The Case Against “Viral” Genomes

I’ve come across quite a few people who seem to believe that the existence of “viral” genomes and “viral” RNA or DNA sequences somehow proves the existence of “viruses.” One person even believed that the genome was a representation of purified/isolated “viruses.” Disregarding the fact that random A,C,T,G’s that exist only inside a computer database is at best INDIRECT evidence (does not prove; only allows for inference), there is no DIRECT evidence of a PHYSICAL entity called a “virus.” The genomes said to belong to “viruses” are never sequenced from purified/isolated particles taken from the samples directly from a sick person. They are either sequenced from unpurified bodily fluids containing many sources of host and other “non-viral” microorganisms or they are taken from unpurified cell cultures which contain numerous sources of foreign contaminants.

Purification and isolation are two criteria that must be satisfied first before any particles claimed as a “virus” can be said to actually exist and before any genome could theoretically be considered valid evidence. Remember the definitions for purification/isolation:

Purification

1. to make pure; free from anything that debases, pollutes, adulterates, or contaminates:
2. to free from foreign, extraneous, or objectionable elements:

https://www.dictionary.com/browse/purification

Isolation

the act of separating something from other things: the act of isolating something

https://www.merriam-webster.com/dictionary/isolation

However, the CDC knows that the purification and isolation of “viruses” directly from human samples is impossible:

When you break down the steps for sequencing a genome, you will realize that there is absolutely no way that this process can be said to fulfill these two basic criteria, starting with the very cell culture process used to get the sample for sequencing. Thus it must be understood that no matter what process is used, no “viral” genome ever comes from anything that has been proven to exist physically in an isolated state. It is always assumed that the “virus” is hiding within the mixed fluids/culture and that it can be broken down into pieces and put back together again from within a mixed soup.

Charting the Course

Previously, I detailed the various steps that are used to create a “viral” genome. As there are different ways to sequence a genome, I followed the blueprint set forth by the CDC in the image below.

In this post, I have broken it down into the main steps from the image and provided a brief summary for each one. I included the different ways in which each step can be contaminated and/or introduce errors that are further propagated into the final product. I also included links to articles I did focusing specifically on each step, providing further details to help flesh this process out. At the end are a few important links to articles exposing the inaccuracy and inability to reproduce genomes as well as the fact that genomics fails as a science. My hope is that this serves as a guide to understanding this complex process as well as evidence for why “viral” genomes can never stand as valid evidence for an entity never shown to physically exist in the first place.

“Viral” Cell Culture:

In order to get enough RNA/DNA needed to sequence a “virus,” the sample taken from a sick person is usually cultured first. Why do they do this? Because, as the CDC stated, purification is not possible as there is not enough “virus” within the bodily fluids of a human so more “virus” must be grown by adding it to a cell culture first. Keep in mind that the original “SARS-COV-2” genome was supposedly sequenced straight from the unpurified broncoalveloar fluid of one patient without cell culturing first. Somehow, there was enough “virus” in the fluids to sequence a genome but not enough to purify and isolate the particles said to be “viruses” beforehand.

Regardless of the above blatant contradiction, the cell culture process used by the CDC consists of taking the unpurified sample, subjecting it to “viral” transport media, and adding the mixture to either human cancer or animal cells. This concoction has further substances added to it such as fetal bovine serum, antibiotics/antifungals, DMEM, “nurtrients,” etc. There are numerous sources of contamination which they admit can only be mitigated at best, not eliminated. The added chemicals can lead to changes in gene expression, characterization, and genomic instability. The stress from the culture process itself can alter the cells and the final product. There are also problems with cell-line misidentification and reproducibility.

