A lot of Cochrane
“It must be remembered that there is nothing more difficult to plan, more doubtful of success, nor more dangerous to manage than a new system. For the initiator has the enmity of all who would profit by the preservation of the old institution and merely lukewarm defenders in those who gain by the new ones. ” ― Niccolò Machiavelli
It is not news that the scientific publishing model (not to say national politics and the media) needs a serious revamp. In every walk of life (such as fossils fuels vs climate change), the many existing vested interests seek to protect their territory at the expense of the greater good, where truth is seen as secondary. Just as in the control of the mainstream media by politicians, control of the scientific media by vested interests is both undesirable and commonplace. Editors of scientific journals are very powerful and largely immune from the control of working scientists whose views they do not choose to espouse (nor even understand). Similarly, scientists who are maybe more interested in politics and funding can thereby profit by infiltrating themselves and/or their ex-staff into the agencies that control funding and publication in vanity journals. Despite the fact that the vanity journals have to publish more retractions than the majority (some accessible links here and here)(and the ‘top 10’ retractions are all in the Life Sciences), they often decline to publish the papers that point out their errors (I have other examples).
I wrote a blog on this some time ago, and recent events surrounding our research on Long Covid now require me to do so again, for similar reasons.
Cochrane reviews have been widely seen as authoritative surveys of areas of medicine and therapy, though recent changes, seemingly to a more ‘commercial’ model, have seen a major decline in their prestige as well as the withdrawal of NICE/NIHR funding. In response to what amounted to an opinion piece by Fox et al. attacking our work while masquerading as a serious review, Prof Resia Pretorius and I submitted the below response on August 3rd, 2023, and received from ‘Eva’ (support@cochrane.org) an acknowledgment of receipt, and on August 10th, 2023 a reply from Christine Schorfheide, Cochrane Evidence Production & Methods Directorate (comments-cdsr@cohrane.org) stating “Thank you for your comment on the Cochrane Review ‘Plasmapheresis to remove amyloid fibrin(ogen) particles for treating the post-COVID-19 condition’. Given the sensitive nature of its concerns, we are currently seeking advice from our publisher before posting the comment.”
Since then, more than three months ago, we have heard precisely nothing despite multiple attempts to email Cochrane at comments-cdsr@cohrane.org. No comments presently appear (November 12th, 2023) on the relevant part of the Cochrane website, although Comments appear on another review related to clotting. Consequently, since the non-appearance of our rebuttal might be mistaken for acceptance of the views espoused in the paper that attacked us (and it is not the only one by some of these authors), we simply place our rebuttal online here as a matter of public record. If Cochrane eventually decides to publish our comments properly we’ll add a suitable link on this website. A second rebuttal, submitted at the same time by Nico Pretorius and Dr Asad Khan, received the same treatment from Cochrane. While it is openly available on Substack, we also reproduce this below.
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Dear Dr Soares-Weiser,
We are writing to express our deep concern about a recently published paper entitled “Plasmapheresis to remove amyloid fibrin(ogen) for treating the post‐COVID‐19 condition” by Tilly Fox et al. (Cochrane Database of Systematic Reviews, July 26, 2023) [1]. We do so because, as well as being a transparent and purposive attack on a small subset of our own published findings, it falls so far below acceptable scientific standards that it imperils the reputation of your journal.
One of the most troubling aspects of the paper is the suggestion that our findings about amyloid fibrin(ogen) or “microclots” in Post-COVID-19 Condition (PCC) support the use of plasmapheresis. As advocates for evidence-based research, we want to clarify that we have not published any data supporting plasmapheresis as a treatment for PCC. The paper mistakenly links our research on amyloid fibrin(ogen) to the endorsement of plasmapheresis without any evidence that we have done so, which is both misleading and unfounded. Incidentally, the authors seem to conflate heparin-induced extracorporeal LDL/fibrinogen precipitation (H.E.L.P.) apheresis (e.g. [2; 3]) (that involves heparin) with plasmapheresis (e.g. [4; 5]) (that normally does not), in the mistaken belief that they are the same thing.
This review heavily relies on a limited number of laboratory studies. We firmly believe that conducting a comprehensive Cochrane review should entail a more robust and extensive examination of available evidence, considering a broader range of studies and data sources.
