|Viruses do not replicate themselves|
Today's post is about the virus realm called "Coronaviridae".
That virus realm is discussed in the context of several subgroups that are called "Alpha, Beta, Delta, Gamma, and Mers" since they are distinguished that way in the GenBank database.
Each subgroup will be covered by reports and graphs.
Concerning each subgroup, today's post contains two types of reports, and several graphs associated with those reports.
The two report formats are Report A ("compare") and Report B ("detail").
The Report B ("detail") contains the values related to a particular virus in each subgroup.
The Report A ("compare") contains the results of a comparison of each virus in the group to the original (oldest) virus in that group.
Report "type A" has the following format:
It is simply the characteristic values of the genes of the viruses to wit:
version: the GenBank unique id of the virus (like a person's social security number)
virus_type: e.g. AL-HS-RN-CG (Alpha=AL, Beta=BE, Gamma=GM, Mers=MR, HS=homo sapien, AN=animal, RN=RNA, CG=complete genome)
NL: Nucleotide size
GC: number of genes in the virus
GB_1: where gene 1 begins (GB_2 means gene 2, etc.)
GE_1: where gene 1 ends (GB_2 means gene 2, etc.)
GL_1: gene 1 length (number of a,c,t,g, or u nucleotides, GB_2 means gene 2, etc.)
Report "type B" uses the same data, however, "type B" is a comparison report, showing the results of comparing all the subsequent gene data lines with the first virus data, to wit:
In the comparison reports, if the compared values at each virus' NL, GC, GB_1, GE_1, GL_1... location match the original values of the first virus, then a 'y' is shown, otherwise an 'n' is shown.
Here is the link to the graphs (Graphs; Note that the gene lengths are averages for that virus).
The purpose of this post, like a couple of other posts on the subject, take a look at the data on the viruses and discuss whether or not the virology reports make sense.
The story told by the commercial virologists (those who work for Big Pharma corporations) is that viruses contemplate their environment and make changes to themselves so as to make themselves more virulent, more pathogenic.
That is, viruses engineer their own evolution via 'recombination' and the like (e.g On The Origin of Genieology - 2).
There is no consensus:
"Although RNA viruses were initially thought to experience only limited recombination, both experimental studies and analyses of the rapidly growing database of viral gene sequences have revealed not only that recombination [or damage] occurs in many families of RNA viruses, but also that it can sometimes have a major impact on their evolution, emergence and epidemiology. Indeed, recombination has been associated with the expansion of viral host range increases in virulence, the evasion of host immunity and the evolution of resistance to antivirals. However, despite the growing evidence for the action of recombination in RNA viruses, the evolutionary reasons for its occurrence remain uncertain."
(Why Do RNA Viruses Recombine, emphasis added). But my argument in this series is that the evidence does not support the 'uncertain' hypothesis (accord "Here, we analyse the extant genomic diversity of SARS-CoV-2 and show that, to date, there is no detectable hallmark of recombination", bioRXiv).
The evidence tells me that the GenBank genomes analyzed in this series indicate that the genomes exhibit evidence of a mass destruction of the microbes that host the Coronaviridae realm, which leads to malformed (not recombined) viruses.
The reports contain the actual measurements of genes and nucleotides in the Coronaviridae viruses so you can peruse the results.
The graphs show how those measurements change in a very haphazard way over a relatively short time span.
This haphazard mixing is not the way change happens, except in chemical warfare.
Take for example, the 1918 epidemic virus that was recovered and reactivated after some eight decades (On The Origin Of The Home Of COVID-19 - 9).
The comparison of the Alpha, Beta, Delta, Gamma, and Mers phases of the Coronaviridae viruses have virtually no matching values to speak of like the 1918 virus segments have.
III. Closing Comments
Genes have to do with quality and quantity of arms, legs, eyes, ears, toes, and the like (humans would not even be born without the advent of a virus gene).
The two videos give us an idea of the delicate, complicated, intricate, and utterly awesome machinery that replicates viruses inside microbes (think mutualistic replication).
If that machinery is damaged when antibiotic and other toxins attack and damage or destroy the microbe's replication machinery, then defective viruses will be the result.