The Human “Virome”

“Viruses are microscopic parasites, generally much smaller than bacteria. They lack the capacity to thrive and reproduce outside of a host body. 

https://www.google.com/amp/s/www.livescience.com/amp/53272-what-is-a-virus.html

When most people think of “viruses,” they think of invisible floating invaders from outside which find a way to inhabit the body taking over host cells and multiplying out of control until disease occurs. They are under the false assumption that what are referred to as “viruses” do not belong to our own bodies (endogenous) but must come from some outside source (exogenous). However, this is clearly not the case according to the newest scientific evidence as it is claimed that the human body is full of what virologists call “viruses.” In fact, when you look at the evidence presented to us today, the human genome is primarily made up of “viruses:”

The non-human living inside of you

“The human genome contains billions of pieces of information and around 22,000 genes, but not all of it is, strictly speaking, human. Eight percent of our DNA consists of remnants of ancient viruses, and another 40 percent is made up of repetitive strings of genetic letters that is also thought to have a viral origin.”

“For many years, biologists had little understanding of how that connection worked—so little that they came to refer to the viral part of our DNA as dark matter within the genome. “They just meant they didn’t know what it was or what it did,” explains Molly Gale Hammell, an associate professor at Cold Spring Harbor Laboratory.”

Due to the power of metagenomic sequencing, it has been determined that at least 48% of our genome is made up of “viruses.” Gramted, they have no understanding of what this genetic “dark matter” is nor whether it is even “viral” at all. However, the discovery of these vast amounts of repetitive strings of RNA/DNA assumed to be of “viral” origin has given way to what has now become known as the human “virome:”

Virology: a scientific discipline facing new challenges

“Many host districts of the human body and its mucous membranes are heavily ‘colonized’ by viruses that are not associated with any disease. This has led to the concept of the virome, which can be considered as the set of all viruses, eukaryotic and prokaryotic, present in the human body. The virome includes viruses that infect host cells, viruses that infect the majority of other types of microorganisms harboured by the body, and virus-related genetic elements in our chromosomes [[1]]. Viruses, which can no longer be invariably considered pathogens, interact with the host and other members of the microbial communities (Archaea, bacteria and eukaryotes) in a variety of complex and meaningful ways. These complex interactions have just begun to be investigated but it is common opinion that they profoundly affect health status [[2]]. Due to the existence of commensal viruses, we should probably redefine chronic viral infections and focus our attention on the host rather than on infectious agents to dissect disease determinants.”

https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(18)30775-4/fulltext

The explosion of genomic sequencing in the early 2000’s gave way to numerous sequences of unknown origin. As genomic databases were in their infancy and just starting to be built, anything that did not fit with already existing references were set aside. Rather than assuming that these strings of DNA were of human origin, it was decided that they must be either bacterial or “viral.” While the bacterial side of the microbiome has been studied extensively, the “viral” side has been neglected and thus very little is actaully known about it. In fact, they do not know whether the sequences belong to bacteriophages (“viruses” of bacteria) or other “virus” types. Essentially, they have a massive amount of data with no idea what to do with it as there are no references avaliable to compare these sequences to, so assumptions were made and stories were built to justify the collection of meaningless data:

The human virome: assembly, composition and host interactions

“The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the ‘virome’. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral ‘dark matter’.”

“We are becoming accustomed to the idea that healthy humans are colonized by a rich diversity of microorganisms — the microbiome. However, less well known is that healthy humans are also colonized by a remarkable diversity of viruses — the virome. The human virome comprises bacteriophages (phages) that infect bacteria, viruses that infect other cellular microorganisms such as archaea, viruses that infect human cells and viruses present as transients in food.”

“Centuries of medical research have linked infection by specific viruses with characteristic disease states; however, the nature and importance of whole viral populations were mostly not appreciated until the development of advanced DNA sequencing methods that could report the structures of whole communities. Untargeted sequencing of purified viral samples, termed ‘shotgun sequencing’, was first applied to environmental viral populations in 2002 by Breitbart et al. Viral particles were prepared from seawater, and then shotgun metagenomic sequencing was employed to characterize the viral communities present8, revealing highly abundant and diverse phage genomes, as well as a large proportion of viral ‘dark matter’ (that is, sequences that looked like nothing in available databases).”

“Most constituents of the human virome are inferred to be phages. This is an inference because, in most cases, the majority of sequences uncovered in a virome metagenomic sequencing experiment do not align with any information present in existing databases (Box 1), so it is unknown whether they are phages or some other virus types.”

“However, within a healthy adult, the virome is usually relatively stable over time, paralleling stability in the cellular microbiome. For example, one study found that ~80% of viral contigs present persisted over a span of 2.5 years in the gut of one individual6. Another recent study tracked the gut virome of 10 individuals and found that >90% of recognizable viral contigs persisted in each individual over 1 year39. Studies on the oral virome revealed similar stability40,41.”

https://www.nature.com/articles/s41579-021-00536-5

These “viruses” that make up our virome are not considered pathogenic, are said to be integrated elements within our genome, and are believed to interact with the body in complex and MEANINGFUL ways. It has been estimated that while our microbiome is made up of 38 trillion bacteria, our “virome” contains 380 trillion “viruses.” Essentially, we are walking, talking “viruses.” With that many of these “microscopic parasites” living inside of us, you would think we would be in a perpetual state of sickness. However, that is obviously not the case.  Still, as with most of science it seems, much is unknown about the virome as it remains a vastly understudied area. Study of the “virome” lags far behind bacteria as there is a lack of standardized technology necessary to decipher what it all means. Still, this hasn’t stopped scientists from assuming that these strings of genetic material show that we have “viruses” in every part of our body:

Meet the trillions of viruses that make up your virome

‘If you think you don’t have viruses, think again.

It may be hard to fathom, but the human body is occupied by large collections of microorganisms, commonly referred to as our microbiome, that have evolved with us since the early days of man. Scientists have only recently begun to quantify the microbiome, and discovered it is inhabited by at least 38 trillion bacteria. More intriguing, perhaps, is that bacteria are not the most abundant microbes that live in and on our bodies. That award goes to viruses.