In particular this review is full of nonsequiturs and blatant misrepresentations, it fails to understand the most elementary definitions of sensitivity and specificity, it fails to cite a huge body of our other work on fibrinaloid microclots, and it ignores a large and entirely self-consistent body of evidence that entirely fulfil the Bradford Hill criteria for the causation and aetiology of a disease. In our previous research on Long COVID, we have consistently discussed the pathophysiology, emphasizing the presence of thrombotic endothelialitis and the occurrence of “microclots” or amyloid fibrin(ogen) that entrap various inflammatory molecules, along with hyperactivated platelets. Since 2006 [6], we have extensively detailed the existence of dense matted deposits of amyloid fibrin(ogen) in inflammatory conditions, which we more recently referred to as microclots. Regrettably, the authors of this paper chose to disregard this longstanding work in its entirety.
Our research is based on the discovery and significance of what we term fibrin amyloid microclots. We have argued that these fibrinaloids might have the ability to impact on microcapillaries and thereby inhibit oxygen transfer to tissues can account for a large majority of the symptoms of Long COVID [7; 8]. The authors state [1] “We first appraised the term ‘microclots’. It appears that the term ‘clots’ or ‘microclots’ which is adopted throughout the laboratory studies is not an accurate definition of the blood components involved.” Well it simply is. They are definitely clots, formed as part of the normal clotting cascade involving the polymerisation of fibrinogen, but catalysed here in the presence of SARS-CoV-2 spike protein [9], but they clot into an anomalous amyloid form (amyloid is a kind of structure) that stains with stains such as thioflavin T and Amytracker dyes (which is how you detect them) and they are small (‘micro’). They also entrap inflammatory molecules, as we have demonstrated through proteomics [10; 11] The process of amyloidogenesis is very common; we happened to discover [12; 13] that it could occur during blood clotting. Not one of our papers cited in this paragraph was mentioned by Fox et al [1].
Moreover, we wish to emphasize that the main focus of the papers by Pretorius et al. (2021) [11] and Kruger et al. (2022) [10] was on proteomics studies aimed at determining the protein content of plasma samples. While these papers did include data on microclots, it is essential to recognize that microclot data were presented as supporting data and not the primary focus of these studies. The 2021 paper [11] discusses the fact that plasma from acute and Long COVID samples exhibited resistance to trypsin digestion and after developing a 2nd trypsin digestion step, we could show that the digested plasma contained various molecules of interest, including alpha-2 antiplasmin, that prevent clot breakdown. On the other hand, Kruger et al. (2022) [10] served as a follow-up paper, reiterating the importance of the supporting data. Furthermore, we would like to clarify that both papers explicitly state that the raw data are available upon request. In the 2021 paper, a functional link is provided, leading the reader to the raw data files. Additionally, all micrographs were taken at 63x magnification, and the scale bar was included as standard practice for providing accurate measurements. It is incorrect and unfair to imply that the omission of the scale bar was intentional. Given the nature of these papers and their primary focus on proteomics and supporting data for microclots, we believe that they should not be the sole basis for a Cochrane review with implications for clinical decision-making.
The Pretorius et al 2022 [14], apart from providing micrograph data, also provided an extensive data analysis of data collected from the participants’ self-reported symptoms and comorbidities. This was done in the absence of a diagnostic marker, and thus such data are of great value to understand this new condition.
Furthermore, the review suggests that amyloid fibrin(ogen) is not unique to the post-COVID-19 condition and can even occur in controls. Indeed, we have published several papers to this effect [15-20] (again not cited). The existence of background levels of biochemicals in controls is entirely normal, and equally many inflammatory diseases share inflammatory markers [21]. Our microclot methods for Long COVID have 100% sensitivity and an as-yet-unknown specificity. This is the appropriate distinction.
It is also very worrying that the authors also seem biased by not reviewing data from a paper that Prof Ariëns and Prof Hunt themselves have published, a paper with the title Plasma from patients with pulmonary embolism show aggregates that reduce after anticoagulation [22]). In this paper, their own data actually corroborate the existence of microclots or aggregates in diseases associated with venous thromboembolism. Furthermore, they write that it is important that questions are raised regarding their pathophysiological relevance and further studies are warranted to investigate whether they represent cause or consequence of clinical thrombosis.
This apparent inconsistency raises significant concerns about the objectivity of their review and interpretation of the literature. Indeed, the paper “Plasma from patients with pulmonary embolism show aggregates that reduce after anticoagulation,” could then also be viewed as providing evidence about the potential usefulness of ‘plasmapheresis’.
Returning to the review paper’s conclusions, based on their review of a tiny number of laboratory studies and purposefully omitting others, raise concerns about bias and reporting discrepancies, rendering the results insufficient to support their purported link between the treatment modality “plasmapheresis” and amyloid fibrin(ogen) (microclots) with Long COVID.
