Global Biosurveillance

This analysis is based on past experience and studies applicable to SARS-CoV-2, and the Omicron variant in particular. I still maintain that SARS-CoV-2 is an animal virus, a generalist, and opportunist with an imposed human bias. It has kept its options to infect and be maintained in animal species other than humans. Humans have just provided a profound opportunity for viral amplification and transmission with travel, global contact, disregard for sanitary precautions, socioeconomic disparity (poor vaccine distribution and preferential access to life saving treatments), and political interference (positive and negative influence). Omicron can be viewed as the natural evolutionary progression of the virus under these circumstances. Recent data have shown the first indications that Omicron is following an animal coronavirus pattern that I have described in several earlier posts. The confusion in the press and the debate amongst the scientific community over Omicron being more transmissible (clearly) and less pathogenic (awaiting more data) is an unclear relationship, if any connection at all, between pathogenicity (morbidity and mortality) and transmissibility. Transmissibility seems to follow a logical course of higher transmissibility leading to greater incidence and prevalence of a variant like Omicron, but it has its limitations. Transmissibility is not linear but asymptotic in its evolution. Too much transmissibility and vulnerable hosts become harder too find; too little and the virus infectivity dies out with distance between and immunity of hosts. An inhibition of immunity by the virus leads to greater viral production and lower infectious dose, but too much and the virus spreads throughout a host’s tissues that leads to incapacitation (limited mobility for viral spread) or lethality (eliminating a viral host for replication and spread); too much or too quick induction of immunity and not enough virus is available for transmission. These are the tensions pulling on virus mutations, governing its evolution.

Omicron has, in a preliminary study, shown a preference for infecting human upper respiratory tissue over lung tissue in culture. The omicron variant multiplies about 70 times faster inside human respiratory tract tissue than the delta variant does, according to a University of Hong Kong report (https://www.med.hku.hk/en/news/press/20211215-omicron-sars-cov-2-infection?utm_medium=social&utm_source=twitter&utm_campaign=press_release). This is supported by the fact that, in the U.S., cases caused by the Omicron variant jumped seven times in a week, from 0.4% to 2.9% total cases, according to Centers for Disease Control and Prevention estimates. The infection incidence is approaching 13% of cases in the region including New York and New Jersey. This is close to the prevalence of other coronaviruses in animal populations at any given time (10-15%). The preponderance in the upper respiratory tract (including bronchi) assures large amounts of virus will be expelled with coughs and sneezes and will most likely take hold in exposed susceptible people. Localized immunosuppression in these tissues before recovery is more than adequate to rapidly reproduce and provide time to spread the virus. No increase in pathogenicity is necessary.

However, a shift from preference for receptors deep in the lungs to those of the upper respiratory tract assuring more likely human to human transmission has been seen before in influenza. Avian influenza prefers deeper receptors in the human respiratory system and is more pathogenic. When it reassorts with other strains like those of pigs and humans, it becomes more transmissible in these species, mostly less pathogenic, but not always and without assurance of such a result. So no assurance of Omicron’s decrease in pathogenicity.

The increase in lethality of an infectious entity is often indifferent to transmissibility, especially if it is quick and a living host is not required to spread the agent. Sometimes the dead are a greater source of transmissible agent than the living and the agent is thus selected for lethality as it mutates or against attenuation that would allow recovery and elimination of the infectious form. This situation describes anthrax that is transmitted through spores that form upon death and dismemberment of the host. Even Ebola, until recently, was most likely to be transmitted from person to person by preparation of the dead for burial. Today, not just the dead and dying transmit it but also the recovered through chronic infection and sexual transmission. Its nature has changed as it has moved from being an East African sporadically occurring zoonoses to an endemic urban virus in West Africa. SAR-CoV-2, like other animal coronaviruses, is not so infectiously persistent in the environment, but rather spreads through constantly maintained susceptible populations and by acute and chronic viral shedders (in animals, mostly by the GI tract, yet to be fully demonstrated in human hosts infected with adapted coronaviruses). Time will tell if SARS-CoV-2, Omicron in particular, follows this well tread coronavirus path.

Did Omicron come out of animals? Sequences shared with coronaviruses in rats (https://media.nature.com/original/magazine-assets/d41586-022-00215-2/d41586-022-00215-2.pdf). Spreading to hamsters then back to humans (https://deliverypdf.ssrn.com/delivery.php?ID=905122026003114127079123119001002108070000006036012087096100017005026012108069005085117079006123024016028096075124024095120029035039092080082014103069087050015051047119025019073007018096068101116122057113095048023013018003005127004003074071116075102028010112004123113020012112075020103113022&EXT=pdf&INDEX=TRUE). We have recently seen that even Omicron is mutating toward more transmissibility (Omicron Subvariant 1.5 Times More Contagious Than Omicron: https://www.medscape.com/viewarticle/967541) but not necessarily more pathogenicity, following the course predicted in an earlier version of this posting. Are we approaching the asymptotic maximum?

Isn’t it time for a totally new approach that is both specific and versatile? An approach that can be applied immediately before an emerging infectious disease goes pandemic? A means to “out evolve” a virus or antibiotic resistant bacteria or other microbe before it escapes its origin ? Yes, Nanobes . “I’ve seen things you people wouldn’t believe….all those moments will be lost in time like tears in the rain”.

