The Coronaviridae - 6

Concept: Genes And Nucleotide-gaps Between Them

The Coronaviridae RNA genome is not composed completely of genes, there are nucleotide strands between the genes.

In today's post the variability of the "gaps" between genes will be shown to be more variant than the genes.

Notice the graphic above, which shows genes and "gaps" (purple squares) of nucleotides between the genes.

Today's appendices (Countries A-C, Countries D-Z, USA SARS-CoV, USA SARS-CoV-2) are composed of the latest download of the GenBank database of SARS-Cov-1 and SARS-Cov-2 GBFF files mentioned in previous post (The Coronaviridae - 5). 

They are tables of genomes in the GenBank recording the variations of genes and the gaps between the genes.

This picture can indicate chemical damage and mutation:

"Cellular fitness relies heavily on the ability of the cell to cope with mistakes resulting from biological processes being intrinsically imprecise and from exposure to a multitude of endogenous and exogenous insults. Damaging agents alter the chemical composition and, hence, the function of biomolecules, including DNA, RNA, protein, and lipids. Nucleic acids are specifically susceptible to chemical damage primarily due to the reactivity of the nitrogen and oxygen atoms of the nucleobase with a variety of chemicals. These chemical assaults include reactive oxygen species (ROS), ultraviolet light, and alkylating agents. Curiously, certain species of damaged RNAs, typically oxidized, have been linked to a number of neurodegenerative disorders. These observations suggest that the inability of the cell to clear damaged RNAs could contribute to disease or that certain diseases may interfere with cellular handling of damaged RNA.

Unlike naturally occurring modifications of specific nucleotides in rRNA and tRNA, unwanted modification [of nucleotides] resulting from chemical agents typically has deleterious effects on RNA’s function. Specifically, some modifications can prevent base pairing completely, while others alter the base-pairing properties of the modified nucleotide. Consistent with these ideas are recent discoveries showing that chemically damaged RNAs pose significant hurdles to translational fidelity and efficiency. Modifications interfere with the decoding process on the ribosome, whereby codon–anticodon interactions are disrupted and, depending on the type of damage, result in stalling or miscoding."

(Quality control of chemically damaged RNA, emphasis added). Antibiotic chemicals are a cause of ROS:

"The radical-based theory proposes that three major classes of bactericidal antibiotics, i.e., B-lactams, quinolones, and aminoglycosides, have in common the downstream formation of lethal levels of reactive oxygen species (ROS) as part of the killing mechanism."

(Influence of Reactive Oxygen Species [ROS], emphasis added). The issue of where the damage to microbes that replicate viruses comes from (chemical mistreatment of food-animals) was discussed in a previous Dredd Blog series (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21).

Other researchers are getting closer to checking out the mass-production-of-animals-for-food industry:

"The WHO team also examined more than 80,000 samples from cattle, sheep, chickens, ducks, geese, and pigs from 31 provinces across China. There wasn't a single positive case among them. None of the animals had coronavirus-specific antibodies, either, which would have indicated a past infection." 

(Yahoo, emphasis added). If not in China, then where (On The Origin Of The Home Of COVID-19, WHO SARS Report)?

The the next post in this series is here, the previous post in this series is here.