As researchers dedicated to advancing our understanding of Long COVID and its treatment, we believe that scientific literature should encourage collaboration and accurate representation of research findings. We are deeply concerned that this paper may mislead the scientific community and impact clinical decision-making. In conclusion, we urge you to consider our perspective, and we insist on an erratum associated with this paper, where the authors acknowledge that the 5 of which 2 are preprint papers, from our research group that Fox et al chose to include, do not claim that plasmapheresis is a suitable treatment modality, OR most importantly do NOT present data to suggest that. We would also want an acknowledgement that their own paper could then also imply the usefulness of plasmapheresis. We insist that it is essential to address any misunderstandings and inaccuracies that might have influenced its content. Scientific integrity and collaboration are vital for the progress of medical knowledge.
We are also very concerned that one of the authors (Garner) is a member of your Editorial system (so may have had an influence in allowing this paper to be published), and has a public persona in which he has tried to maintain the entirely discredited psychological theories of diseases such as Long COVID and ME/CFS. Clearly organic findings such as our own show that the psychological explanations are nonsense.
Thank you for your attention to this matter, and we hope that you will take our evidenced concerns into consideration in the interest of scientific rigour and credibility.
Sincerely,
Resia Pretorius and Douglas B Kell
REFERENCES
[1] Fox, T., Hunt, B. J., Ariëns, R. A. S., Towers, G. J., Lever, R., Garner, P. & Kuehn, R. (2023). Plasmapheresis to remove amyloid fibrin(ogen) particles for treating the post-COVID-19 condition. Cochrane Database of Systematic Reviews CD015775.
[2] Winkler, K., Contini, C., Konig, B., Krumrey, B., Pütz, G., Zschiedrich, S., Pecks, U., Stavropoulou, D., Prompeler, H., Kunze, M. & Markfeld-Erol, F. (2018). Treatment of very preterm preeclampsia via heparin-mediated extracorporeal LDL-precipitation (H.E.L.P.) apheresis: The Freiburg preeclampsia H.E.L.P.-Apheresis study. Pregnancy Hypertens 12, 136-143.
[3] Jaeger, B. R., Arron, H. E., Kalka-Moll, W. M. & Seidel, D. (2022). The potential of heparin-induced extracorporeal LDL/fibrinogen precipitation (H.E.L.P.)-apheresis for patients with severe acute or chronic COVID-19. Front Cardiovasc Med 9, 1007636.
[4] von Baeyer, H. (2002). Plasmapheresis in thrombotic microangiopathy-associated syndromes: review of outcome data derived from clinical trials and open studies. Ther Apher 6, 320-8.
[5] Harris, E. S., Meiselman, H. J., Moriarty, P. M., Metzger, A. & Malkovsky, M. (2018). Therapeutic plasma exchange for the treatment of systemic sclerosis: A comprehensive review and analysis. J Scleroderma Relat Disord 3, 132-152.
[6] Pretorius, E., Briedenhann, S., Marx, J. & Franz, R. C. (2006). Structural changes in the fibrin network of a Pretoria family with dysfibrinogenemia: a scanning electron microscopical study. Ultrastruct Pathol 30, 167-76.
[7] Kell, D. B., Laubscher, G. J. & Pretorius, E. (2022). A central role for amyloid fibrin microclots in long COVID/PASC: origins and therapeutic implications. Biochem J 479, 537-559.
[8] Kell, D. B. & Pretorius, E. (2022). The potential role of ischaemia-reperfusion injury in chronic, relapsing diseases such as rheumatoid arthritis, long COVID and ME/CFS: evidence, mechanisms, and therapeutic implications. Biochem J 479, 1653-1708.
[9] Grobbelaar, L. M., Venter, C., Vlok, M., Ngoepe, M., Laubscher, G. J., Lourens, P. J., Steenkamp, J., Kell, D. B. & Pretorius, E. (2021). SARS-CoV-2 spike protein S1 induces fibrin(ogen) resistant to fibrinolysis: implications for microclot formation in COVID-19. Biosci Rep 41, BSR20210611.
[10] Kruger, A., Vlok, M., Turner, S., Venter, C., Laubscher, G. J., Kell, D. B. & Pretorius, E. (2022). Proteomics of fibrin amyloid microclots in Long COVID/ Post-Acute Sequelae of COVID-19 (PASC) shows many entrapped pro-inflammatory molecules that may also contribute to a failed fibrinolytic system. Cardiovasc Diabetol 21, 190.