How can symptoms of COVID-19 persist after the virus is gone? The answer may lie in the type of immune response triggered by SARS-CoV-2, which resembles one more familiar to those studying the immune response to worm and protozoan parasites. I mentioned this in earlier posts citing observations of clinical characteristics of COVID and how they resembled the response to a parasite rather than a virus. Parasite immunology more closely resembles tumor immunology than that of responses to many viruses and bacteria. This cross reactivity between tumor immunity and the immune response to SARS-CoV-2 has been dramatically illustrated in a recent case of a rare remission of advance Hodgkin lymphoma in conjunction with COVID (https://onlinelibrary.wiley.com/doi/10.1111/bjh.17116). The host must mount a different kind of response to parasites because of their many strategies to evade the immune system, the innate and adaptive components. Therefore, animals and humans have developed a different series of cellular and humoral components unique to parasites, but often with potentially severe collateral damage to normal tissues and organs. There is a delicate balance between controlling a parasite infestation so that it does not consume the host and so completely destroying the parasites that the host “burns down the house to get rid of the rats”, auto destruction of the host in the process of eliminating the parasite and confusion between parasite antigen and self antigens (autoimmunity) https://downloads.hindawi.com/journals/iji/2014/651503.pdf. The remaining “memory” of this response, after the virus is gone, is continuously reactivated by a broad range of stimuli https://jlb.onlinelibrary.wiley.com/doi/epdf/10.1189/jlb.0313113. This primitive process, discussed in my book Type B Cytochromes: Sensors and Switches and cited in previous posts, is built on anticipatory responding to potential pathogens, toxins and physical insults before those insults are actually known or specifically identified. This is good for evolutionary survival but can lead to unnecessary overt nonspecific responses and collateral damage. What is the evidence for such a hypothesis in regards to COVID-19 and how might it lead to treatments, especially for long haulers? As stated in a previous post, the immune response of hospitalized COVID-19 patients falls across a spectrum of immune responses in 3 categories: (1) antiviral (some macrophages and dendritic cells, natural killer cells, cytotoxic T cells, helper and suppressor T cells, antibody making B cells and plasma cells, and gamma interferon; other interferons made by tissue cells: alpha and beta); (2) anti-parasitic granulocyte white blood cells (some special B cells that make IgE, eosinophils, basophils (in tissue mast cells), and all kinds of biochemical mediators: histamine, prostaglandins, leukotrienes, and kinins); and (3) anti-bacterial and fungal (granulocyte: neutrophils, and monocytes and macrophages). COVID-19 can move through all three types. The worst and most likely cause of the long hauler syndrome is type 2 which was meant for worms and other multicellular localized parasites and can be locally severe and if generalized, fatal. The serum concentrations of IL-17A (a protein that recruits monocytes and neutrophils to an inflammatory site produced by Th17 lymphocytes) and IFN-γ, but not TNF-α or IL-6 (the pro-inflammatory culprits), decrease with age of patients (this might argue against Th17 memory cells being the source of long haulers); therefore, gamma interferon’s ability to prevent viral replication but not induce oxidative damage to host cells, as with TNF-α, is more important in children’s responses. However, as stated in a previous post, evidence supports decline in soluble IL17A receptors, which block TNF-alpha and interferon gamma production by competing with the cellular T17 cellular receptors, leads to more severe COVID19 (supporting Th17 cell involvement). Adults show a more robust T cell response to the viral spike protein compared to pediatric patients shown by increased expression of CD25+ on CD4+ T cells and the frequency of IFN-γ+CD4+ T cells. Also, serum neutralizing antibody titers and antibody-dependent cellular phagocytosis are higher in adults than in pediatric COVID-19 patients. The neutralizing antibody titer increases with age while the IL-17A and IFN-γ serum concentrations decrease. Children seem to be resistant to the severe effects, except in some instances when they display multiple organ inflammation, Kawasaki-like syndrome, because they produce a lot of the anti-inflammatory cytokine IL10. The responses of neonates compared to adults change from increased IL-10 as neonates to balanced IL-10/T helper type 1 (Th1)/Th2/Th17 cytokine levels early in life. This allows protection from pathogens but reduces the chances of severe inflammatory reaction. Th17 cells are the most probable mediators in many human autoimmune and chronic inflammatory disorders, including psoriasis, Crohnˈs disease, rheumatoid arthritis, Multiple Sclerosis, and uveitis https://www.frontiersin.org/articles/10.3389/fimmu.2018.01112/full. The development of pathogenic Th17 cells relies on signals from multiple cytokines: IL‐1, IL‐23, IL‐6 and TGF‐β,transforming growth factor, that can promote Th17 development and induce a Th17 response which promotes intestinal muscle hypercontractility that drives worm expulsion. TGFβ-activation by dendritic cells yields this Th17 induction and intestinal contractility and facilitates the expulsion of the parasite Trichinella spiralis in mice. This unique immune response of intestinal helminth expulsion beyond that of classical Th2 driven immunity, highlights the importance of IL-17 in parasitic disease. Th17 protection against parasites is very broad spectrum extending to Th17 cells’ providing robust protection against Trypanosoma cruzi, the intracellular protozoan parasite that causes Chagas disease. Parasites that establish long term chronic infections suppress Th17 immunity by modulation of antigen-specific CD4+ T responses. This is seen in human infection with the worm parasite Strongyloides stercoralis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546867/pdf/nihms-704134.pdf. Th17 cells of infected people showed significantly decreased responses upon antigen-stimulation, but following treatment, significantly increased the antigen-specific responses of Th17 cells. Th17 cells produce pro-inflammatory cytokines, including IL-17A, IL-17F, and IL-22. This cytokine production not only promotes accumulation of immune cells, such as macrophages, neutrophils and lymphocytes, at inflammatory sites, but also can cause collateral tissue damage. Other Th17 cells can negatively regulate immune responses by secreting immunosuppressive factors, such as IL-10 as noted in the response of children to COVID. Th17 cells are required for vaccine-induced protection against pulmonary infection with the pathogenic fungi Coccidioides posadasii, Histoplasma capsulatum, and Blastomyces dermatitidis, fungal pathogens causing systemic mycoses in humans. IL-17 is required for neutrophil and macrophage recruitment to the lungs. This balance is evidently what helps dispose of or suppress parasites and perhaps SARS-CoV-2 virus, or, if out of balance, severe acute or chronic persistent long hauler pathologies https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cell-analysis-learning-center/immunology-at-work/t-helper-17-cell-overview.html. Some in vitro experiments suggest a benefit from Vitamin D because of its effects on Th17 cells. These cells are characterized by the chemokine receptor CCR6, RORC expression, and production of IL-17A, IFNγ, and TNFα. Using rheumatoid arthritis (RA) as a model of autoimmune disease, investigators demonstrated that pro-inflammatory memory CCR6+ Th cells can switch into anti-inflammatory cells by treating them with the active vitamin D metabolite 1,25(OH)₂D₃. Memory CCR6+ Th cells were sorted from healthy controls or treatment-naïve patients with early rheumatoid arthritis (RA) and cultured with or without 1,25(OH)₂D₃. Vitamin D₃ inhibited pro-inflammatory cytokine production, IL-17A, IL-17F, IL-22 and IFNγ, in memory CCR6+ Th cells from both healthy controls and RA patients. This inhibition was accompanied by induction of anti-inflammatory factors, IL-10 and CTLA4 https://www.frontiersin.org/articles/10.3389/fimmu.2019.01504/full. Perhaps, this approach provides a means to test the hypothesis that Th17 memory cells are the root cause of long haulers. Also, antioxidants may help because the pro-inflammatory cytokines enhance the production of reactive oxygen species which are mediators of the anti-parasitic effector mechanism and collateral pathology. These benefits remain to be seen.

The anti-parasitic immune response leading to long haul and neurological disease has gained further support in a new paper showing the involvement of the cytokine CCL11, eosinophil chemotactic protein and eotaxin-1 (https://www.biorxiv.org/content/10.1101/2022.01.07.475453v1.full.pdf).

A prophet is not a soothsayer. Prophets are interpreters of the past, now and future. They see through the fog with clarity that is obvious to them and frustrating because of their lack of understanding of others inability to see. They are compelled, no driven, to tell what they see, even to the detriment of themselves and those they love. They have but one measure, the truth, to tell even if they would rather not. It is a Hand of what is Greater than themselves that leads, pushes, compells the way forward. Voices that cannot be silenced until they are spoken, even to the end. My book “Type B Cytochromes: Sensors and Switches”, the past, this blog, the now, “The Black Dragon Trilogy”, the vision, the dreams dreamt of the future. The last, the alternatives and options mapped out on the plain of space and time to be chosen with inevitable outcomes determined by the path chosen. “All those moments lost in time”, if ignored. Professionally dead but still alive.

This analysis is based on past experience and studies applicable to SARS-CoV-2, and the Omicron variant in particular. I still maintain that SARS-CoV-2 is an animal virus, a generalist, and opportunist with an imposed human bias. It has kept its options to infect and be maintained in animal species other than humans. Humans have just provided a profound opportunity for viral amplification and transmission with travel, global contact, disregard for sanitary precautions, socioeconomic disparity (poor vaccine distribution and preferential access to life saving treatments), and political interference (positive and negative influence). Omicron can be viewed as the natural evolutionary progression of the virus under these circumstances. Recent data has shown the first indications that Omicron is following an animal coronavirus pattern that I have described in several earlier posts. The confusion in the press and the debate amongst the scientific community over Omicron being more transmissible (clearly) and less pathogenic (awaiting more data) is an unclear relationship, if any connection at all, between pathogenicity (morbidity and mortality) and transmissibility. Transmissibility seems to follow a logical course of higher transmissibility leading to greater incidence and prevalence of a variant like Omicron, but it has its limitations. Transmissibility is not linear but asymptotic in is evolution. Too much transmissibility and vulnerable hosts become harder too find; too little and the virus infectivity dies out with distance between and immunity of hosts. An inhibition of immunity by the virus leads to greater viral production and lower infectious dose, but too much and the virus spreads throughout a host’s tissues that leads to incapacitation (limited mobility for viral spread) or lethality (eliminating a viral host for replication and spread); too much or too quick induction of immunity and not enough virus is available for transmission. These are the tensions pulling on virus mutations, governing its evolution.

