Virology: A Reappraisal

I have written the following as a comprehensive, detailed and hopefully cogent explanation of the methods used in modern virology and their flaws. I have gained this knowledge from medical professionals and from my own verification and research. I have examined published scientific papers to this end. I hope you find it informative and this should also enable you to compare the methods described herein to published papers, not least those claiming isolation of SARS-CoV-2. I am packaging this monograph free with every copy of Paper View: In Print but you can of course just print-out your own copy if you so wish.

Virology: A Reappraisal
by Daniel Ford

The study of virology dates back to the early 19th century. The field of virology has made significant advancements since the 1800’s while its methods remain questionable. In this monograph, I shall explore and describe the flaws of this particular field of study still present today, and in so doing, explain not only an alternative methodology for the discovery and identification of viruses but the only true methodology. I shall also relate my findings to the current SARS-CoV-2 virus and explain what this means for the disease known as Covid-19, now presently considered a global pandemic.

What is a virus?

A virus is a microorganism on the nanometer scale, beyond the range of human sight. A virus contains RNA or DNA (genetic material) and this genetic material is housed in a casing which allows for contact with receptors (receivers) inside the body. For example, the spikes of the coronavirus allow for a lock-and-key mechanism, whereby the spikes bind to the receptor and then the virus can release its genetic material into cells and replicate.

Viral Identification

The process of identification of a new virus includes three key stages – isolation (purification), sequencing and characterisation. Without all these stages being completed, a new virus cannot be proven to exist and cannot be fully understood. Isolation is the single most important step because everything else that follows, including in the governmental and societal sphere, is based on the assumption that the infectious agent has been isolated. The process of isolation or purification of a virus, for instance, a respiratory virus, involves taking a sample of lung fluid or sputum from a sick individual and filtering the sample, which removes material like bacteria and other material which is bigger than viral particles and bigger than the size of the filter, thus leaving only viral particles. Lung fluid (commonly referred to as bronchoalveolar lavage fluid or BAL in scientific papers) can contain bacterial cells; debris from dead or dying cells; exosomes (which are very similar to viruses); free genetic material, and other material so filtration is necessary. The filtered fluid is then added to a density gradient reagent, a liquid solution with a specific density measurement, and a centrifuge, which is a piece of laboratory equipment with a wheel powered by a motor, which is used to spin the sample material at high-speed using centrifugal force. The viral particles eventually form a sediment, or band of material, and the particles can then be extracted using a pipette. The viral particles can then be visualised and examined under an electron microscope, which can see material on the nanometre scale, and sliced open to reveal the genetic material inside and this genetic material can then be sequenced, meaning understood from a genetic perspective and characterised, which means compared to other previously identified viral genetic material. Published papers claim to have isolated the SARS-CoV-2 virus. However, further examination of their methods reveals lack of filtration and centrifugation.

Proving Infection

An often-cited method to prove infectious capacity and nature is a set of criteria known as Koch’s Postulates, which have been in use since 1890. These are the 5 stages:

The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.

The microorganism must be isolated from a diseased organism and grown in pure culture. The cultured microorganism should cause disease when introduced into a healthy organism.

The microorganism must be re-isolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent. In other words, the infectious agent must only be found in abundance in people or animals suffering from the disease it is claimed the infectious agent is causing but not in healthy people or animals.

The infectious agent must necessarily be found in abundance as it is not only the presence of an infectious agent which causes disease and illness but the amount replicating and circulating within the body of the person or animal. In virology, this is known as viral load. The infectious agent must be isolated in the above described manner, and introduced into a healthy person or animal, and they must show symptoms.

The infectious agent must then be re-isolated from another infected person or animal and proven to be identical to the original infectious agent and introduced into another healthy person or animal and they must again show symptoms.

This proves a clear cause-and-effect. This process may be repeated one or two times to prove repetition, an important scientific principle. Another set of criteria, building on Koch’s Postulates, were introduced in 1936 known as Rivers’ Criteria, after Thomas Milton Rivers, an American bacteriologist and virologist, a former director of the Rockefeller Institute for Medical Research. Rivers proposed that a specific virus must be found associated with a disease with a degree of regularity; this is significant because as any virologist knows, association is not causation. Rivers also proposed that it is not obligatory to demonstrate the presence of a virus in every case of the disease caused by the virus; this would mean not proving that the infectious agent is the cause of the disease which runs counter to the entire foundation of germ theory. Rivers claimed that satisfaction of his modification of Koch’s Postulates does not necessarily indicate the active agent was present in the original material used for inoculations of experimental hosts and that upon satisfaction of the criteria, one can be fairly confident that a disease is caused by an infectious agent. Rivers’ Criteria would seem to be a shortcut compared with Koch’s Postulates while only capable of proving a weak association between a virus and the cause of a disease. Rivers stated, as recently as 1936, that it was obvious that Koch’s Postulates had not been satisfied for viral diseases. Neither Koch’s Postulates nor Rivers Criteria have been satisfied for the SARS-Cov-2 virus.