It has been estimated that there are over 380 trillion viruses inhabiting us, a community collectively known as the human virome. But these viruses are not the dangerous ones you commonly hear about, like those that cause the flu or the common cold, or more sinister infections like Ebola or dengue. Many of these viruses infect the bacteria that live inside you and are known as bacteriophages, or phages for short. The human body is a breeding ground for phages, and despite their abundance, we have very little insight into what all they or any of the other viruses in the body are doing.

I am a physician-scientist studying the human microbiome by focusing on viruses, because I believe that harnessing the power of bacteria’s ultimate natural predators will teach us how to prevent and combat bacterial infections. One might rightly assume that if viruses are the most abundant microbes in the body, they would be the target of the majority of human microbiome studies. But that assumption would be horribly wrong. The study of the human virome lags so far behind the study of bacteria that we are only just now uncovering some of their most basic features. This lag is due to it having taken scientists much longer to recognize the presence of a human virome, and a lack of standardized and sophisticated tools to decipher what’s actually in your virome.”

“Viruses may inhabit all surfaces both inside and outside of the body. Everywhere researchers have looked in the human body, viruses have been found. Viruses in the blood? Check. Viruses on the skin? Check. Viruses in the lungs? Check. Viruses in the urine? Check. And so on. To put it simply, when it comes to where viruses live in the human body, figuring out where they don’t live is a far better question than asking where they do.”

“So the race is on to find those viruses in our viromes that have already figured out how to protect us from the bad guys, while leaving the good bacteria intact.”

Many people believe that these “viruses” must come from the outside the body and invade us, integrating into our cells and DNA. However, seeing as the RNA making up the “virome” is found within humans, the logical conclusion would be that this genetic material must come from us and be human in nature.  Take, for instance, ENDOGENOUS (internal origin) “retroviruses.” These are “viruses” that are said to be a part of our genetic makeup. While a story was concocted stating that they must be remnants of ancient “viruses” that ended up mixed into our genetic code, the case could easily be made that these were never “viruses” and that the assumed “viral” sequences were in fact human all along:

“About 8% of our genome is composed of sequences with viral origin, namely human Endogenous Retroviruses (HERVs). HERVs are relics of ancient infections that affected the primates’ germ line along the last 100 million of years, and became stable elements at the interface between self and foreign DNA.”

https://www.frontiersin.org/articles/10.3389/fimmu.2018.02039/full

“The viral component of the human microbiome is referred to as the “human virome.” The human virome (also referred to as the “viral metagenome”) is the collection of all viruses that are found in or on humans, including viruses causing acute, persistent, or latent infection, and viruses integrated into the human genome, such as endogenous retroviruses.”

https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC3701101/

“Although there are exceptions, the vast majority of ERVs (particularly the ancient ERVs) is not closely related to known exogenous retroviruses, is no longer capable of expressing virus, and has no other associated biological or phenotypic properties to facilitate classification.”

https://www.sciencedirect.com/topics/medicine-and-dentistry/endogenous-retrovirus

As can be seen by the above three sources, endogenous “retroviruses” are a part of us and make up about 8% of our genome. They are said not to be related to exogenous “retroviruses” and can not express “virus.” These sequences are of human origin. They have been labelled as “viral” when that obviously is not the case. How many other sequences claimed to be “virus” are in fact nothing but human genetic material incorrectly labelled as such?

It is becoming clearer to scientists that “viruses” are an integral part of human biology.  It is now theorized that many of these “viruses” are beneficial to us and actually promote health, which doesn’t really sound like the classical definition of a “virus,” now does it? In fact, “viruses” thought pathogenic and seen as causes of the common cold have been found in completely healthy children. Thus, it is now being considered that “viruses,” or at least the strings of non-classifiable RNA claimed to be them, are in fact a part of us rather than something that lives in or on us:

The vast virome

“The most abundant inhabitants of what many researchers are calling “the human ecosystem” are the viruses. So Pérez-Brocal reasoned they were worth a closer look.

Viruses are deceptively simple organisms consisting of genetic material packed in a protein shell. They are tiny and can’t replicate on their own, relying on human or other cells to reproduce.

And yet, scientists estimate that 10 quintillion virus particles populate the planet. That’s a one followed by 31 zeros. They outnumber bacteria 10-to-1 in most ecosystems. And they’re ubiquitous in and on humans.

Pérez-Brocal and others are learning that viruses, once seen only as foreign invaders that make people sick, are an integral part of human biology. Some cause major diseases, including influenza, AIDS and some cancers. Others, conversely, may promote health. Some may even help us gauge how well the human immune system works.”

“We know a lot about the bacteria that inhabit humans,” says David Pride, an infectious disease doctor at the University of California, San Diego. In comparison, “we know absolutely nothing about the viruses.”

“Not that scientists haven’t been interested in viruses. Until recently there was just no good way to identify them, an important first step toward understanding the biology of health and disease. As a consequence, virome research is in its infancy.”

“Virus hunters aren’t so lucky. There is no analogous virus-identification tag. Instead, to look for viruses, researchers must sequence hundreds of thousands of bits of DNA from a sample — skin swabs, saliva, feces or mucus, for example. Scientists have gotten really good at generating these DNA sequences; the trick is figuring out what they are.

Some of these DNA bits come from human cells, some from bacteria and other microbes that occupy the body, such as archaea and fungi. Some bits may come from viruses, but it is hard to tell for sure, says Pérez-Brocal, because scientists have a limited set of characterized viruses to use as a guide for spotting new ones.”

“Healthy subjects are just loaded with viruses,” Wylie says. Even viruses known to cause diseases such as the common cold were found in healthy kids. That makes it difficult to determine whether a particular virus is really making someone sick.”