Omicron has, in a preliminary study, shown a preference for infecting human upper respiratory tissue over lung tissue in culture. The omicron variant multiplies about 70 times faster inside human respiratory tract tissue than the delta variant does, according to a University of Hong Kong report (https://www.med.hku.hk/en/news/press/20211215-omicron-sars-cov-2-infection?utm_medium=social&utm_source=twitter&utm_campaign=press_release). This is supported by the fact that, in the U.S., cases caused by the Omicron variant jumped seven times in a week, from 0.4% to 2.9% total cases, according to Centers for Disease Control and Prevention estimates. The infection incidence is approaching 13% of cases in the region including New York and New Jersey. This is close to the prevalence of other coronaviruses in animal populations at any given time (10-15%). The preponderance in the upper respiratory tract (including bronchi) assures large amounts of virus will be expelled with coughs and sneezes and will most likely take hold in exposed susceptible people. Localized immunosuppression in these tissues before recovery is more than adequate to rapidly reproduce and provide time to spread the virus. No increase in pathogenicity is necessary.

However, a shift from preference for receptors deep in the lungs to those of the upper respiratory tract assuring more likely human to human transmission has been seen before in influenza. Avian influenza prefers deeper receptors in the human respiratory system and is more pathogenic. When it reassorts with other strains like those of pigs and humans, it becomes more transmissible in these species, mostly less pathogenic, but not always and without assurance of such a result. So no assurance of Omicron’s decrease in pathogenicity.

The increase in lethality of an infectious entity is often indifferent to transmissibility, especially if it is quick and a living host is not required to spread the agent. Sometimes the dead are a greater source of transmissible agent than the living and the agent is thus selected for lethality as it mutates or against attenuation that would allow recovery and elimination of the infectious form. This situation describes anthrax that is transmitted through spores that form upon death and dismemberment of the host. Even Ebola, until recently, was most likely to be transmitted from person to person by preparation of the dead for burial. Today, not just the dead and dying transmit it but also the recovered through chronic infection and sexual transmission. Its nature has changed as it has moved from being an East African sporadically occurring zoonoses to an endemic urban virus in West Africa. SAR-CoV-2, like other animal coronaviruses, is not so infectiously persistent in the environment, but rather spreads through constantly maintained susceptible populations and by acute and chronic viral shedders (in animals, mostly by the GI tract, yet to be fully demonstrated in human hosts infected with adapted coronaviruses). Time will tell if SARS-CoV-2, Omicron in particular, follows this well tread coronavirus path.

Did Omicron come out of animals? Sequences shared with coronaviruses in rats (https://media.nature.com/original/magazine-assets/d41586-022-00215-2/d41586-022-00215-2.pdf). Spreading to hamsters then back to humans (https://deliverypdf.ssrn.com/delivery.php?ID=905122026003114127079123119001002108070000006036012087096100017005026012108069005085117079006123024016028096075124024095120029035039092080082014103069087050015051047119025019073007018096068101116122057113095048023013018003005127004003074071116075102028010112004123113020012112075020103113022&EXT=pdf&INDEX=TRUE).

Isn’t it time for a totally new approach that is both specific and versatile? An approach that can be applied immediately before an emerging infectious disease goes pandemic? A means to “out evolve” a virus or antibiotic resistant bacteria or other microbe before it escapes its origin ? Yes, Nanobes . “I’ve seen things you people wouldn’t believe….all those moments lost in time like tears in the rain”.

What the USAF/AFRL Counterproliferation Team learned 1989-2011. What I continued as a contractor for USAF and DTRA 2011-2015:

“trying to define, or at least approach the value, as calculus would for an instantaneous velocity and trajectory, the timeless prediction of infectious disease emergence which defines pathogenic ecology as if it were a law of physics rather than an account of history.”

— The Black Dragon Trilogy by JOHNATHAN KIEL
https://a.co/91rCMnQ

Detection and identification : Finding it early, very early: This is easier said than done because what is really required is finding the pathogen, or even worse, an emerging potential pathogen, before it emerges. For a well characterized pathogen, that has not genetically or phenotypically changed, this may be done with straightforward genetic testing like rapid PCR in the field or with an antibody-based test, like a lateral flow antigen test. But there is still a problem with sampling, so one does not end up with “garbage in, garbage out”, or worse an empty sample because what is sampled is mostly empty space in respect to the pathogen (appropriate sample volume). The problem is most boldly illustrated with the following statistical prediction of what it takes to find a positive at a given prevalence level of an infectious disease:

The above is a graph applied to sampling birds for avian influenza, in which the birds amplify the virus making it more likely to detect. When a microbe is diluted in air, soil, water or across surfaces, the sampling problem becomes more acute. These samples in which a pathogen or its toxin does not replicate will require concentrating and/or pooling of samples to find pathogens. This is why agents might not reveal themselves unless contact of a host is made with a naturally concentrated source or the rare event of contact with a susceptible host allows for replication and distribution to more susceptible hosts. Therefore, there is need for screening samples at the source with the appropriate assay to not merely collect “empty” samples and depend on statistics alone to find the pathogen. The key here is an appropriate assay: if it is too specific, a related but unknown potentially emerging pathogen will be missed, and if too broad, many non-pathogens may be detected and confound the analysis. The following pictures illustrate examples of these problems and attempts to solve them:

Knowing where to look: Lately, GIS (geographic information systems) models have become more useful in finding pathogens in the environment. However, one must know what parameters are required for the likeliness of the pathogens’ presence. As rapid whole nucleic acid sequencing moves out of the laboratory into the field and into the real time domain, confirming the presence of a pathogen in a sample will be more likely. However, for previous unknown potentially emerging pathogens, even a whole genome sequence may be necessary but insufficient for predicting pathogenicity. The following pictures illustrate examples of these problems and attempts to solve them:

Knowing how to respond before mitigation is necessary: Once a potential pathogen has been detected, tentatively identified, and isolated in the field. Then, the next decision is how to respond. Should animal and potential human infections be identified and isolated or quarantined? How long and where? There are basically two types of bio defense, active and passive. The former is the essence of Counterproliferation (a corollary of the more general Active Defense against other Weapons of Mass Destruction), keeping bio agents in non-permissive territory, where there are political, territorial, and resource limitations. Passive and consequence management bio defense includes medical countermeasures like vaccines and pharmaceutical therapies and engineering and sanitary controls of infection. We are in this mode globally with COVID-19. This is more difficult and haphazard and less effective, but more likely to be supported because if the former is effective no one knows it because no epidemics or pandemics materialize. The production of influenza vaccines for different emerging strains every year is an example of rare anticipatory passive biodefense that has proven effective time and time again rather than the consequence management approach used for SARS-CoV-2 vaccines; albeit their development and deployment was in record time. However, the virus is still outrunning us with mutations leading to new Variants of Concern. Effective active defense is still a work in progress.

The Unfinished Solution for early active bio defense, closest to the point of origin, counteracting an emerging or re-emerging infectious disease before it becomes an epidemic or pandemic. The solution to which the AFRL Counterproliferation Team was finally led, as the ultimate goal, was the Nanobes. They were meant to be synthetically selected to detect, identify, isolate and kill specific biological agents seamlessly. An added objective was the biological replication of the Nanobes in the target microbe or cell infected with the objective virus to kill or make the respective pathogen susceptible to elimination.