Viral Culturing

The criteria stipulate that the infectious agent must be grown in a pure culture which is used to observe the reproduction and effects of a microorganism by allowing it to grow in a petri dish in a replication of its ‘natural’ environment. Viruses, however, given that they are not living organisms in the first place, cannot be grown in a pure culture as they cannot survive without the provisions of a living host cell, in human or animal cells, for example. Viruses are cultured in a host cell and cytopathic effects are observed, meaning the effect of the virus on cells. Viral culture is cited as evidence of isolation of the virus even though isolation means separation from anything else. Viral culture has nothing in common with genuine viral isolation previously described. Viral culture has been the standard method of viral identification since 1954 after John F. Enders perfected the method to allegedly identify the virus of measles. Viral culture would be better called tissue culture or cell culture as nothing about the method proves a virus without first isolating the virus which is often the case. Viral culturing in virologic study is commonly subject to serious flaws and a lack of control experiments. The first flaw is the lack of isolation of the viral material. For the study of human viruses, human host cells are often not used, instead, Vero cells, particularly, Vero E6 cells, which are monkey cells or monkey rhesus kidney cells, are the most commonly used form of host cell. A solution claimed to contain the virus, without the virus being first isolated, is inoculated into the host cells, and over a specific time period, cytopathic effects are observed. Another flaw is the host cells are not cultured with the viral material and left to thrive in a replication of their optimal, natural environment but are given minimal growth media, meaning the cells are starved of nutrition and mixed with antibiotics, known to be toxic to cells, and very often, bovine calf serum, which can itself contain various types of material including genetic material. Naturally resulting cytopathic effects from such an environment are then claimed to be the effects of the virus. Two forms of control experiment should include inoculating healthy cells with viral material in a culture which allows the cells to thrive and healthy cells in a culture without the viral material but with the antibiotics and other toxic or infected material. The first form would prove the virus is the cause of the cytopathic effects and the second form would prove the culturing with toxic and infected material was the cause of the cytopathic effects.

Sequencing

When a virus’ genetic material has been extracted and fully sequenced end-to-end, the viral genome is compared against a database of previously sequenced viral genomes (RNA or DNA sequences) to understand the kind of virus being compared. However, viruses are often ‘identified’ using the methods previously described and, in such cases, entire intact viral genomes are not being sequenced, only tiny snippets of RNA or DNA not correctly established to be of viral origin. RNA and DNA are composed of base pairs, which bond together. A-T or G-C in the human genome, for example. In viral sequencing, only short snippets of RNA or DNA base pairs from an unpurified tissue or fluid sample out of 30,000, for example, may ever be sequenced. Computer sequencing software is then used to fill in the blanks. Even in the event of correct and genuine isolation, purification and sequencing of a virus, characterisation is limited as so many viral sequences are, for the most part, computer-generated. As a result of this method, attempts at sequencing by several study groups will produce different sequences as the computer software will produce different genomes. The actual genome is finally decided upon merely by consensus. A common form of sequencing is Next Generation Sequencing, which is designed to identify genetic fragments from already identified genetic sequences extracted from previously purified infectious agents, not to identify the genome of a new infectious agent, although it is often used for this purpose.