“To figure out which viruses are friends, foes or neutral passengers on the human body, scientists first need to identify them. Researchers still aren’t very good at recognizing new viruses, says Brian Jones, a molecular biologist at the University of Brighton in England. Hence the large pool of unknown samples in Pérez-Brocal’s and other researchers’ virome studies. But even if scientists improve their identification skills, it may take a long time to figure out what the viruses are doing in the body.”

“Based on what researchers have learned so far about the virome, Jones is convinced that viruses and other microbes “should be viewed as a part of us rather than something that lives in or on us.” They are part of the puzzle, the intricate ecosystem composed of human and microbial cells, all pushing and pulling at one another and subject to local conditions, such as diet and environment.”

https://www.google.com/amp/s/www.sciencenews.org/article/vast-virome/amp

The “magic” of metagenomics.

Hopefully, after reading the above sources, it is now more clear what all the human “virome” entails. You should be able to see that, according to the latest scientific evidence, not only are we surrounded by “viruses” everywhere, we are almost more “virus” than human based on the latest sequencing technology. It’s important, however, to keep in mind that what they are calling “viruses” in the “virome” are nothing more than “repetitive strings of genetic letters” stored in a computer database. These are not particles that have been purified and isolated directly from a sample and proven pathogenic in a natural way. It is a collection of A,C,T,G’s taken from a mixed population of organisms within a sample. The particles assumed to be “viruses” are never seen nor characterized. Every organism, whether bacterial, fungal, “virus,” or whatever else could potentially be contained within the sample are broken down into free-floating RNA/DNA and sequenced by computer algorithms. This is done through a process known as metagenomics:

“Metagenomics” is the two words “meta” and “genomics”. So genomics is obtaining the DNA sequence, but meta implies that we’re doing it of many organisms together. And metagenomics is usually used when we are studying microbial communities where we can’t separate one microbe from another. Like there may be two bacteria that grow together, and so when you take the DNA sequence, you’re getting the DNA sequence of two bacteria together. Now, as an example of this, you can imagine that I could go in and take the DNA sequence of a person who lives in New York City. But if I were to come in and take the DNA from everyone who lives in New York City and sequence it together, that would be the equivalent of what we’re doing when were sequencing the DNA of all of the bacteria that live in one place on your skin or your intestine together. So we’re not just looking at one organism, we’re looking at the DNA sequence of all of the organisms together. Because we could imagine sequencing the DNA of an individual in New York, but imagine if our technology was limited and we couldn’t separate these people in New York. If we need to take the DNA sequence of every person in New York together, and then later we try to figure out which DNA belonged to which person, that’s often what we are doing when we’re studying bacterial and fungal communities together.”

https://www.genome.gov/genetics-glossary/Metagenomics

Nothing but “random genetic strings” in a computer database.

This process of breaking down and sequencing all organisms in a sample is not without its flaws. There are challenges based on the limitations of the technologies. It is admitted that human tissue samples as well as lung mucus, such as that used for the sequencing of “SARS-COV-2,” make it difficult to reliably obtain and interpret genomic data. It is also admitted that the use of metagenomics actually fails Koch’s Postulates, the very criteria used to determine a pathogen exists, as there is no direct host information available. Thus, obtaining the potential etilogical agent from a diseased organism and then growing it in pure culture can not be properly fulfilled. It has been attempted to modify the Postulates for the genomic era to allow that the sequence only needs to be found more regularly in a diseased host rather than a healthy one. However, these sequences are regularly found in healthy individuals, as seen by the massive amounts of healthy “asymptomatic” people testing positive for “SARS-COV-2” and other diseases. Metagenomes are also primarily assembled and created using short reads which can often lead to erroneous, inaccurate, and incomplete genomes:

Metagenomics in Virology

“Metagenomics has quickly become a major tool for exploring viral diversity, yet several challenges need to be addressed in order to fully leverage the potential of these methods. First, metagenomes built from limited input material are still difficult to reliably obtain and interpret, and do not yet provide a comprehensive and quantitative view of the viral community present in the sample. This includes environments with low biomass such as some human tissues, hydrothermal vents, ice cores, or ancient samples, but also samples with a thick substrate or matrix to which cells and virus particles tend to adhere such as human lung mucus or coral samples. Improvement in the recovery of cells and virions from this type of substrates and in the generation of quantitative libraries from sub-nanogram input will help better survey these viral communities.

The second major challenge lies in the absence of direct host information for genomes assembled from metagenomes. In a clinical context, this means that one of Koch’s postulates, which requires that the candidate etiological agent be isolated from a diseased organism and grown in pure culture, cannot be fulfilled. Already, several smacoviruses which had been detected in human samples metagenomes and suspected to represent new human viral pathogens have been found to likely infect prokaryotic cells from the human microbiome instead. In a similar way, evidence is emerging that picobirnaviruses, which are believed to be eukaryotic viruses, might actually infect bacterial cells. These examples should thus serve as a cautionary tale when trying to detect entirely new viral pathogens from mixed samples containing both human and microbial cells. A modified Koch’s postulate for the metagenomic era has been proposed in which potential new pathogens must first be present and more abundant in the diseased subject compared to matched control. Then, experiments using either a sample from a disease subject or an artificial virus obtained through DNA synthesis and expression in cell cultures must be performed to demonstrate that this agent induces disease in another healthy subject. While not trivial, these additional experiments based on metagenomic results could still lead to the identification of viral pathogens much more quickly than classic culture techniques.

In an ecological context, associating uncultivated viruses to their host is also critical to understand their impact on microbial communities and to meaningfully integrate viruses into ecosystem models. Because viral ecology studies typically include hundreds to thousands of viruses of interest, these host associations are typically derived from in silico approaches based on various types of genome sequence comparison. While methods for in vitro confirmation of these metagenome-derived virus-host pairs are currently being developed, they will need to improve both in terms of scale and resolution to provide meaningful host association for the vast diversity of uncultivated viruses.