“The Defense Advanced Research Projects Agency (DARPA) is soliciting proposals for the development and demonstration of advanced pathogen countermeasures, which will be a key component of DARPA’s overarching goal to remove the threat of biological weapons as a factor in the planning and conduct of U.S. military operations.” Really? And we hadn’t already done this? Now it is forgotten-“tears in the rain.”

“Revelations of poor practices at a contract research company helping to carry out Pfizer’s pivotal covid-19 vaccine trial raise questions about data integrity and regulatory oversight. Paul D Thacker reports” https://www.doximity.com/newsfeed/ed907e95-12e1-48cd-bed0-10774520e526/public.

Here’s the problem. In none of the complaints were there any real data to say the vaccine was not efficacious. All this is about breaking standard protocols (they did in a clinical trial I participated in). Adverse reactions can be reported by anyone at anytime to FDA (not just the company) regardless if they are actually caused by the vaccine. We have now undergone the largest clinical trial in history with over 196 million fully vaccinated (59.4% of the population) in US and all adverse reactions are being reported and do not exceed what is seen with many established vaccines. Doses given 7.81 billion, fully vaccinated 3.33 billion, 42.7% fully vaccinated worldwide (https://www.google.com/search?q=number+vaccinated+worldwide&ie=UTF-8&oe=UTF-8&hl=en-us&client=safari&dlnr=1&sei=naqnYYvHD-SyqtsP5uqXoA8).

This kind of slipshod work by the largest drug company in the world only feeds the antivax fires and demonstrates at least in my eyes the problem with “free market” development of and control of data for vaccines in general. This can only hurt ending the pandemic where being unvaccinated is largely responsible for deaths, severe illness, overburdening the medical system and wrecking it, generating more resistant mutants, and periodicallly shutting down businesses and schools with superspreader events. Not to mention feeding insane antivax and anti-mask politics.

Recently, SARS-CoV-2, COVID, has shown that it has more surprises for us. The following diagram is based on the comparison of all the genomes of SARS-CoV-2 isolates grouped into related variants. The South African recent isolate variant (red lines) did not evolve from other current variants. The 91 genomes from Omicron viruses (@GISAID) were from specimens collected between Nov 11 and Nov 23 in Botswana, South Africa and Hong Kong. On 26 November, the World Health Organization (WHO) designated SARS-CoV-2 variant B.1.1.529, as a variant of concern and named it Omicron, on advice of scientists in the WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution. Omicron was added to WHO list of current variants of concern: Delta, Alpha, Beta and Gamma. The Omicron variant has a high number of mutations especially in the spike protein. The extremely long red branch (>1 year) below indicates an extended period of circulation in a highly localized geographic area with poor genomic surveillance (not in South Africa proper but some contiguous or connected area by travel) or continual evolution in a chronically infected individual before spilling back into the population. It is not likely an animal source, as some have suggested, but has a peculiarity of one coronavirus, feline infectious peritonitis virus, in particular, that has been observed for many years and in another, originally zoonotic virus, that has been maintained in a slow but enduring pandemic, HIV.

The sources of this diagram are https://twitter.com/trvrb/status/1464353224417325066?s=21 and https://www.pango.network/.

For these changes to occur in such isolation, mutations forced by natural selection in a small number of hosts or in a single host, there must be one or more mechanisms of immune evasion and survival of the host(s) to allow for the time for these mutations to occur and to select for survival of the virus. How could one get Omicron variant ? Two CoVs could infect the same cell at once and share genetic material to make a new virus (homologous recombination). HIV generates mutations frequently, even within the same individual, because of the sequence mistakes made by reverse transcriptase, which converts the RNA to DNA, which is, in turn, inserted into the host genome from whence it is expressed as new virus. Even though coronaviruses have a proof reading RNA dependent RNA polymerase, they still make mistakes in replication, and mutations are also produced in the viral RNA templates by the active oxygen and nitrogen compounds produced by inflammatory cells which produce chemical changes in the RNA nucleotides which alter replicated sequences. The viral selection process is driven by the host immune system against the frequently changing protein structure, eliminating the variants for which it is specific and leaving behind the evading ones to enter new host cells and replicate. The anti-parasite immunity described in earlier posts may also be, at least in part, responsible in allowing the SARS-CoV-2 time to mutate and escape the immunity in a single host. This is seen in such parasitic diseases as African Sleeping Sickness (trypanosomiasis) and malaria, and may even produce a stalemate with the host called premunition, infectious immunity ( https://www.frontiersin.org/articles/10.3389/fimmu.2019.02738/full). It appears SARS-CoV-2 has chosen to enhance anti-parasite immunity like that used by the hosts to control parasitic worm, pathogenic protozoan and fungal infestations and infections. This response often controls the number of parasites to a tolerable, but not immediately lethal, level and prevents further infestation (process premunition), but does not totally eliminate the parasite. But is there any precedent for this in other coronaviruses in animals?

Cats get an enteric coronavirus which has little or no signs, but, in certain young cats, it becomes disseminated, causing peritonitis with lethality, usually 100%. Cell-mediated immunity provides an effective immune response that resolves the infection in the enteric, intestinal form. If it does not, a strong humoral response kicks in and selects for a more pathogenic form of the virus which infects and replicates in macrophages https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112361/pdf/main.pdf. Also, autoantibodies form. There seems to be genetic predisposition toward this resulting in peritonitis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819880/. Peritonitis pathology involves severe systemic inflammatory damage of serosal membranes and widespread pyogranulomatous lesions in the lungs, liver, lymph tissue, and brain. The clinical finding of hypergamma-globulinemia-associated feline infectious peritonitis is indicative of over production of antibody against an antigen which cannot be cleared, allowing time for viral mutations that allow the virus to escape elimination. Therefore, like COVID-19, the feline coronavirus virus disease has this dichotomy, based on viral dissemination and autoantibodies. The right antigen for the right vaccine must be selected to prevent such adverse effects.

SARS-CoV-2, continues to evolve by mutation and selection toward being more efficient at infection and transmission within close, tight social groups but falling off quickly when vaccination and moderate barriers, like masks and good ventilation, and social distancing are implemented.

Vaccination does NOT guarantee protection from infection by Delta, Omicron, or any new variant or transient release of virus from asymptomatic vaccinated individuals. Vaccination is NOT for elimination of all possible virus but to reduce infection level below the point of symptoms of disease in immunized people (varies from person to person somewhat, but is more likely to be overcome with higher circulating viral loads). It is the circulating of more infectious particles over and over so there can be accumulation and increased probability of developing more mutants, therefore, variants, that is problematic. Omicron is just SARS-CoV-2 testing the perimeter for weaknesses.

The first Omicron case has arrived in the US in California in a person returning from South Africa Nov 22. Fully vaccinated, this person has displayed mild symptoms, is in quarantine, and all contacts tested have been negative so far (CDC).