[11] Pretorius, E., Vlok, M., Venter, C., Bezuidenhout, J. A., Laubscher, G. J., Steenkamp, J. & Kell, D. B. (2021). Persistent clotting protein pathology in Long COVID/ Post-Acute Sequelae of COVID-19 (PASC) is accompanied by increased levels of antiplasmin. Cardiovasc Diabetol 20, 172.
[12] Pretorius, E., Mbotwe, S., Bester, J., Robinson, C. J. & Kell, D. B. (2016). Acute induction of anomalous and amyloidogenic blood clotting by molecular amplification of highly substoichiometric levels of bacterial lipopolysaccharide. J R Soc Interface 123, 20160539.
[13] Kell, D. B. & Pretorius, E. (2017). Proteins behaving badly. Substoichiometric molecular control and amplification of the initiation and nature of amyloid fibril formation: lessons from and for blood clotting. Progr Biophys Mol Biol 123, 16-41.
[14] Pretorius, E., Venter, C., Laubscher, G. J., Kotze, M. J., Oladejo, S., Watson, L. R., Rajaratnam, K., Watson, B. W. & Kell, D. B. (2022). Prevalence of symptoms, comorbidities, fibrin amyloid microclots and platelet pathology in individuals with Long COVID/ Post-Acute Sequelae of COVID-19 (PASC) Cardiovasc Diabetol 21, 148.
[15] Nunes, J. M., Kruger, A., Proal, A., Kell, D. B. & Pretorius, E. (2022). The Occurrence of Hyperactivated Platelets and Fibrinaloid Microclots in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Pharmaceuticals (Basel) 15, 931.
[16] Pretorius, E., Akeredolu, O.-O., Soma, P. & Kell, D. B. (2017). Major involvement of bacterial components in rheumatoid arthritis and its accompanying oxidative stress, systemic inflammation and hypercoagulability. Exp Biol Med 242, 355-373.
[17] Pretorius, E., Mbotwe, S. & Kell, D. B. (2017). Lipopolysaccharide-binding protein (LBP) reverses the amyloid state of fibrin seen in plasma of type 2 diabetics with cardiovascular comorbidities. Sci Rep 7, 9680.
[18] Pretorius, E., Page, M. J., Engelbrecht, L., Ellis, G. C. & Kell, D. B. (2017). Substantial fibrin amyloidogenesis in type 2 diabetes assessed using amyloid-selective fluorescent stains. Cardiovasc Diabetol 16, 141.
[19] Pretorius, E., Bester, J., Page, M. J. & Kell, D. B. (2018). Reversal of amyloid formation in the plasma fibrin of individuals with Alzheimer-type dementia using LPS-binding protein J Alzheimers Dis.
[20] Pretorius, E., Venter, C., Laubscher, G. J., Lourens, P. J., Steenkamp, J. & Kell, D. B. (2020). Prevalence of readily detected amyloid blood clots in ‘unclotted’ Type 2 Diabetes Mellitus and COVID-19 plasma: A preliminary report. Cardiovasc Diabetol 19, 193.
[21] Kell, D. B. & Pretorius, E. (2018). No effects without causes. The Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases. Biol Rev 93, 1518-1557.
[22] Baker, S. R., Halliday, G., Ząbczyk, M., Alkarithi, G., Macrae, F. L., Undas, A., Hunt, B. J. & Ariëns, R. A. S. (2023). Plasma from patients with pulmonary embolism show aggregates that reduce after anticoagulation. Commun Med (Lond) 3, 12.
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The commentary from Nico Pretorius and Dr Asad Khan:
Critical Reflections on the Cochrane Review of Long Covid Research: Where Is the Line Between Scientific Discourse and Prejudice?
We are writing to present a detailed critique of the recent Cochrane review evaluating Long Covid research conducted by Resia Pretorius, Douglas Kell, and their collaborators.
The Cochrane review uses a set of criteria to evaluate five articles from the Pretorius research group. However, the suitability and appropriateness of the Cochrane framework for evaluating these specific pieces of research are questionable. The Cochrane framework is generally employed to consolidate and evaluate a wide range of studies on a given topic to minimize bias. Yet, this review focuses solely on early-stage research from a single group, which makes it difficult to avoid a narrow perspective.
The authors’ decision to conduct a systematic review—despite the early-stage nature of the research and the potential for perceived bias—prompts significant inquiry. It calls into question whether a systematic review, typically used to synthesize mature research, was the most appropriate methodology to evaluate such nascent studies.