Among the expected technological improvements, two stand out as likely to benefit the field of viral metagenomics in the near future. First, long-read sequencing technologies are progressively amenable to the sequencing of environmental viral communities. Pragmatically, this means that instead of having to assemble virus genomes from short reads, a process which can yield potentially erroneous and/or incomplete genome sequences, a complete viral genome could be sequenced as a single read.”

https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7157462/

In Summary:

  • It is said that eight percent of our DNA consists of remnants of ancient “viruses,” and another 40 percent is made up of repetitive strings of genetic letters that is also thought to have a “viral” origin
  • Many host districts of the human body and its mucous membranes are heavily ‘colonized’ by “viruses” that are not associated with any disease
  • This has led to the concept of the “virome,” which can be considered as the set of all “viruses,” eukaryotic and prokaryotic, present in the human body
  • The “virome” includes “viruses” that infect host cells, “viruses” that infect the majority of other types of microorganisms harboured by the body, and “virus-related” genetic elements in our chromosomes (in other words, these “viruses” are a part of our genetic makeup)
  • Due to the existence of commensal “viruses,” it is stated that we should probably redefine chronic “viral” infections and focus our attention on the host rather than on infectious agents to dissect disease determinants
  • “Viruses” are believed to be the most abundant and diverse biological entities on our planet with an estimated 10^31 particles on Earth
  • The human “virome” is similarly vast and complex, consisting of approximately 10^13 particles per human individual, with great heterogeneity (i.e. diversity)
  • The human “virome” comprises:
    1. Bacteriophages (phages) that infect bacteria
    2. “Viruses” that infect other cellular microorganisms such as archaea
    3. “Viruses” that infect human cells
    4. “Viruses” present as transients in food
  • In other words, the RNA claimed to be “viruses” comes from many sources
  • The nature and importance of whole “viral” populations were mostly not appreciated until the development of advanced DNA sequencing methods that could report the structures of whole communities
  • Early metagenomic sequencing in 2002 found a large proportion of viral dark matter” which is sequences that looked like nothing in available databases
  • Most constituents of the human “virome” are inferred to be phages
  • This is an inference because, in most cases, the majority of sequences uncovered in a “virome” metagenomic sequencing experiment do not align with any information present in existing databases so it is unknown whether they are phages or some other “virus” types
  • Within a healthy adult, the “virome” is usually relatively stable over time
  • One study found that ~80% of “viral” contigs present persisted over a span of 2.5 years in the gut of one individual
  • Another recent study tracked the gut “virome” of 10 individuals and found that >90% of recognizable “viral” contigs persisted in each individual over 1 year
  • While it is estimated that 38 trillion bacteria reside inside of us, they are not the most abundant microbes that live in and on our bodies as that award goes to “viruses”
  • It’s estimated that there are over 380 trillion “viruses” inhabiting us, a community collectively known as the human “virome”
  • These “viruses” are not the dangerous ones you commonly hear about
  • The human body is a breeding ground for phages, and despite their abundance, we have very little insight into what all they or any of the other “viruses” in the body are doing
  • One might rightly assume that if “viruses’ are the most abundant microbes in the body, they would be the target of the majority of human microbiome studies, however, that assumption would be horribly wrong
  • The study of the human “virome” lags so far behind the study of bacteria that we are only just now uncovering some of their most basic features
  • There is a lack of standardized and sophisticated tools to decipher what’s actually in your “virome”
  • To put it simply, when it comes to where “viruses” live in the human body, figuring out where they don’t live is a far better question than asking where they do
  • Keep in mind, when they claim that ‘viruses” are found everywhere within the human body, what they are referring to is “viral” RNA, not purified/isolated “viruses”
  • The race is on to find those “viruses” in our “viromes ” that have already figured out how to protect us from the bad guys, while leaving the good bacteria intact
  • About 8% of our genome is composed of sequences with “viral” origin, namely human Endogenous “Retroviruses” (HERVs) and they interface between self and foreign DNA
  • Endogenous “retroviruses” are integrated into the human genome
  • The vast majority of ERVs (particularly the ancient ERVs) are not closely related to known exogenous “retroviruses” and are no longer capable of expressing “virus”
  • Pérez-Brocal and others are learning that “viruses,” once seen only as foreign invaders that make people sick, are an integral part of human biology
  • It is said some “viruses” may promote health while others may even help us gauge how well the human “immune system” works
  • According to David Pride, an infectious disease Dr., “we know absolutely nothing about the viruses” that inhabit us
  • Until recently there was just no good way to identify “viruses,” an important first step toward understanding the biology of health and disease
  • As a consequence, “virome” research is in its infancy
  • Researchers must sequence hundreds of thousands of bits of DNA from a sample — skin swabs, saliva, feces or mucus, for example, to find “virus” RNA/DNA
  • Scientists have gotten really good at generating these DNA sequences; the trick is figuring out what they are
  • Some of these DNA bits come from human cells, some from bacteria and other microbes that occupy the body, such as archaea and fungi, and some bits may come from “viruses,” but it is hard to tell for sure, says Pérez-Brocal, because scientists have a limited set of characterized “viruses” to use as a guide for spotting new ones
  • “Healthy subjects are just loaded with viruses,” Wylie says
  • Even “viruses” known to cause diseases such as the common cold were found in healthy kids
  • That makes it difficult to determine whether a particular “virus” is really making someone sick
  • Researchers still aren’t very good at recognizing new “viruses,” says Brian Jones, a molecular biologist at the University of Brighton in England
  • But even if scientists improve their identification skills, it may take a long time to figure out what the “viruses” are doing in the body
  • Based on what researchers have learned so far about the virome, Jones is convinced that “viruses” and other microbes “should be viewed as a part of us rather than something that lives in or on us”
  • The process used to study the “virome” is known as metagenomics
  • Genomics is obtaining the DNA sequence, while meta implies that the sequencing is of many organisms together
  • Metagenomics is usually used when studying microbial communities where one microbe can’t be separated from another
  • They are not just looking at one organism but rather at the DNA sequence of all of the organisms together
  • “If we need to take the DNA sequence of every person in New York together, and then later we try to figure out which DNA belonged to which person, that’s often what we are doing when we’re studying bacterial and fungal communities together.” – Julie A. Segre, Ph.D.
  • Metagenomes built from limited input material are still difficult to reliably obtain and interpret, and do not yet provide a comprehensive and quantitative view of the “viral” community present in the sample
  • This includes environments with low biomass such as some human tissues, hydrothermal vents, ice cores, or ancient samples, but also samples with a thick substrate or matrix to which cells and virus “particles” tend to adhere such as human lung mucus or coral samples
  • The second major challenge lies in the absence of direct host information for genomes assembled from metagenomes
  • In a clinical context, this means that one of Koch’s postulates, which requires that the candidate etiological agent be isolated from a diseased organism and grown in pure culture, cannot be fulfilled
  • A modified Koch’s postulate for the metagenomic era has been proposed in which potential new pathogens must first be present and more abundant in the diseased subject compared to matched control
  • Because “viral” ecology studies typically include hundreds to thousands of “viruses” of interest, these host associations are typically derived from in silico (in a computer) approaches based on various types of genome sequence comparison
  • While methods for in vitro (i.e. outside the living body and in an artificial environment) confirmation of these metagenome-derived “virus-host” pairs are currently being developed, they will need to improve both in terms of scale and resolution to provide meaningful host association for the vast diversity of uncultivated “viruses”
  • Currently, metagenomics assembles “virus” genomes from short reads, a process which can yield potentially erroneous and/or incomplete genome sequences

