARS-CoV-2 safely and efficiently, our vaccine candidate Biovacc-19 was designed by first carefully analysing the biochemistry of the Spike. We ascertained that it is highly unusual in several respects, unlike any other CoV in its clade. The SARS-CoV-2 general mode of action is as a co-receptor dependent phagocyte. But data shows that simultaneously it is capable of binding to ACE2 receptors in its receptor binding domain. In short, SARS-CoV-2 is possessed of dual action capability. In this paper we argue that the likelihood of this being the result of natural processes is very small. The spike has six inserts which are unique fingerprints with five salient features indicative of purposive manipulation. We then add to the bio-chemistry a diachronic dimension by analysing a sequence of four linked published research projects which, we suggest, show by deduction how, where, when and by whom the SARS-CoV-2 Spike acquired its special characteristics. This reconstructed historical aetiology meets the criteria of means, timing, agent and place to produce sufficient confidence to reverse the burden of proof. Henceforth, those who would maintain that the Covid-19 pandemic arose from zoonotic transfer need to explain precisely why this more parsimonious account is wrong before asserting that their evidence is persuasive, most especially when, as we also show, there are puzzling errors in their use of evidence.
Introduction: Why does this matter? No-one has ever produced a safe and effective vaccine against a coronavirus. In the context of a forthcoming paper addressing contingency actions cognizant of this fact, the potentialities for 'trained immunity' from 'new old friends' in the form of Bacillus Calmette–Guérin (BCG), Microbacillus vaccae (IMM-102) and most especially Microbacillus obuense (IMM101) by stimulating the innate immune system and especially Delta Gamma T cells are explored; and a salutary review of failed vaccine programmes is included (Kleen et al., 2020). On 28th April 2020, Nature published a graphical guide to eight conceptual approaches featuring in current explorations of around 90 vaccine development programmes intended to counter SARS-CoV-2 (Callaway, 2020).
We have just (2nd June 2020) published Biovacc-19 in QRB-Discovery: a candidate vaccine for this daunting task (Sørensen et al., 2020). Its mode of action is unique and therefore is not included in the Nature review. In our paper we gave reasons why the virus vector or RNA vector based approaches that are the basis of the eight methodologies reviewed in Nature are unlikely to prove immunogenic and why either, but especially RNA vectored models, may carry significant risk of Antibody Dependent Enhancement (ADE). As we have detailed in QRB-D, we have seen such a story before over thirty years in the failure of all three mainstream vaccine approaches to HIV, which we predicted but were disbelieved.
As with our HIV vaccine, the methodology underpinning Biovacc-19 first analysed fully the virus target. In this case we published the general mode of action for infectivity of SARS-CoV-2. Doing this took us into a fundamental exploration of the biochemistry and structure of the SARS-CoV-2 Spike which is highly singular, possessed of features that we have not seen before and which are not present in other SARS viruses of that clade. We posited that the SARS-CoV-2 general mode of action is as a co-receptor dependent phagocyte. But unusually, simultaneously, data shows that it is capable of binding to ACE2 receptors in its receptor binding domain. In short, SARS- CoV-2 is possessed of dual action capability. How do we think this was made possible? That is the subject of this paper. We shall argue from evidence below that the likelihood of this being the result of natural processes is very small.
The co-receptor dependent phagocytic general method of action for infectivity and pathogenicity of SARS-CoV-2 appears to be specifically related to cumulative charge resulting from inserts placed on the surface of the Spike receptor binding domain, right next to the receptor binding motif. That SARS-CoV-2 has charged inserts is not in dispute (Zhou et al., 2020) What we have shown that is new is that the SARS-CoV-2 Spike carries significant additional charge (isoelectric point (pI) pI=8.2) compared to human SARS-CoV Spike,( pI = 5.67) and the implications thereof. Basic domains - partly inserted, partly substituted amino acids and partly redistributed from outside the receptor binding domain - explain the salt bridges formed between the SARS-CoV-2 Spike and its co-receptors on the cell membrane. We comment further on the significance of this in the next section.
An influential paper was published in Nature Medicine on 17 March 2020. Andersen et al observed that several mutationshave occurred in the receptor binding domain of SARS-CoV-2. These, they suggested, therefore sustain an hypothesis ofnatural evolution (Andersen et al., 2020). We do not agree. We do agree that it is indeed correct that several such mutations are to be seen and in a forthcoming companion article to this one, about three other viruses of interest, we will discuss further Andersen et al's evidence and argumentation in that context. But here we observe only that the contention that it is improbable that Covid-19 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus because the ACE2 binding is not ideal is weakened because Andersen et al cite two authorities which actually say there verse of what they say that they say.Wan et al are cited by Andersen et al but offer them no support (Wan et al., 2020). Wan et al say, correctly in our view,that computational structural modelling of complex virus-receptor interactions can be used for structural predictions and that such models can potentially be used for Gain-Of-Function modelling. It is well known that models have been developed from data generated in animal model systems such as the palm civet. Wan et al say that the SARS-CoV-2 binding to the ACE2 receptor confirms the accuracy of the structural predictions. Therefore the data and conclusion in Wan et al contradicts Andersen et al's opinion that it is improbable that the virus could have emerged through laboratory manipulation.
There is a similar problem with (Sheahan et al., 2008). This deals with research on a civet strain SZ16 and the infectivestrain SARS-CoV Urbani. These strains were used to create a chimeric virus icSZ16-S. Sheahan et al go on to explain that by in vitro evolution of the chimeric virus icSZ16-S on human airway epithelial (HAE) cells in the lab, they have been able to produce two new viruses binding to such HAE cells. Therefore this reference supports the very opposite of the Andersen et al hypothesis. We are immediately wary of any paper containing such egregious errors.
Our discovery of the high pI number, the high accumulated charge and how it comes about, in the course of our bio-chemical analysis, suggested several features which individually seem unlikely to be the result of natural evolution andwhich, taken together, and applying Occam's Razor to hone the most parsimonious hypothesis, make natural evolution aless likely explanation than purposive manipulation, specifically for Gain of Function.