Science has dramatically and classically demonstrated its failure to communicate to the general populace with fatal consequences in the last 2 years (2019-2021) for COVID. I have not been exempt from this failure. In the last 10 years, I have published eBooks with catchy titles (making them available from popular outlets as cheaply as possible), used social media: Facebook, Twitter and LinkedIn and this blog to attempt to educate the public in science, in general, and infectious diseases, specifically. I shouldn’t have been surprised by the underwhelming response. Even among scientists, communication among disciplines is very difficult and seemingly fails because of specialization, jargon and disinterest and because of stove piping, mostly because of funding mechanisms and not seeing how this “other science” could possibly benefit their scientific pursuits. Type-B Cytochromes : Sensors and Switches, my specialized science book by CRC Press, Taylor & Francis Group, CRC Revivals 2018, now 8 editions published between 1995 and 2018 in English is held by 147 WorldCat member libraries (including Harvard, Stanford, Johns Hopkins, Princeton, etc) worldwide, costing between $51-$237, while my popularized book The Black Dragon Trilogy, 2012-2018, Amazon eBooks $0-$2.99, has been read by almost no one. I have not received any royalties from these; the first because it was done while I was a Federal employee and the latter because no one has bought it. I published them more to convey knowledge and wisdom than to make any money.

The latter book collection is about my general interest in science and my last unfinished scientific work, and the former specifically about my research for the Air Force Research Laboratory up until it was published. But I am really about conveying to the public the joy of scientific discovery and the benefits of science to human kind. I deeply admire and tried to emulate Carl Sagan, who was one of the few in Science able to and succeeded at doing this.

Another more successful engagement of the public in science and technology has been through movies, like Star Trek, although less scientifically accurate, but even inspiring scientists to try to attain their fictional achievements in the real world. I also find the James Bond series has a similar technological appeal, discounting its early misogyny, continued sexism, action and romantic appeal (cultural sophistication and beautiful places besides people). But the most amazing thing about it is its timely relevance to current events and technologies (even if the characters covered too much time and changed without changing its suspension of disbelief). There appears an unlikely connection between my science and technology work and the James Bond technology themes. In particular, two movies Golden Eye (Release date: November 13, 1995,USA) and the most recent “No Time to Die” (https://www.007.com/no-time-to-die/). The former (Golden Eye) involved a Soviet era electromagnetic pulse weapon that destroys electronic devices, including aircraft. We investigated such a potential Russian weapon during the Cold War, not only for its electronic warfare effects but for its potential health effects on military personnel. Later, after the fall of the Soviet Union, the Russians offered to sell us such a prototype device. The theme of “No Time to Die” mirrors my last research, before my retirement, for USAF and DoD, that remains unfinished. The technological theme of the movie engages the MI6 scientist Valdo Obruchev who is kidnapped from an MI6 laboratory. With M‘s approval Obruchev had developed Project Heracles, a bioweapon containing nanobots that infect like a virus upon touch and are coded to an individual’s DNA, rendering it lethal to the target and their relatives but harmless to others.

We developed bionanotechnology that has the potential for similar nefarious use. My attempts to further develop it for biomedical applications post retirement failed for unknown reasons (https://link.springer.com/book/10.1007/978-3-031-63006-4). The proof of the technology is in 30 years of basic and applied research documented in peer-reviewed scientific publications, government reports and patents in the public record. Also, my books, particularly Nanowarfare (2016), and its subsequent inclusion in The Black Dragon Trilogy (2018), describe the bionanotechnology, designated Nanobes in further detail. One component of the technology, developed in collaboration with the Nobel Laureate who discovered PCR, Dr Kary Mullis, was transferred through a US affiliate, to a British company Centauri LTD, and is still being developed in the United Kingdom to fight antibiotic resistant bacterial infections. Many of the other posts in this blog describe various aspects of this technology. However, I will describe its salient features here, again, in brief, in comparison to the fictional technology in “No Time to Die”. Perhaps, the detail and specifics I have given in the past are too much and only create a fog obscuring its good and bad potential. The comparison may make it crystal clear and make the technology more plausible for all its various applications. Sometimes we draw patterns from observations that are not really there, but the similarities I am about to describe are uncanny and the potential nefarious applications, especially by our potential adversaries, have been noted and described and the warnings given years before the movie. Suspicion that others following our progress were contemplating such nefarious use was clearly illustrated in an open literature publication: “Ultramicro, Nonlethal, and Reversible: Looking Ahead to Military Biotechnology by Colonel Guo Ji-wei, The People’s Liberation Army, China, and Xue-sen Yang, MILITARY REVIEW July-August 2005, https://www.armyupress.army.mil/Portals/7/military-review/Archives/English/Dir-Select/nano-technology.pdf. I presented a paper at the Twelfth Annual Directed Energy Symposium, 2-6 November 2009, San Antonio, Texas, titled “Biotechnological Nanowarfare: Directed Electromagnetic Energy Control” which warned: 1) Chinese and Russian researchers follow our (Brooks Team) research on genetic engineering of microbes and animal/ human cells and their interactions with directed energy. 2) The Chinese are hotly pursuing aptamer development, biotechnological manipulation and nanoparticle delivery systems, especially for the brain. 3) Even if we never make Nanobes, we will have to face them. So the mood was set to be aware of the technology being subverted into a nefarious military offensive use to selectively attack, control, or even dispatch undesirable individuals or ethnic groups just like in the movie while eliminating collateral damage, “infection” and injury to non-targeted individuals.

Here we are at 2021 and a James Bond movie is describing a nanobot comparable to our Nanobe, which has been described as a nanomachine (“nanobot” is more an engineering term describing a mechanical nano device and the term “Nanobe” is more biological but closer to the viral substitute description and energized by an external wireless electromagnetic power source, especially pulsed radio frequency or microwave radiation). These Nanobes are able to induce the host cells to make enzymes which manufacture more polymer to encapsulate more Nanobe DNA or RNA equivalent sequences to be transferred to new naive host cells just like a virus, but not coated with proteins which would trigger a host immune response. Thus Nanobes evade immune clearance and enzymatic breakdown in a host. In the movie, the nanobots infect individuals for life even if they do not kill them, but can be transferred to another targeted individual with lethal consequences. The nanobots are programmed with the target’s DNA. Nanobes are programmed with synthetic DNA or RNA which hybridizes to host DNA sequences, selected or designed to bind specifically to proteins, specific nucleic acid sequences, or other biological molecules or whole cells and specific tissues and organs. They can re-direct an immune response to a new antigen, transfer functional genetic material, or simply mark a small target like a microbe, virus or even a cancer cell for very focused electromagnetic radiation energy mediated destruction. Both nanobots and Nanobes can penetrate skin. The latter can penetrate the host by inhalation into the lungs or the mucous membranes of the nose and directly enter the brain. The Nanobes, unlike the nanobots, have a fail safe function triggered by absorbing enough electromagnetic energy locally to destroy them. The bionanotechnology is described in detail in Bionanotechnology: Radio Controlled Antimicrobial and Genetic Vectors, Springer-Nature, 2024, https://link.springer.com/book/10.1007/978-3-031-63006-4.

In the end, the USAF (Agent Defeat Weapons: CrashPAD) reality and the movie both destroy the manufacturing and storage facilities of bioweapons with munitions and incendiaries.

The following illustrations and photographs display tracing the Nanobes in target cells with fluorescent quantum dots and polymerase chain reactions (PCR) to show gene transfer and the final Nanobe design:

The performance of vaccines is based on three fundamental factors: (1) the vaccine antigen (immunogen); (2) the host (human or animal) immune response; and (3) the pathogen (infectious or effective dose; replication rate in the host ; pathogenicity: tissues infected, immune avoidance responses, and damage to the immune system).