If we are to take the latest genomic science at face value, then we are as much “virus” as we are human. It is estated that we have 380 trillion “viruses” within us and integrated into out genome. It is said that at least 48% of our genome is “viral” and that 8% of this is endogenous, meaning it comes from humans. We have within us what is now referred to as the human “virome.”

However, it is also admitted that what are claimed to be “viral” sequences are only thought to be so as the data is vastly understudied. The data is derived from metagenomics, which is the mass sequencing of multiple unknown and unrelated microorganisms within a sample using computer algorithms. No actual “viral” particles are ever found and characterized. The human “virome” is nothing but a giant collection of sequencing data assumed to be “viral” in nature. Much of the data comes from the early 2000’s when the sequencing technology was even more hampered by limitations than it is said to be now. However, even today, the technology does not exist to completely separate and characterize these genomes. They are assembled and put together using short reads which can lead to inaccurate and unreliable genomes (cough…”SARS-COV-2″…cough).

With so much of the human body composed of what virologists claim is of “viral” origin, it is clear that the idea of the exogenous pathogenic “virus” is the unproven exception to the rule and not the norm. It is also clear that they are sequencing normal human genetic material and assuming it is “viral” based on nothing but computer-generated data. There are no purified/isolated particles. There is no proof of pathogeniticity. These “scientists” have taken massive amounts of data and created a fictional narrative around it. They are trying to make us believe that there is an ocean of undiscovered “viral” genetic material out there. In this way, they can pull out any random sequence at any time from amongst this “viral dark matter” and claim a new pathogenic “virus” exists. In reality, all that they are doing is pulling out normal human fragments from our own “genome” and selling back to us the new boogeyman created from our own genetic material.

35 comments

  1. Such a great post, as usual!! I am starting to think that the entire germ theory model is rooted in our concepts of “evil”. I put that word in quotes for a reason! Does evil actually exist? I realize this is a touchy question for sure! But in the spirit of questioning all of our assumptions, it’s a good question to ponder.

    I am not saying evil acts do not exist, not at all. This isn’t about denying evil acts, just like asking the question, “Do viruses actually exist, and if so how, and if not why not?” is NOT denying the existence of illness!!!! It’s just an inquiry. So, in the spirit of inquiry: does evil exist as an entity, force, concept, being (or whatever) that is SEPARATE from the human mind? This is how I ponder the question, at least.

    The reason I bring this up in this context (of virology) is because I really am noticing that “bugs” (whether conceived as viral, bacterial, fungal, parasitical or whatever) have replaced the idea of “the devil”. I think the human psyche (when not in a healthy, sane, calm state) an enemy, a force that we can blame for our unhappiness. So, we get sick. That’s human, that’s the body and mind doing it’s thing: healing itself. And we freak out!!!!! This isn’t fair, it isn’t right, it’s scary, I could die (like we aren’t going to die at some point anyway!) goes through our mind.

    That’s my point: personally, and I don’t expect people to agree with me, I think our concept of evil as being a inherent force in nature is in error. It’s real, it’s VERY VERY real as a created force that we create for perhaps good reasons, but it’s not ACTUALLY part of nature. Destruction and decay and pain and suffering are part of the human experience. But is this “evil”??? To me, evil connotates “something random, crazy, unreasonable, purposeless, relentlessly destructive, something that destroys for NO REASON, meaningless suffering that comes from nowhere or from some source that is equal to “good”. That’s what I don’t agree with. That suffering and decay are meaningless. I mean, animals and plants and rocks don’t worry about evil. They endure storms, decay, death, etc…. but don’t come up with that concept. We do.

    That’s okay, humans come up with concepts. But is it serving us? Viruses are a concept Is it serving us? Is it true? Is it real? Is this idea creating a healthy way of being in the world? Is there actual evidence that parasitical tiny units of information (that are dead, but not really dead, they say!) are attacking us? Do bacteria have intent to kill us? Are there “good” and “bad” bacteria? It’s the same as asking, is there “good AND evil”? Or is Nature, Reality, God actually GOOD inherently (look at nature!) and we THINK that bad exists inherently?

    Is it all a big misunderstanding? And we project out our ideas about evil onto our ideas about the body and disease? What is the cause of disease? Evil little bugs? Really? It’s a cartoonish, simplistic, myopic view of how nature and reality really work.

