John Sanford: Is The COVID-19 Virus Degrading?

Continuing the discussion from Explaining the shape of a typical COVID 19 epidemic curve:

An important technical question came up about Sanford’s work I would like to resolve. I’m sending him an email pointing here. (Click the arrows below to expand details)

Does Genetic Information Loss Explain COVID-19 Death Curves?

We do have alternate explanations that explain this curve and much more without appealing to genetic entropy. But we also doubt that genetic entropy is attenuating the COVID virus.

The Paper In Question

Information Loss: Potential for Accelerating Natural Genetic Attenuation of RNA Viruses

by Wesley H. Brewer, Franzine D. Smith, and John C. Sanford

Loss of information is not always bad. In this paper, we investigate the potential for accelerating the genetic degeneration of RNA viruses as a means for slowing/containing pandemics. It has previously been shown that RNA viruses are vulnerable to lethal mutagenesis (the concept of inducing mutational degeneration in a given pathogen). This has led to the use of lethal mutagenesis as a clinical treatment for eradicating RNA virus from a given infected patient. The present study uses numerical simulation to explore the concept of accelerated mutagenesis as a way to enhance natural genetic attenuation of RNA viral strains at the epidemiological level. This concept is potentially relevant to improved management of pandemics, and may be applicable in certain instances where eradication of certain diseases is sought.

We propose that mutation accumulation is a major factor in the natural attenuation of pathogenic strains of RNA viruses, and that this may contribute to the disappearance of old pathogenic strains and natural cessation of pandemics. We use a numerical simulation program, Mendel’s Accountant, to support this model and determine the primary factors that can enhance such degeneration. Our experiments suggest that natural genetic attenuation can be greatly enhanced by implementing three practices. (1) Strategic use of antiviral pharmaceuticals that increase RNA mutagenesis. (2) Improved hygiene to reduce inoculum levels and hence increase genetic bottlenecking. (3) Strategic use of broad-spectrum vaccines that induce partial immunity. In combination, these three practices should profoundly accelerate loss of biological information (attenuation) in RNA viruses

And @glipsnort’s analysis with emphasis added:

I will be checking for myself if this is a good assessment, and I will also ask Dr. Sanford for this thoughts. I have three specific questions for him:

  1. Responding to @glipsnort, how does he reconcile his choice of the parameters in his study with reference 35?

  2. Does he believe that SARS-CoV-2 is being attenuated by the information loss mechanism he explains in this paper? What evidence can he point to that shows this is the case?

  3. How did this new virus come to be? Why is it so effective if new functions cannot evolve? If evolution can only degrade functions, and it does so rapidly, shouldn’t this virus have gone extinct thousands of years ago?