Visualisation

Viruses can be mistaken for other forms of particle. SARS-CoV-2 particles are often mistaken for exosomes. These are secretions of a poisoned cell. The body releases exosomes regularly, but they are especially released upon poisoning, toxification or irradiation (including the non-ionising form of wi-fi, Smart meters and 5G). Exosomes are extracellular vesicles, which are used for communication with other cells. Exosomes are a natural response of the immune system. SARS-CoV-2 particles can be indistinguishable from exosomes in all the major ways. Exosomes are said to be 500nm (nanometres – billionth of a metre) inside the cell. Exosomes are housed inside multivescicles, which are 500nm in length. When released from these multivesicles, the exosomes themselves are actually 100nm, the length attributed to SARS-CoV-2 particles. Variation in size does occur however. Exosomes are believed to bind to the angiotensin converting enzyme-2 receptors on the cell just as SARS-Cov-2 particles are said to do and both can be found in lung fluid. The damage to the lungs generates the release of exosomes. Viral culturing with toxic drugs and starvation of the cells in the previously described manner will generate the release of exosomes. When viewed under an electron microscope, exosomes can easily be confused with other viral or other forms of particle. It is not guaranteed that viral particles will be visualised under an electron microscope in a viral culture constituted of the previously described material, but it is guaranteed that exosomes will be visualised as a recipe has been used in the culture which leads to their release from the host cells. When electron micrograph ‘images’ of a virus are shown, in many cases, they are particles or vesicles from the tissue culture with the cytopathic effects. The particles or vesicles are claimed to be discovered by zooming in to the tissue culture and claiming a certain particle or vesicle is the virus particle. However, the tissue culture contains toxic and poisonous material, leading to particles or vesicles not of viral origin to break away from an infected or dying cell. Electron micrograph images claiming to show virus particles are distributed by health bodies as evidence of isolation of the virus. The point is, however, that virus images derived from tissue or cell culture constituted in the previously described manner may contain a variety of particles or vesicles. Another case of mistaken identity is what are known as clathrin-coated vesicles. A vesicle is a structure within or outside of a cell and is used for secretion, excretion or transport of material within the membrane of a cell, which surrounds and encloses the cell’s contents. Clathrin-coated vesicles resemble SARS-CoV-2 particles with visible ‘spikes’ on their surface. This is also the case for Copi and Copii coated vesicles.

Testing

A common means of testing for infection with a virus, and indeed, the method most used to test for SARS-CoV-2, is known as the RT-PCR test (real-time reverse transcription polymerase chain reaction). The test is used to reverse transcribe RNA into DNA. The test uses an enzyme called reverse transcriptase to transcribe the genetic material allowing for a pre-determined amount of copies to be made to allow for easier study of the genetic material. The test is calibrated using primers, which are pre-set genetic sequence codes, the viral genome. Each test will be using a certain primer. The primer is basically the viral genome template which the test will search for within the sample from the test subject. The test takes a minute amount of RNA and ‘amplifies’ the material; in other words, more of the genetic content in the sample is made available for the test to detect. The amount of amplification of material informs the likelihood of a positive result as the more material is amplified, the more other material present in the body, which may or may not be of sufficient viral load or potency to cause illness and may or may not even be viral or bacterial, can be detected by the test and register as positive. Samples can also be diluted or used neat which can also inform the result. In the case of SARS-CoV-2 and other viruses, the entire, intact genome has never been extracted from a purified viral particle and has never been discovered. The RT-PCR test cannot detect SARS-CoV-2 because the primer sequence is based on a largely computer-generated sequence created in the previously described manner. Also, some viruses are known as symbiotic viruses, which are naturally present in the body and each will have their own genetic material. When a virus infects a sperm or egg cell, providing fertilisation occurs, the viral genome will be copied into each and every cell of the offspring, and that offspring can then pass a copy of the viral genome onto its offspring. This is known as a fully endogenous retrovirus, which forms part of the human genome. Without correct isolation and purification of a viral particle, short snippets of RNA or DNA from retroviruses can be extracted from a body sample and declared viral and used as part of a template for a test and register positive. Junk DNA, or non-coding DNA, meaning DNA which does not code for a protein, may be involved with facilitating retroviruses. The antibody test is claimed to detect the presence of previous infection with a specific infectious agent to which the body responds by releasing antibodies. However, antibodies can be present from a wide variety of different causes and SARS-CoV-2 is only one form, it is claimed, of a family of coronaviruses, known as Coronaviridae, which are present in many people’s bodies and generally never make their presence known, even for people with weakened immune systems. Vaccinations are claimed to prompt the production of antibodies due to the presence of a live virus being inoculated into the body, thus generating an immune response. However, with the toxic nature of vaccine ingredients, the body will be generating antibodies in response to the vaccine ingredients. These antibodies are then cited as evidence the vaccines are effective. If the infectious agent, in the case of SARS-CoV-2, a virus, has never been isolated and therefore, proven to exist, and has never been proven in viral culturing to be infectious to human cell lines, what, then, is the body producing an immune reaction against? Vaccines are produced by ‘growing’ the virus in a cell culture in the previously described manner and then adding the constituents of the cell culture to adjuvants, including aluminium and mercury, to form the vaccine. The body will respond with antibodies to such toxic material. Antigens, which prompt the release of antibodies, can be present in the body from a wide variety of different causes, including toxicity. Exosomes, which can be confused for viral particles and contain genetic material, may serve the role of absorbing toxins to transport them out of the body, and also warning other cells about the toxicity and poisoning to activate an immune response.