    Again, I am not bringing this up in terms of a religious or spiritual debate, but just in the context of looking at virology. If there is a “virome” inside of us that can at any moment “activate” disease by “taking over our cells”. well, that’s a BIG CLAIM to make. And the fact that people “buy into it” easily is testament to the fact that it’s rooted in deeper ideas, like that of “good vs evil”. In my opinion. 🙂

    Liked by 1 person

    1. I love your philosophical view of things Carolyn! You always give me a lot to think about. I can definitely see where you are coming from. I do believe evil exists as pedophilia, murder, and physical torture/abuse are all acts that scream pure evil to me. I can’t put those actions into a context that does not define evil. I believe they go against our very nature. To me, that which goes against the inherent good in us, the innate ability to determine right from wrong, is where evil belongs. That may be too narrow as there are those things which we know are wrong which may not necessarily be evil, but hopefully you get what I’m saying. Those who willingly give into that which pulls them away from that inherent goodness within are often on a path towards evil. Whether or not there is an evil force driving them to do so is debatable for sure.

      I’m not sure if I explained everything as best I could. You always give me so much to think about and ponder. I hope you are working on that book! 😉

      Liked by 1 person

      1. lol, the book! haha, thanks, yeah, maybe some day…. same with you! I hope your work gets into print in some form, some day. Thanks for your kind words. Absolutely, evil exists. It’s here, it’s there, it’s everywhere. One could say “it” rules the world right now. But….. the question is, then, where does it come from? Why does it perpetuate itself and gain such power? Does it exist INHERENTLY within the plan of creation, as a necessary component for life, even for human life? Does it exist as an essential part of creation? Or is it created and MADE REAL by the human mind and beliefs, then experienced as freaking REAL.

        This is a HUGE question, I hope I am not coming across as seeming to “have the answer” but I do admit I am fascinated by the topic. My motivation is because I am tired of evil ruling the world! I think if we don’t understand it, if we don’t examine it like we are examining viruses, then we will just keep perpetuating it because it has momentum and we fear it and we keep making it MORE real, and those in power just use it as a weapon. It’s all too easy to call the other side evil! Even if we don’t use that word.

        I think in philosophy they call it “the problem of evil” so even those high minded philosopher types don’t seem to have it figured out! I do believe (choosing that word carefully here) that beliefs themselves are extremely powerful. So, if we believe evil exists, it will. We make it happen. If we are in denial about evil, like if we are in denial about child abuse, and we don’t look for the real causes, then it will just keep happening. If we are too ashamed to look at the real causes of evil, it doesn’t exactly help to rid evil from the world.

        So, the beliefs we hold about these “big ideas” make a big difference. That’s my main point.

        There is a process there that occurs. If we assume evil is “just there, like goodness”, as if it is EQUAL in power to goodness, then we get a world that reflects that belief and assumption. We end up accepting evil as part of life! Okay. On the other hand, if we assume that evil is a concept, an idea, a projection of mind, an aspect of the human psyche….. something that have some relationship to creating…. then we can see how we might be able to change our way of being with it. If it’s seen as inevitable, like a force of nature that is in all nature, then what can we do?

        If we work from the assumption that evil exists but is not EQUAL to goodness, or God, then we get another and very different world. Less fear, more ability to address evil tendencies. Less shame about it all, more ability to bring it to the light.

        So, all I am saying is that how we view evil is going to lay the foundation for the world we experience and perpetuate and create etc.

        So, the same with viruses. If we choose to believe there are these things out there, or in our body, that cause illness, seemingly “for no reason”, then we get one world. If we think of all the components of our body (even the tiniest units of information) as being there for GOOD reason, for the benefit of the overall health of the body, the forest, the earth etc, … then we get a different world.

        So it’s how we look at these concepts. It’s hard, these aren’t easy topics. To be honest, I deal with chronic pain everyday, and tend towards depression, and really struggle a lot to maintain my own sanity in light of what I COULD call evil forces… .meaning, I could just say I am being attacked by evil, or viruses. And I HAVE been told I have “infections” like Lyme disease (even though the tests came back negative! and the tests are totally useless and misleading, I now know…). So, I am just saying that in our personal lives, we all have tragedy and struggles and it is tempting to lay blame on an outside agent. But where does that get us? And is it even true? I am doing a lot of healing practices (or trying to!) that bring it all back to ME. Instead of blaming outside agents. I read a lot of metaphysics (for lack of a better word) and have for many years. So my views come from my own struggles with my own mind, really.

        But back to what you were saying: pedophilia, and other horrific acts…. it’s so horrific, it seems to constitute a “force”. Yes. And in that sense it is a force, I mean it is VERY powerful! But is it EQUAL to what we call “good” or is it a REVERSAL of good? See what I mean? If it’s a distortion, a DENIAL of good, then that means that evil is DEPENDENT upon good, not a force unto itself.

        That last thing I want to do is deny evil, because that IS denial, and denial isn’t going to get us anywhere. It’s just that I also don’t want to give evil itself, or evil doers, any more power.

        Dorothy was ignorant. She didn’t know the Wizard was just a man behind a curtain. In her ignorance, the Wizard was very very very REAL. But when Toto pulls the curtain, she could see that it was just a story in her head. She believed the story, and beliefs frame how we think and perceive, and the human mind is super powerful, so her belief made it real. But does the Wizard actually exist?

        I do think this relates to the idea of viruses. To me, germ theory “works” as a form of control so very well because it triggers really deep fear in people, fear of the unknown. It’s a powerful story. What if what we were calling viruses were actually just cell debris, the process of decay and death and rebirth misconceived? What if the scary story was just a scary story? Well, that is what it seems to be! We are Toto pulling back the curtain, I think. I think the body is intelligent and good and so is all of creation, really. We can’t deny evil, but we might be able to see that in the deepest sense it is just a story, a misreading of reality. Maybe we are all really living in a safe and loving universe and we just don’t know it yet. (I hope I am not preaching too much! I don’t want to mar your wonderful blog with my comments and opinions! It’s just my opinion and my take on it… I do think this virus stuff relates to our ideas on evil. That’s it in a nutshell.)