For a breakdown of the numerous problems inherent with this cell culture process, read the post below:

THE CASE AGAINST CELL CULTURES

Step 1. Extracting RNA

This initial step after cell culturing utilizes various methods to attempt to “purify” RNA from the cell culture supernatant. The methods used for extraction consist of chemical and physical means. They are:

1. The phenol/chloroform method
2. The spin column/column chromatography method
3. The magnetic beads method

It is important to understand that through this process, they are not separating whole “viral” particles from everything else. They are breaking down all of the substances within the sample into RNA by either physical or chemical processes in order to establish a DNA library for genome sequencing. This means that “purifying” RNA is not “purifying” particles said to be “virus.” It is essentially a pool of RNA created from a mixed population of genetic material from many different sources. All of the methods used for extracting the RNA have their own drawbacks and contamination is a guarantee as well as the possibility of RNA degradation. Any errors in this first crucial step will affect the following steps in the sequencing process and lead to problems with the reliability and accuracy of sequencing a genome. 

THE CHALLENGES RELATED TO RNA EXTRACTION FOR GENOME SEQUENCING

Step 2. DNA/RNA Shearing/Fragmentation

The next step consists of breaking the RNA into fragments. This is done as the sequencing technology is based on cutting DNA into small fragments and performing massive parallel sequencing. The multiple overlapping segments termed “reads” are then assembled using computer algorithms and consensus into a contiguous sequence. This fragmentation step can be done either before or after converting the RNA into cDNA for library preparation. The main methods used for RNA fragmentation include using metal ions or using RNase III. These two methods can introduce bias, RNA degradation, and contamination. After conversion to cDNA, methods used for fragmenting include:

1. Enzyme-based treatments
2. Acoustic shearing
3. Sonication
4. Centrifugal shearing
5. Point-sink shearing
6. Needle shearing

As with the previous RNA shearing methods, contamination, sequencing errors, bias, degradation, and loss of sample can and do occur with these DNA shearing practices. The size of the fragments needed are dependent on the technology that is selected and used. If any problems arise during fragmentation, these errors will be propagated and compounded down the line into the final genome.

DNA AND RNA SHEARING/FRAGMENTATION

Step 3. Converting RNA into cDNA

It is claimed that RNA is highly unstable and as the PCR process used to create the sequencing library can only use DNA, there is an added step of converting the RNA into the more stable complementary DNA, or cDNA, for “viral” sequencing. The theory to explain cDNA relies heavily on the “virus” fraud as the only way for cDNA to exist is either through the use of reverse transcriptase, an enzyme created through the “natural” processes of “retroviruses” as they hijack host cells or as synthetically engineered DNA in a lab using the synthetically created reverse transcriptase. The conversion of RNA to cDNA in order to generate a sequencing library is as fraught with issues relating to contamination, biases, artifact creation, sequencing errors, false-results, etc. as are the prior steps related to “purification” and fragmentation of the RNA. This is primarily due to the error-prone process called Reverse Transcription (RT) PCR. These errors can then be further propagated into the final product. Seeing a theme yet?

THE HYPOTHETICAL CONVERSION OF RNA INTO cDNA

For more information on the various problems with PCR amplification and contamination, please see this article:

PCR CONTAMINATION AND LIMITATIONS

Step 4. Library Construction

After extracting the RNA, fragmenting it, and converting it into cDNA, the sequencing library must be prepared. The library is essentially just a set of DNA fragments used for sequencing. The steps listed previously are used to prepare the library and once this is done, the library is loaded into a DNA sequencer to create “reads.” As stated before, the process of generating this library is rampant with contamination, batch errors, sequencing errors, biases, etc. They openly admit that bias can not be eliminated and can only be mitigated and that batch effects are inevitable with no way to detect or remove them. 

THE CHALLENGES IN GENOME LIBRARY CONSTRUCTION

Step 5. DNA Sequence Analysis

Now that the library has been prepped and loaded into the sequencer, the sequencer produces millions of DNA reads and specialized computer programs put them together. They commonly refer to this part of the process as putting together a jigsaw puzzle. Granted, it is done by automated algorithms. However, if you have incorrect pieces due to contamination, bias, batch errors, degraded RNA, low quality DNA, sequencing errors, etc. from the proceeding steps, how accurate will the picture truly be?