Immunity

The body has different immune responses to an incoming threat based on the severity of the threat and the efficiency of the immune system in question. The body does not always need to fight infection with antibodies, and this explains why some who test positive for a virus have no antibodies. Symptoms of a viral or other infection are the body’s response to an invading agent or toxin. A fever is actually the immune system using heat to attack a threat. A runny nose is the body detoxing after the mucus membranes in the nasal cavity have trapped an allergen or bacteria and the nose runs to literally drain away the allergen or bacteria from the body. As it does, mucus may drain down to the back of the throat and cause coughing, and a tickly throat will result. Throwing up is the body literally flushing out a virus or bacteria or toxins through the mouth. This is why people throw up when they have a hangover because alcohol is a toxin and the body is flushing out the toxin. This is why pure alcohol, ethanol, is so dangerous to the body so the alcohol content has to be diluted to make the drink safe to consume. Too much alcohol (poison) kills the bodies’ own microbes. The body is dealing with the threat by instigating these immune reactions. Mainstream medicine treats these immune system responses as a problem in themselves and will prescribe a drug to suppress symptoms when the symptoms are the immune response. Lack of correct identification of viruses limits understanding and options to instigate immunity.

Conclusion

Virology is far from an exact science. We have seen that laboratory methods used for identification of viruses and their genetic make-up are open to interpretation, and what are judged to be exacting standards leave the field and its practices open to confusion and misinterpretation. Virologic study would benefit greatly from a revision of its methods, a crucial step necessary in the field given the societal, governmental, economic and personal implications of relying on its methods and conclusions.

Published papers falsely claiming isolation of SARS-CoV-2 which I have read:

https://wwwnc.cdc.gov/eid/article/26/6/20-0516_article
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7045880/
https://pubmed.ncbi.nlm.nih.gov/32080990/
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238614
https://www.nejm.org/doi/full/10.1056/nejmoa2001017
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314506/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239045/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7303940/
https://pubmed.ncbi.nlm.nih.gov/33152198/
https://www.jstage.jst.go.jp/article/yoken/73/4/73_JJID.2020.137/_article
https://www.nature.com/articles/s41586-020-2008-3
https://pubmed.ncbi.nlm.nih.gov/32237278/
https://www.mja.com.au/journal/2020/212/10/isolation-and-rapid-sharing-2019-novel-coronavirus-sars-cov-2-first-patient
https://www.sciencedirect.com/science/article/pii/S120197122030566X
https://jvi.asm.org/content/94/11/e00543-20
https://jamanetwork.com/journals/jamaotolaryngology/fullarticle/2768621
https://jvi.asm.org/content/94/11/e00543-20#ref-5
https://journals.lww.com/cmj/fulltext/2020/05050/identification_of_a_novel_coronavirus_causing.3.aspx
https://www.europeanreview.org/wp/wp-content/uploads/5186-5188.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366528/
https://www.pnas.org/content/117/13/7001
https://www.medrxiv.org/content/10.1101/2021.01.12.21249603v1.full
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493737/
https://www.mdpi.com/2077-0383/10/2/309/pdf
https://www.biorxiv.org/content/10.1101/2020.03.02.972927v1.full
https://revistabiomedica.org/index.php/biomedica/article/view/5834
https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1760144?scroll=top&needAccess=true
https://www.pathologyjournal.rcpa.edu.au/article/S0031-3025(20)30939-9/fulltext
https://www.sciencedirect.com/science/article/pii/S2214250920302687?via%3Dihub
https://www.ijidonline.com/article/S1201-9712(20)30566-X/fulltext
https://www.acpjournals.org/doi/10.7326/M20-1176
https://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762020000100344&tlng=en
https://jvi.asm.org/content/jvi/94/11/e00543-20.full.pdf
https://ophrp.org/journal/view.php?doi=10.24171/j.phrp.2020.11.3.02
https://onlinelibrary.wiley.com/doi/full/10.5694/mja2.50569
https://link.springer.com/article/10.1007%2Fs12250-020-00241-2
https://www.icgeb.org/wp-content/uploads/2020/04/Journal-of-Virology-2020-Licastro-JVI.00543-20.full_.pdf
https://www.tandfonline.com/doi/full/10.1080/22221751.2021.1884003
https://www.nature.com/articles/s41467-020-19619-7#Sec7
https://link.springer.com/article/10.1007/s11262-021-01826-z
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001006
https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001453
https://www.sciencedirect.com/science/article/pii/S1201971220303428
file:///home/chronos/u-77d5309fe881975d711b51311be761f8ce97e3ea/MyFiles/Downloads/jcm-10-02696-v2.pdf
https://www.nature.com/articles/s41586-020-2313-x
https://link.springer.com/article/10.1007/s12250-020-00241-2
https://www.ijmr.org.in/temp/IndianJMedRes1512244-8106046_223100.pdf
https://www.ijidonline.com/article/S1201-9712(20)30566-X/fulltext
https://www.researchgate.net/publication/344877119_SARS-CoV-2_Isolation_from_Cuban_COVID-19_Patients
https://nanoconvergencejournal.springeropen.com/articles/10.1186/s40580-021-00281-8
https://www.researchgate.net/publication/344367092_Sars-CoV-2_isolation_from_a_10-day-old_newborn_in_Italy_A_case_report
https://www.researchgate.net/publication/344418051_SARS-CoV-2_isolation_from_the_first_reported_patients_in_Brazil_and_establishment_of_a_coordinated_task_network
https://www.scienceopen.com/document_file/4a04bea0-683a-4201-a3c4-580c1e3bd046/PubMedCentral/4a04bea0-683a-4201-a3c4-580c1e3bd046.pdf