        Liked by 1 person

      2. Are you kidding me??? Your words don’t mar my blog. I love reading your insights! It gives me so much to think about. I typically look at the surface yet you go to a deeper level that challenges me to examine the beliefs and preconceptions I hold. I think you have very insightful views and sometimes I respond too fast without sitting and reflecting first. There is so much in what you wrote that hit me and I completely agree with. Never feel like your comments don’t belong. The world is.a better place for being allowed to share in your insight. I am serious about you needing a book deal. Do you ever talk with Jordan about this stuff? He gets very deep into the philosophical side as well. I feel I am still scratching at the surface. Thank you for giving me some deeper layers to ponder!

        Liked by 1 person

      3. @forcgd and @Mike Stone…
        “Does evil actually exist?”
        In one sense, no. >> Just as ‘darkness’ is the absence of light, evil is the absence/’privation’ of good.
        In another sense, yes. >> At https://www.vatican.va/archive/ENG0015/_INDEX.HTM , search for the following separately:
        1) The Fall
        2) Evil Acts
        Click through into each and read, (including the footnotes in the former).
        Mike, – kudos! Keep up the nice work! 🙂

        Liked by 1 person

    2. I’ve seen people reduce Lyme by using ivermectin. The horse stuff works well, same shit.
      I would guess 2x the typical dose for 3 days straight then a week off and do it again.

      Viruses do sound like the devil. Made up fears to attribute things to a singular cause, like when they used to think that Zeus caused lightning or the swamps killed because of spirits (swamp gas has hydrogen sulfide, a killer if you stay in it)

      The tiredness might be connected to the Lyme. Dr Hudla Clark a decade ago said we have tiny parasites that can be in our liver etc.

      Anyway that’s also why I think ivermectin cures other things unrelated…. Our medical system doesn’t care to look for them, like they don’t care to check for vitamin D or C levels.

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      1. I haven’t looked into ivermectin enough to say one way or the other. However, I don’t believe pharmaceuticals really can cure anything. They may suppress or delay symptoms, but the symptoms tend to come back eventually, often worse than before.

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  2. There’s a joke I once heard at a dinner party: Q. What’s a virus? A. It’s what the doctor says when he doesn’t know what’s wrong with you. An answer with some merit although, in defence of doctors (I’m one of them), one should add the rider ‘And he doesn’t think it’s serious and it will last long’. Mike Stone’s latest introduces creationist virology: Any computer-generated nucleic acid sequence that can’t be matched to any other computer-generated nucleic acid sequence is a virus.

    Liked by 2 people

      1. You think that’s a joke, but it’s not. It’s the term doctors always use to explain what they fail to recognize as a detoxification process/detoxification symptoms, when they can’t find evidence of a so-called bacterial “infection”. That too, is a detoxification process or the recycling of cellular matter, but most allopaths can’t conceive that another paradigm exists besides the germ theory model, as doctors are chained to dogma and faux science.

        “In nature nothing is created, nothing is lost, everything changes.” Antoine-Laurent de Lavoisier

        I would like to know all your quote sources. There’s no formatting (on the mobile version) to figure out which quotes are from where or whom, and what parts of the text are specifically yours, besides the last few paragraphs.

        Thanks.

        Liked by 1 person

      2. If I quote something, I always put it it quotations and usually under the heading of the article with the link. My comments are those that are not in quotations. In the summary, my comments are italicized.

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    1. Absolutely, they are attempting to label anything and everything as “viruses” and they have massive amounts of sequencing data they can continue to pull out from thin air to claim as the next big threat. It’s ridiculous.

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    2. Northerntracey, do you mean Mike Stone’s article is based on nonsense? He isn’t calling anything a virus. I will look at your links. I do have a question for you: I thought microzyma (same thing as protits, somatids, correct?) can only be seen (as little lights) under a dark field microscope? And, as I understand it, they are theorized to (or seen to, I think there is visual real-time evidence) be what morphs into all sorts of microrganisms, ie bacteria. So they are from what bacteria, say, emerge from. That’s the part of the pleomorphic theory, yes?

      Liked by 1 person

      1. Yes, to be clear, I am definitely not calling anything a “virus.” The article is pointing out that they can claim any sequences found within us as “viruses” when these sequences are most likely a part of us, if they even have any relevance whatsoever.

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      2. Microzyma were spotted by Bechamp before dark field microscopy so they can be seen under a good microscope, but Rife and Naessens invented microscopes which can see live cells etc and somatids which are the same thing yes. Yes they are kind of ‘spores’ and do morph into many bacterial forms and it’s called pleomorphism.

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  3. NorthernTracey, thanks. I don’t know the history as well as you. Still learning. But, these are super important distinction to make and I think we need to use our language as clearly as possible. So, are you saying that what “they” mistakenly call “viruses” are actually the microzyma, and not cell debris? It’s all one process (decay/rebirth) in pleomorphic terms, but in terms of the discussion we are having during these times, most people that are awake to the fraud of virology and germ theory don’t say that the “scientists” of today are mistaking the microzyma for viruses. At least that’s my take on it. In the simplest terms, the most basic critique of virology is a deconstruction of the methodology, which reveals that there simply is no evidence of a “thing” at all. There is no there there. But going a step further, they are saying that they are mistaking the effects for the cause, ie they are saying the cell debris (genetic debris, fragments) that occur during the decay process are called viruses, which is of course absurd. But you are saying something new, to my ears at least. You are saying that they are mistaking microzyma for viruses. That’s pretty profound, because that means that WAY BACK WHEN during the era of Bechamp and Pasteur, that they already could SEE very small things (calling these microzyma “things”, which really in my mind it’s more of a verb, a process, than a noun… it’s an emerging) and they wanted to call them the cause of disease. I thought they couldn’t see anything smaller than bacteria back then, or fungus, but I don’t have a background in the history of microbiology, I guess I am totally wrong on that point? Anyway, just my thoughts. If you could clarify that would be great. Thanks

    Liked by 1 person

  4. I’m wondering if this virome concept isn’t related to the HIV/AIDS retrotranscriptase theory or something, I gotta research more about it cause this whole “8% of our DNA is viruses” is a very big thing. Makes people believe about this whole concept of co-evolution with random non-living genetic materials generated by god random in the whole “darwinian evolution” mindset.
    Very very bad.