Before I discuss the above factors, I need to address an obvious question, “How is a veterinary microbiologist and parasitologist qualified to discuss human vaccines and those for COVID specifically?” First, of 30 plus new human pathogens, including SARS-CoV-2, detected in the last three decades, 75% came from animals. Furthermore, in addition to having a DVM, I have a PhD from a medical school in biochemistry and microbiology concerning human metabolic and infectious diseases, respectively. I am board certified in veterinary microbiology and parasitology (Diplomate of the American College of Veterinary Microbiologists, 1984, and a Charter Diplomate in Veterinary Parasitology, 2011). I have served the USAF and other agencies and Military Services of the Department of Defense in countering biological warfare for over 30 years. I was consultant to the USAF Surgeon General on Veterinary Microbiology (the last one). I retired as the USAF Senior Scientist in Chem/Bio Counterproliferation and Electromagnetic Bioeffects in 2011. And, I have advised them as a contractor from time to time in these areas ever since, including on how to neutralize SAR-CoV-2 in the air using electromagnetic radiation and how to counter biotechnological weapons.

In respect to the first factor, antigens, it is very important to select the proper one as an immunogen to induce protective immunity against initial infection and/or specific disease manifestations. Vaccines may not fully prevent infection (as with SARS-CoV-2 delta variant), but can reduce or prevent disease. However, recent evidence from Sweden and Finland show that they inhibit transmission within family units containing unvaccinated individuals as the number of family members vaccinated increase (45% to 97% lower risk of contracting COVID-19 as the number of immune family members increased). Also, mild infections have recently shown to provide strong enduring immunity which meets the Sabin Rule, “that a vaccine cannot give any better immunity than that derived from a recovered infection.” The exception is when a dysfunctional immune pathway is triggered as in “ long hauler” COVID or when non-neutralizing antibody is induced as is abundantly seen in such other infectious diseases as HIV AIDS or symptomatic progressive rabies. SARS-CoV-2 infection, especially if widespread in tissues prior to immune resolution, has a propensity for triggering a detrimental immune pathway. Also, aborted upper respiratory infections, as in children, are mitigated by innate immune responses such as those driven by interferon which truncates the development of a lasting specific immune response to COVID and can lead to re-infections as children age and become adults. The virus is in a race with the immune system to replicate, transmit and cause disease before it can be eliminated by the immune system. This principle being recognized, one must be aware that vaccine induced immunity is not absolute and can be overcome in a spectrum of infection and disease states. In countering biological warfare, those investigators, such as myself, had to be acutely aware of this fact in order to gauge effective responses to various levels of attack and exposure, from overwhelmingly massive bio weapon attacks to collateral release from destroying biological weapon production and storage facilities. Also, the route of exposure from aerosol, to skin contact, to ingestion had to be considered. I once had to answer a Special Forces General Officer Commander on why his vaccination against anthrax did not remove the necessity for other physical barrier and sanitary precautions in a massive attack or exposure scenario. To quote a Russian military proverb, “Quantity has a quality all its own”. Vaccines are meant to provide logs of protection (10-fold increases in the infectious dose) which can be overcome by very high exposures rather than absolute protection. This is why talking about percent protection of a population can be misleading. These percentages are based on an average dose of agent under ordinary circumstances. They are assuming everyone receives the same dose and just have variations in their immune responses to the infectious agent, SARS-CoV-2, specifically. Acceptable vaccines give about 2 logs of protection, good ones 3 logs and excellent ones more than 3 logs. Some of the best vaccines are against toxins and fall into the last category, such as those against diphtheria, tetanus and clostridial toxins (vaccination with inactivated toxins called toxoids). These limitations are why we need to reduce viral output within a population and within a certain exposure circumstance regardless of vaccination status. Why we need to reduce the number in a population producing large amounts of transmissible virus to stop the pandemic. Also, viruses do not mutate with intent. The mutations beneficial to their survival, replication and transmission are directly related in their probability to the amount of virus produced and circulating.

The second factor, the host immune response can become the limiting factor for any vaccine no matter how well designed and it is performing in the general population. This is why the tragic example of Colin Powell’s dying of COVID because of immunosuppression by multiple myeloma, a cancer of plasma cells that suppresses the body’s immune response, is so illustrative. Again, it demonstrates that percentages of protection are no assurance for the protection of an individual unless most of the population around that person is vaccinated. The probability of overwhelming an individual’s immune system by the virus goes down precipitously as the amount of viral exposure goes down. The measure of circulating neutralizing antibody is only one indicator of protective immunity, cell-mediated immunity is also and sometimes more important over the long term. This is carried by lymphocytes and also mediated by other immune cells such as macrophages. Another very important measure is the “immune memory” which resides in specialized lymphocytes. This anamnestic response usually occurs within 3 days. For most natural infections, this response time is sufficient, but for overwhelming exposures with agents, especially by aerosol, and/or with very low infectious doses (as with Q Fever agent, that needs only one organism to infect), the race between the immune system and the pathogen can be very close. Again vaccination is necessary, but not sufficient under circumstances of high infectious dose exposure.

The final factor to be considered here is the pathogen itself. Vaccines may prevent disease but not be able to prevent infection especially if the infectious agent can hide from antibody and immune cells in “privileged” sites such as intracellular, in the brain or kidney, gastrointestinal tract, etc. or if they attack the immune system itself as HIV does and SARS-CoV-2 does to a much more limited extent. This could potentially lead to carrier states, but these are more likely with large viral loads as in naive infections rather than lower viral loads in vaccinated individuals. For COVID, intranasal vaccines are being pursued to induce IgA, a secretory antibody, that stops and neutralizes the virus at the mucosal surface. This would prevent the possibility of widespread tissue invasion by the virus before the immune system could kick in to neutralize it, greatly decreasing the potential for damage and disease seen in the slow response of an initial immune response (2 weeks or greater). The latter is why single vaccination individuals get infected and show symptoms during the two weeks after initial vaccination. It is not a failure of the vaccine. It is just that the virus won the race. This is why mutations that lead to variants that rapidly replicate and disseminate in tissues are such a threat. Our military group addressed such rapid, low dose infecting microbes by developing small synthetic DNA which could be selected in the test tube rapidly to bind to new variants for immediate neutralization and with an additional binding site to attract antibody induced by earlier vaccines to redirect the immune system against these new “rapid variants”. We even showed it could be delivered by inhalation. All these statements are supported by my other posts and data in the references of this blog, and by experience with many other especially dangerous pathogens. The final word: No one is safe until we are all safe.

I have found it necessary to re-post this post. The only way vaccines have affected reproduction is when live attenuated vaccines are given to pregnant hosts, infect the fetus and cause defects or abortion—the mRNA vaccines in particular are not of this class and even the aforementioned effects do not result in sterility and should not be confused with it.

A recent popular article has suggested, that because the SARS-CoV-2 spike (fusion) protein has a homologous polypeptide to Syncytin 1, a protein that forms the syncytium of cells by fusion binding the fetus to the uterus through the placenta, the vaccines against the spike protein would develop antibodies against the placenta and cause sterility, but the data does not support this https://edwardnirenberg.medium.com/are-covid-19-vaccines-going-to-cause-infertility-939bbdb62b64. The fusogen proteins that allow enveloped viruses to fuse with their target host cells are related but not necessarily identical to the placenta protein. In fact, Syncytin 1 and 2 were originally viral proteins and are necessary to the development of placentas in mammals. This was accomplished by infection with a Type D retrovirus which became integrated into the mammalian and human genomes. HERV–W genome integrated into its host’s germ-line around 63 million years ago, spread into Old and New World monkeys and then evolved independently. The viral genes were incorporated into the germ cells and, therefore, for all subsequent generations. This endogenous retrovirus, HERV-W, is the source of Syncytin I. The env gene from HERV-W produced a functional class I fusion protein capable of merging cells into a syncytium. Such syncytia are at the placental interface between the embryo and mother; preferential expression of HERV-W occurs in embryo cells that become part of the placental interface. This virally derived fusion protein is syncytin, later called syncytin-1; a second such protein from HERV-FRD, is called syncytin-2.