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REFERENCES

These are some of my references but this is far from an exhaustive list:

Krug, Robert; Wagner, Robert – November, 2020, Virus, Encyclopedia Britannica, https://www.britannica.com/science/virus

Andrew Kaufman MD – April, 2020, Rooster in the River of Rats, https://www.andrewkaufmanmd.com/therooster-in-the-river-of-rats/ vi Isolation

Culture and Identification of Viruses, Lumen Learning – Microbiology. https://courses.lumenlearning.com/microbiology/chapter/isolation-culture-and-identification-of-viruses/

Andrew Kaufman MD, Sally Fallon Morell, Thomas Cowan MD - 2020, Statement on Virus Isolation - https://andrewkaufmanmd.com/sovi

Thomas Cowan MD - October 15, 2020, Only Poisoned Monkey Kidney Cells Grew The Virus - https://drtomcowan.com/only-poisoned-monkey-kidney-cells-grew-the-virus/

Enders, F. John - Jun 1954, Propagation in tissue cultures of cytopathogenic agents from patients with measles - https://pubmed.ncbi.nlm.nih.gov/13177653/

Gianessia, Flavia - May 2020, The Role of Extracellular Vesicles as Allies of HIV, HCV and SARS Viruses - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291340/

Segre A. Julia - July 11, 2013, What does it take to satisfy Koch’s Postulates two centuries later?, US National Library of Medicine – National Institutes of Health, https://ncbi.nim.nih.gov/pmc/articles/PMC3775492

Rivers, M. Thomas – December 29, 1936, Viruses and Koch’s Postulates, https://ncbi.nim.nih.gov/pmc/articles/PMC545348/pdf/jbacter00773-0005.pdf

Harcourt, Jennifer et al. – June 2020, Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with Coronavirus Disease, United States, United States Centers for Disease Control and Prevention, https://wwwnc.cdc.gov/eid/article/26/6/20-0516_article

Ryu, H. Ann – August 8, 2017, Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation, Nature, https://nature.com/articles/s41598- 017-0775

Andrew Kaufman MD – March, 2020, A Breakdown on Current Testing Procedures (or Humanity is Not a Virus), https://andrewkaufmanmd.com

Miler, E. Sarah and Goldsmith E. Cynthia – September, 2020, Caution in Identifying Coronaviruses by Electron Microscopy, Journal of the American Society of Nephrology, https://jasn.asnjournals.org/content/31/9/223

Dittmayer, Carsten et. Al – October 5, 2020, Why misinterpretation of electron micrographs in SARS-CoV-2 infected tissue goes viral, The Lancet, https://thelancet.com/journals/lancet/article/PIISO140

Aquino, Erika – July 3, 2020, Covid-19 testing: What does it mean for me?, British Society of Immunology, https://www.immunology.org/news/covid-19-testing-what-does-it-mean-for-me

Schraer, Rachel – September 5, 2020, Coronavirus: Tests could be picking up dead virus, BBC News Online, https://www.bbc.co.uk/news/health-54000629

Arnold, Carrie – September 28, 2016, The Viruses That Made Us Human, PBS (Public Broadcasting Service), https://pbs.org/wgbh/nova/article/endogenous-retroviruses/

Kaiser, Gary – August 15, 2020, 14.1: Cell-mediated Immunity – An Overview, https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Kaiser)/Unit_6%3A_Adaptive_I mmunity/14%3A_Cell-Mediated_Immunity/14.1%3A_Cell-Mediated_Immunity_-_An_Overview