    Liked by 1 person

  5. Re: Quantum mechanics. Yes, great channel (see also Karma Peny’s channel tearing quantum entanglement to shreds).

    There are reasons to believe in science the method but never science the institution. If even physics and math, as the king and queen of the sciences, have had the institutions named after them thoroughly corrupted in the 100 years, what hope is there for other sciences-as-institutions?

    Conflation of the scientific method with the output of academia and its method for distilling truth (or worse, media/gov’s method for distilling truth, aka “the science”) is the core problem.

    Liked by 1 person

    1. Thanks for the other link that challenges quantum theory and math!
      A few months ago I met my gf’s brother in law who was a big chemistry and physics geek (he’s a research biologist by trade).
      He had an old physical chem book that he picked up from a yard sale and we were looking through it. I loved it! Principles of materials, principles of processes, and other observable things!
      Then I asked him about how electron valences were discovered. This is the base theory of chemical reactions.
      He explained there were probability clouds of each level and showed them in his later book. I looked and looked and couldn’t find how they came up with this…
      Then, it clicked, it was a mathematical modeling, since technically the electron is non local, yet acts like it is local in the valences… Another weird contradiction…

      Perhaps the valences are correct, as they do explain affinity with chemical reactions and can be used to predict outcomes with accuracy. But I can see where this kind of mathematical modeling can go awry, like in genetics, quantum physics, etc.

      When science tries to map the unseeable, using instruments and math, there is a lot left to interpretation and belief, which can push the model into la-la land!

      Liked by 1 person

  6. Doing excellent work, but I concur with another poster that it’s a bit tough to tell where the quote ends and the commentary begins – not for my sake, but for the germ-centric friends I share this with, of which there’ve been a handful. Maybe name the source, use italic, or both, just feels like a more cut-throat approach.

    Liked by 2 people

    1. Thanks for the kind words and feedback! I will look into ways to switch it so that it is more clear where the sources are speaking and where I am. I appreciate the heads up. 🙂

      Like

      1. I concur, it needs to be SUPER clear for folks, as you well know, otherwise, the mind gets a wee bit confused….. and this topic is already mega confusing.

        Liked by 1 person

  7. I agree with other posters that it can be a tad hard to follow what is you and what is a quote. I also often find myself wishing for a bit more commentary midway through the long quotes. I’m always glad to see one of those wry italicized interjections.

    I want say I appreciate your fastidious use of quotes around all the mainstream’s FUBAR terminology. “Virus” and the like. Every time we use their words without dis-owning them, we score a little point for them. It’s often socially unappreciated, but this is the cost of rigor.

    To commenter Rob Rob about “probability clouds” (for electrons):

    Yes the problem is they’ve taken probability, which is simply a type of human ignorance about the causal mechanisms of a phenomenon, and claimed that that ignorance is part of nature.

    Which is nonsensical of course. It’s just a word game.

    This is functionally identical to saying, “The baby died of SIDS” after a shot. SIDS = Sudden Infant Death Syndrome. It’s presenting a question (or ignorance) as an answer. The purpose is to stop further investigation into the cause. 💉

    Same with the whole concept of “virus”: it’s a question posing as an answer. “What’s being passed from person to person making them sick?” They said “virus” before Enders ever “proved” there was anything. Ignorance as answer, until eventually they find a way to fool people into thinking ignorance has appeared in the flesh, so to speak.

    Karma Peny’s video on quantum entanglement is truly legendary, a great contribution to the field of physics. It also shows how scientists think in herds and how institutional science cannot be relied upon; institutional distilation of correct information from scientists is NOT the scientific method.

    Liked by 2 people

    1. Is the confusion you are referring to in the main text of the post, the summary, or both? I’ve been trying to figure out the best way to present the information in a clear and concise manner. It has been a little tricky figuring out how to do so on WordPress. Thanks for the feedback!

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      1. Kind of both. I mean it’s clear enough if you really pay attention, but adjusting the font size or indenting or coloring or some other visual offsetting may help. I’m on mobile, for reference, so it may be easier on desktop.

        Liked by 1 person

  8. Below I post a quote about the lie of pathogenic viruses (about how many hypothetical pathogenic viral strains are supposed to exist, without specifying whether the hypothetical mutations are included).

    The Human Virome

    It’s estimated that there are between ten trillion (1 x 1013) and 37 trillion (3.7 x 1013) human cells in the body2. There is somewhere in the vicinity of 38 trillion (3.8 x 1013) bacterial cells in the human body, which makes up the microbiome2. Many people are under the assumption that in the absence of disease, the human body is free from viruses, however this is simply not the case3. There are more than 380 trillion (38 x 1013) viruses in the human body, outnumbering human and bacterial cells by a factor of 104. In fact, there are more than 260 viruses from 25 different families that have been identified in various human tissues3,5,6, a number of which, have been found in blood samples taken from healthy people7. The collective term given to the viruses within the human body is known as the virome, which may be one of the most misunderstood aspects of human biology3,6.

    Despite considerable research being undertaken on the human microbiome over the last decade, we still have an incredibly basic understanding about its role in health and disease5. It would be fair to say, we know far less about the human virome than we do the microbiome6. To put things in perspective, it is estimated that there are somewhere in the vicinity of 1.7 million viruses that have yet to be discovered, and at least half of these are thought to have the potential to infect humans6. Yet the human race has somehow managed to survive for hundreds of thousands of years, despite the constant threat of infection.

    https://www.humanley.com/blog/what-really-makes-us-sick-the-terrain-or-the-germ-part-i?fbclid=IwAR02T1fPDiyMAj2dEVWDUZ70C2KoFxKco59dqfKUoerDZA0JoaVyq2N6FOA

    Liked by 1 person

    1. I look at the human “virome” as the viroLIEgy gift that keeps on giving. With 380 trillion “viruses,” they can pull a new one out of their asses at any point in time whenever they want.

      Like

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