Several instances in the review evoke concerns over its objectivity. Remarkably, the review seems to place undue emphasis on the microscopy images presented in the studies. However, the main thrust of these studies was not centred on microscopy; the images served merely as supportive data. Therefore, it is peculiar that the review overlooks critical findings and statistical analyses derived from proteomics – notably, the discovery of a significant increase in α(2)-antiplasmin, as evidenced in the Pretorius 2021 and Kruger 2022 studies.
The review critiques the staining methodology and the fluorescence microscopy techniques as not being clearly described and questions the repeatability of the studies. However, several international teams have had no difficulty following and repeating the methodology, achieving the same outcomes – an aspect blatantly ignored by the review. This selective focus and critique raise questions about the balance and thoroughness of the review’s examination. Furthermore, contrary to the review’s claim that the data is inaccessible, the data can indeed be accessed via links provided in the journal articles. The review also criticizes the sample sizes and selection criteria, seemingly without acknowledging the unprecedented context of a pandemic in which these studies were conducted. Additionally, the review fails to consider that there are still no standardised guidelines for accurately diagnosing patients with Long Covid.
The Cochrane review also draws certain connections that aren’t present in the original articles – such as the association with plasmapheresis – raising further questions about its purpose. Furthermore, the authors seem to conflate plasmapheresis with H.E.L.P. apheresis.
Whilst H.E.L.P. apheresis has indeed been mooted as a potential treatment for Long Covid, plasmapheresis, on the contrary, has not. This again calls into question the thoroughness and accuracy of the review.
Early research papers by Pretorius, Kell and their team were among the earliest to provide peer-reviewed data on Long Covid. Conducted during lockdown amidst the profound uncertainties of a pandemic, these studies could have been kept under wraps until more mature datasets were available. However, in the spirit of scientific progress and openness the team opted to share their findings promptly, encouraging further investigation by other researchers. Why do the authors of the review not recognize the strategic decision to publish these studies early to catalyse further research—an approach that numerous other research groups have adopted?
In essence, this Cochrane review can be seen as an academic reinterpretation of an opinion commissioned by the BMJ; an opinion which one of its co-authors (Robert AS Ariëns) has now disclosed he published in his capacity as editor.
When the authors of the review express concerns about bias whilst there is clear evidence of potential bias within their own ranks, it appears to be a clear instance of the critic failing to apply the same scrutiny to themselves.
Paul Garner, a co-creator of the Cochrane Reports, has been open about his personal journey of recovery from Long Covid, attributing his recovery to psychological rather than biomedical factors. He has shared his experience in detail and promoted this perspective publicly.
While Garner’s personal story is certainly valuable as an anecdote, it must be considered in the context of his professional role. As a co-author of the Cochrane Review, the potential influence of his personal experience on the interpretation of research findings cannot be ignored. Transparency, especially regarding potential conflicts of interest, is critical in maintaining the credibility of scientific review processes. This point becomes even more salient considering that, besides Garner, at least two other authors, as well as some of the reviewers, also have affiliations with Cochrane.
Another potential source of bias could stem from the choice of reviewers. The Cochrane review appointed a neuropsychiatrist (Alan J Carson) and a systematic reviews expert (Ingeborg Welters) as ‘independent’ peer reviewers. However, their professional affiliations and research perspectives should also be scrutinized for potential alignment with the views of the report’s authors, which could inadvertently influence the objectivity of the review. While the peer review process is designed to ensure rigor and validity, the independence of reviewers is paramount to avoid any inclination towards confirmation bias.
One may question whether the review’s purpose is an attempt to discredit microclot research, potentially stalling or blocking necessary clinical trials. Of utmost importance, however, is the question: how does this review contribute to the understanding and treatment of Long Covid?
In our view, true researchers must fall into da Vinci’s category of ‘those who see’, ever seeking to push boundaries and expand understanding. As we navigate the complex challenges of Long Covid, it is the duty of the scientific community to conduct and evaluate research with the utmost transparency, rigor, and objectivity. To quote Albert Einstein, ‘The right to search for truth also implies a duty; one must not conceal any part of what one has recognized to be true’.
About the authors
Nico Pretorius is an entrepreneur and engineer and the husband of Resia Pretorius and has a personal connection to this work.
Dr M Asad Khan is a Consultant Respiratory Physician in Manchester in the United Kingdom. He has Long Covid and has been demonstrated to have microclots using Pretorius’ techniques on multiple occasions. He has undergone anticoagulation and HELP apheresis with clinical benefit.
ENDS
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