Keep in mind that the technology used to sequence the data has limitations/drawbacks as well. The fact is that the creation of a “viral” genome is heavily dependent upon continually outdated technology in constant need of refinement to ensure an “accurate” end product. The popular and most widely used Illumina sequencer has issues with GC content bias, substitution errors, low sequence diversity, read length limitations, and technical problems related to reproducibility. Thus, the “accuracy” of any genome is limited by the technology of the time.

LIMITATIONS IN GENOME SEQUENCING TECHNOLOGY AND DATA ANALYSIS

It should be apparent that the existence of a genome is not proof of a purified/isolated “virus.” There are far too many issues throughout the sequencing process such as:

1. The contamination/reproducibility issues with the initial cell culturing process
2. The contamination/biases/errors which occur during the extraction/fragmentation/conversion of RNA to cDNA
3. The OVERALL contamination/batch errors/artefacts which are inevitable in the library preparation
4. The technological limitations and reproducibilty issues with the sequencing technology

There is no area of the genome sequencing process that is untouched by serious problems which affect the end result. This laundry list of common and unavoidable pitfalls should make anyone question the overall outcome of any genome sequenced, especially ones that do not come from physical particles ever free from contamination/foreign material nor separated from everything else being sequenced. The particles said to be “viruses” are only ASSUMED to be there. The “viral” RNA is only ASSUMED to be ‘viral” based on sequences from reference genomes previously created without purified/isolated “viruses” using older technology with even more technological issues and limitations.

Next time you hear about a more dangerous variant, just remember the numerous issues outlined above as well as the fact that the WHO admits that the initial cell culturing step leads to mutations and variants in genomes and should be avoided:

“Levels high following culture, but culture may induce artificial variants”

“For samples with a low viral load, the proportion of viral genetic material can theoretically be increased by allowing the virus to replicate in cell culture. However, the biosafety risks associated with virus culture are significantly higher than those associated with uncultured clinical samples. Biosafety level 3 facilities are required, with extensive additional procedures to ensure safe handling and storage. In addition, passage in cell culture can result in artificial
mutations in the sequences, which were not present in the original clinical sample. This can have major implications for subsequent analyses. Using cell culture solely for the purpose of amplifying virus genetic material for SARS-CoV-2 sequencing should therefore be avoided, especially now that other bait-capture and amplicon-based approaches are available to improve sequencing sensitivity.”

https://apps.who.int/iris/rest/bitstreams/1326052/retrieve

Other things to keep in mind:

1. HOW ACCURATE AND RELIABLE ARE GENOMES?
   • The accuracy and reliability of any genome is questionable as they are considered a continual “work in progress.”
2. GENOME CONTAMINATION: A WIDESPREAD PROBLEM
   • Most clinical specimens and tissue culture samples to be used for “viral” genome sequencing are usually contaminated with human cells, other microorganisms and naked DNA and RNA from disrupted cells.
3. THE REPRODUCIBILITY CRISIS IN GENOMICS
   • Genomics is primarily a computationally data-driven “science” and it requires that the technology, software, and data generated are accurate and easily accessible to other researchers in order to reproduce and confirm the findings. However, the ability to generate data has surpassed the technology as well as the ability to store and interpret the massive amounts of data generated. These results from genomic studies are rarely, if ever, reproduced. 
4. THE EPISTEMOLOGICAL CRISIS IN GENOMICS
   • Genomics is not science but is instead driven by statistics. The collection, interpretation, and analysis of data is not science. Genomics does not observe a natural phenomenon and create experiments using valid independent and dependent variables in order to determine cause and effect. It creates an artificial phenomena in a lab using questionable technology. It is concerned with the generation of massive amounts of data and the subjective determination and analysis of that data. 

It’s obvious if you look at the genome sequencing process from start to finish both critically and logically, not only can a genome not be considered DIRECT evidence for a purified/isolated “virus,” it can not count as INDIRECT evidence either.