“These ubiquitous endogenous retroviruses are permanently transmitted in germ cell genomes and almost all have lost their ability to replicate outside of their genome-integrated DNA and to infect other cells horizontally as complete infectious virions. They are associated with resistance to other exogenous retroviruses, the process of xenotropism, and with placental development in mammals.

Endogenous beta retroviruses (enJSRVs) are present in the genomes of sheep and goats. The enJSRVs are highly related to Jaagsiekte Sheep Retrovirus (JSRV) and the Enzootic Nasal Tumor Virus (ENTV), which cause naturally occurring carcinomas of the respiratory tract of sheep. The enJSRV blocks exogenous JSRV replication by a novel two-step interference mechanism acting both early and late during the virus replication cycle. The only retrovirus sequences that have been added to the human genome since humans became a separate species from their common primate ancestor are members of the Human Mouse Mammary Tumor Virus-like 2 (HML-2) group of the beta retrovirus-like viruses. This human endogenous retrovirus is HERV-K whose elements are integrated in all extant human genomes”— The Black Dragon Trilogy by JOHNATHAN KIEL
https://a.co/8OGjRRc

Mammals and humans have become immunotolerant to these viral placental proteins. Although it is possible for there to be cross reactivity between microbial antigens and self, the evolutionary adaptation to this essential viral appropriated protein has minimized the likelihood of this type of autoimmunity. Fusogenic proteins are so pervasive in enveloped viruses, that if this kind of autoimmunity were likely, we would see sterility with many types of viral infection and their developed vaccines. Normal births have occurred and been reported from SARS-CoV-2 infected mothers. Example viruses producing fusogens, including viral class I fusogens, are major human pathogens, including influenza A, Lassa virus, SARS-CoV, Ebola, human parainfluenza virus-3, HIV-1, and human T-lymphotropic virus-1. Class II fusogens come from Dengue fever virus, West Nile virus, Zika virus, and tick-borne encephalitis virus https://www.cell.com/current-biology/pdf/S0960-9822(20)30668-0.pdf. When viruses such as rubella and Zika cause birth defects it is because of the wild viral infection not autoimmunity to a host antigen https://www.ncbi.nlm.nih.gov/books/NBK507879/ and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140214/. Therefore, this extrapolation and extension of a evolutionary relationship between host and ancient viruses have not led to sterility but rather advanced fetal development.

Perhaps the most remarkable interaction of endogenous retrovirus is with HIV (Human Immunodeficiency Virus):

“Recently, it has been shown that the expression of HERV-K proteins suppresses HIV replication, perhaps through tuftsin, an inflammatory macrophage cytokine. Decline in tuftsin and increased expression of HERV-K is associated with advancing AIDS. Activation of HERV-K expression has correlated with the level of HIV-1 production. Studies of autoimmune neurological demyelinating disease (experimental autoimmune encephalomyelitis (EAE)) in rodents indicates that tuftsin administration upregulates immunosuppressive Helper-2 T cell (Th2) cytokine transcription factor and that tuftsin-mediated microglial cell activation results in shifting microglia to an anti-inflammatory phenotype. In return, the T cell phenotype is shifted towards immunoprotection after exposure to tuftsin-treated activated microglia, that is, downregulation of pro-inflammatory Th1 responses triggered in conjunction with upregulation of Th2-specific responses and expansion of immunosuppressive regulatory T cell clones. Macrophages with activated HERV-K expression were more resistant to HIV infection, perhaps in part by its Gag protein being expressed and interfering with the assembly of the HIV virions, and cells expressing HERV-K and infected with HIV were more susceptible to destruction by cellular immunity. Infection of CD4 + T cells with HIV-1 was shown to result in transcription of the HML-2 lineage of HERV-K [HERV-K( HML-2)] and to express the Gag and Env proteins of this virus. HERV-K( HML-2)–specific CD8 + T cells obtained from HIV-1–infected human subjects responded to HIV-1–infected cells in a Viral infectivity factor (Vif)-dependent manner in vitro. HERV-K( HML-2)–specific CD8 + T cells (cytotoxic T cells) eliminated cells infected with globally diverse HIV-1, HIV-2, and SIV isolates in vitro. A second T cell response that exhibited cross-reactivity between homologous HIV-1-Pol and HERV-K( HML-2)-Pol has raised the possibility that similarities between HIV-1 and HERV-K play a role in forming, triggering, and perhaps enhancing, the T cell response to HIV-1. There is even some suspicion, because of the association with HERV-K expression with certain tumor cell lines, that its expression can lead to cancer triggered by HIV infection as was perhaps my brother’s brain lymphosarcoma. HERV-K is both protective, initially through triggering the innate immune system and later specific T cell cytotoxicity, and detrimental by perhaps triggering the formation of cancer. The dilemma with HERV-K and the human immune system is that the initial innate response producing reactive oxygen species could protect against both HERV-K and HIV, simultaneously, but the switch to the inadequate nitric oxide response in human macrophages encourages the replication and release of HIV to infect other recruited and susceptibly activated macrophages to carry the HIV to lymphoid tissue. Evolutionarily, HERV-K’s advantages have outweighed its disadvantages and has led to resistance to such coming plagues as that could result from Viper Plague Virus, at least for now.”— The Black Dragon Trilogy by JOHNATHAN KIEL
https://a.co/57tGvuL

Whereas the following DNA vaccine technologies are no longer being pursued at this time for FDA licensure. India has granted emergency use authorization to a DNA COVID-19 vaccine that uses plasmids, to prime the immune system by synthesizing protein antigen in situ against SARS-CoV-2. The vaccine, ZyCoV-D, was developed by the Indian pharmaceutical firm Zydus Cadila; it is the first DNA vaccine for humans to receive authorization anywhere in the world.

Nov 16, 2020, 07:00 ET, it was announced that INOVIO received approval from the U.S. Food & Drug Administration (FDA) to proceed with Phase 2 of its Phase 2/3 clinical trial for INO-4800, its COVID-19 vaccine candidate. INO-4800 is the only nucleic-acid based vaccine that is stable at room temperature for more than a year and does not need to be frozen in transport, an important factor for implementing mass immunizations. INOVIO’s DNA vaccine plasmid is delivered directly into cells intramuscularly or intradermally using INOVIO’s proprietary hand-held device called CELLECTRA®. The CELLECTRA device uses a brief electrical pulse to reversibly open small pores in cells to allow the plasmids to enter, overcoming a key limitation of other DNA vaccines and mRNA vaccines. Once inside cells, the DNA plasmids enable the cell to produce the targeted antigen. The antigen triggers the normal T cell and antibody-mediated immune responses. The CELLECTRA device ensures that the DNA plasmids are efficiently delivered directly into the body’s cells to drive the immune response. INOVIO’s DNA vaccine does not interfere with or change in any way an individual’s own DNA. The advantages of INOVIO’s DNA vaccine platform are how fast it was designed and manufactured; its stability, not requiring freezing for storage and transport; and the robust immune response, safety profile, and tolerability evident in clinical trials. The CELLECTRA® electroporation device developed by Inovio Pharmaceuticals, Inc., is currently being assessed in clinical studies for both prophylactic and therapeutic applications.

This device delivers square-wave electric pulses by applying an adaptive electric field based on constant current, rather than constant voltage. This system measures electrical parameters and adjusts appropriately for changes in tissue resistance in realtime to avoid tissue damage and diminished DNA cell entry. The device has been evaluated in animal models, including mice, pigs, and rhesus macaques, and demonstrated acceptable immune responses.

DNA vaccines have been criticized in the past because of the possible off-target effects in expression of protein, integration of foreign DNA into the host genome and difficulties in delivery to the right target cells. As noted above INOVIO has provided evidence that they have overcome these limitations by plasmid design and a proprietary electroporation device. The concern about plasmid in comparison to mRNA vaccines is that they must enter the nucleus to be converted into mRNA before being translated into protein in the ribosomes of the cytoplasm. mRNA vaccines do not require entry into the nucleus before this last step. I have spent a lot of time providing accounts and data of the Brooks Counterproliferation Team’s work on these problems for different military applications in previous posts. It is ironic that INOVIO has received a significant level of funding from the Department of Defense independent of our work: On June 23, 2020, INOVIO received a $71 million contract from the U.S. Department of Defense to scale up its manufacture of its CELLECTRA® 3PSP Smart Device and procurement of CELLECTRA® 2000 for COVID-19 DNA Vaccine delivery https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906411/pdf/hvi-9-2246.pdf.

Our work began with efforts to synthesize a microwave and radio frequency electromagnetic radiation interacting polymer starting in 1981. We succeeded (1 March 1988) in making one from the amino acid 3-amino-L-tyrosine which through diazotization ended up with the following structure:

This polymer demonstrates a number of interesting and very applicable physical and chemical properties. It is thermochemiluminescent while oxidizing, binds to DNA without damaging it functionally, and further interacts instantly with pulsed direct current electric fields, and those of pulsed radio frequency and microwave radiation. The classical explanation of its behavior is as an inductor, that it is a passive two-terminal electrical component that stores energy in a magnetic field when electric current flows through it. An inductor consists of an insulated wire wound into a coil around a core. When the current flowing through an inductor changes, the time-varying magnetic field induces an electromotive force (e.m.f.) (voltage) in the conductor, described by Faraday’s law of induction. According to Lenz’s law, the induced voltage has a polarity (direction) which opposes the change in current that created it. As a result, inductors oppose any changes in current through them. The coiled ground state structure of DALM may be responsible for its behaving as a molecular inductor. The discharge of luminescence and/or thermalization are related to the release and conversion of this stored energy.

The next step was to try to make DALM from feedstock chemicals fed to bacteria that have inducible nitrate reductase. When this process was not totally satisfactory, genetic modification with plasmids delivered by electroporation or calcium phosphate was tried and succeeded in enhancing the production of DALM. This even worked with mammalian and human cells harboring nitric oxide producing enzymes (nitric oxide synthase, NOS) which could integrate with a component of the barley plant nitrate reductase to enhance both their activities simultaneously.

Plasmids transferred to target cells with DALM nanoparticle vectors have demonstrated desired functional transfer such as antibiotic resistance for clonal selection, antimicrobial activity, and DALM nanoparticle biosynthetic capability, but also the less desirable transfer and off target effects of genome integration in mammalian and human cells (expected based on plasmid constructs used), and in bacteria, not only the clonal selection antibiotic resistance, but also the off target effects of bacteriophage resistance and hemolytic activity in a pathogen (Bacillus anthracis, anthrax). The DALM nanoparticle vector has demonstrated its broad utility as a potential plasmid DNA vaccine vector and also its ability to be manufactured by microbes’ making biosynthetic complete DALM, nanoparticle, plasmid DNA vectors for genetic transfer.

My colleagues and I answered a call for innovative ideas to fund rapidly responding to emerging infectious disease in a timely and effective way, before COVID-19 was a thought, from The Coalition for Epidemic Preparedness Innovations (CEPI), a global partnership launched in 2017 to develop vaccines to stop future epidemics. We were flatly turned down. CARB-X was launched July 28, 2016, by two divisions of the US Department of Health and Human Services (HHS): the Biomedical Advanced Research and Development Authority (BARDA), which is part of the Office of the Assistant Secretary for Preparedness and Response (ASPR) and the National Institute of Allergy and Infectious Diseases. We had sent in a proposal with a well-known institute to CARB-X in 2017, which was not funded. On 7 January 2020, CARB-X released a press release that CARB-X backs Centauri (a UK biotech company) to advance a new platform that combines antibiotic power with the ability to boost the immune system to fight infections caused by drug-resistant bacteria (this was invented by Dr Kary Mullis, Nobel Laureate and further improved by support from the USAF AFRL Brooks Counterproliferation Team) Centauri therapeutics.https://carb-x.org/carb-x-news/carb-x-backs-centauri-to-advance-a-new-platform-that-combines-antibiotic-power-with-the-ability-to-boost-the-immune-system-to-fight-infections-caused-by-drug-resistant-bacteria/ Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator (CARB-X) is a global non-profit partnership for accelerating antibacterial research to address global rising threat of drug-resistant bacteria. It controls up to US$480 million to invest, 2016-22; CARB-X funds the best science from around the world. The CARB-X portfolio is the world’s largest early development pipeline of new antibiotics, vaccines, rapid diagnostics and other products to prevent, diagnose and treat life-threatening bacterial infections. CARB-X is led by Boston University and funded by US Department of Health and Human Services Biomedical Advanced Research and Development Authority (BARDA), part of the Office of the Assistant Secretary for Preparedness and Response (ASPR), the Wellcome Trust, a global charity based in the UK working to improve health globally, Germany’s Federal Ministry of Education and Research (BMBF), the UK Government’s Global Antimicrobial Resistance Innovation Fund (UK GAMRIF), the Bill & Melinda Gates Foundation, the world’s largest foundation dedicated to improving the quality of life for individuals around the world, and receives in-kind support from National Institute of Allergy and Infectious Diseases (NIAID), part of the US National Institutes of Health (NIH). CARB-X headquarters are at Boston University School of Law. BARDA and the Gates Foundation were appealed to in 2013 and 2012, respectively, for support of the US (our proposal, submitted again to CEPI in October 2019, with Dr Mullis’s collaboration just prior to his passing on August 7, 2019) improvements in chemically programmable immunity using the Nanobe platform, but we were totally ignored by these two. How many times can a good idea be turned down? Until it becomes someone else’s.

For CEPI:

Target pathogens
Pathogen 1: Malaria (Plasmodium falciparum and others): There is no current effective vaccine for this disease and resistance to the most effective treatment with artemisinin is spreading. However, natural resistance has been demonstrated in endemic areas in children, but the effective response requires IgM and not IgG and the target antigen galactose-alpha-1,3-galactose. Vaccines that lead to IgG response development will not be as effective as those that direct the immune system toward an IgM response to alpha gal.
Pathogen 2: Heartworms (Dirofilaria immitis): this disease is not only pervasive in canines across the world, but the current treatment (may be called a “preventative“ but actually kills as a microfilaricide after infection but before worm maturation) uses the same macrocyclide lactones, to which resistance is developing and spreading, used in human filariasis; macrocyclide lactones are the only class of drugs currently available to treat these filarial diseases, which means the development of resistance would eliminate any effective treatment, and they involve altering or blocking the release of an antigen which interferes with the immune response to these filaria and which is effectively activated upon treatment to eliminate microfilaria. There is a robust antibody response which is interfered with by soluble antigen/antibody complex formation which could be overcome by the appropriate redirection or facilitation of immune targeting.
Pathogen 3: Dracunculus medinensis, Guinea worm; the hope to eradicate this parasite, now only in Africa, has recently shown signs of failure after finding that the once thought to be rare infection in dogs (over a thousand infected dogs discovered) is now commonly present in them in Chad. This infection of dogs in areas of re-emerging human infection allows for studies of the platform response in dogs under field conditions which would be most relevant to concurrent human disease.