Three Pathways the RNA-Based COVID-19 Mutates
By: Bruce H. Cottman
Tags: Vaccines, Covid 19 Crisis, Pandemic, Covid 19, Coronavirus

Three Pathways the RNA-Based COVID-19 Mutates

One of those pathways can cause the next pandemic.

COVID-19 virus particles. Binding sites are purple, green, and blue. Source: Unsplash

The Coronavirus Has Been Infecting Humans for 1,000s of Years.

The Coronavirus has existed for a millennium alongside humans, infecting and passing between them. Coronaviruses also has frequently crossed species barriers, and some have emerged as important human pathogens. Those virus variants died off, becoming extinct because they killed the host.

Ancient deadly Coronavirus died off because the virus infection killed the host, and only immune hosts survived. We can assume that COVID-19 is a relatively new mutation of Coronavirus.

Most modern human Coronavirus originated from bats where they are non-pathogenic (to humans or bats), resulting in symptoms as severe as a cold.

So how did the deadly COVID-19 virus mutate from the Coronavirus?

How did COVID-19 become deadly to humans?

We know it mutated. However, infectious experts are not in consensus about which of the three candidate mutation pathways are responsible for the deadly COVID-19 mutation.

One pathway is mutation by replication error. Another possible pathway is jumping from human to animal, where it mutates and incorporates animal RNA and then jumps back to humans (HAH pathway). The human-animal-human transmission is a mutation pathway.

Pathway 1: Mutation by RNA copying mistake

Coronaviruses are successful at mutating because they make a lot of RNA mistakes when they replicate.

All viruses mutate, and the Sars-Cov-2 Coronavirus that causes Covid-19 is no exception. Mutations arise when the virus replicates inside cells and mistakes in copying its genetic code. Unlike humans, whose genes are written in double-stranded DNA, the coronavirus genes are carried on single-stranded RNA. — CDC.gov

RNA virus strand replication has an encoding error rate that can range 100 to 10,000 times higher than DNA-based viruses.

DNA viruses have mutation rates that range from 10−8 to 10−6 substitutions per nucleotide site per cell infection (s/n/c). The mutation rate of RNA-based viruses ranges between 10−6 and 10−4 s/n/c. The mutation rate in DNA-based humans is about 1.5x10–11 base pairs per second.

Note: The higher the mutation rate, the higher probability that the organism becomes un-viable (extinguishes) in 1 or more successive replications.

COVID-19 known variants. Source: Unsplash

Coronaviruses letter replication error causes minor mutation that usually does not induce severe symptoms. The Coronavirus is one of several viruses that causes your flu symptoms one year and is a different virus strain from the one that caused your flu symptoms the next year.

Some Coronaviruses strains are deadly. However, there are pieces of all Coronaviruses that Can Not change, or there is a loss of the ability to replicate and infect human hosts.

The probability of Coronavirus mutating N-letters, where N is the number of the letter changed in the mutation, is proportional to N to the negative power.

Multiple RNA letter change has to result in different and human deadly binding sites, and a viable virus, and human hosts that live long enough for transmission. The probability of another deadly virus by replication mutation is small to non-existent by observation.

The British COVID-19 variant is most likely a letter replication error mutation. The strain was identified by Public Health England (PHE) by investigating the increased number of infections in Kent and London.

The main worry is that the variant is significantly more transmissible than the original strain. It has 23 mutations in its genetic code — a relatively high number of changes — and some of these are affecting its ability to spread. … Scientists say it is about 40%-70% more transmissible. — Reuters.com

PHE has named the variant as VUI — 202012/01. The VUI — 202012/01 strain has made the news because it has a higher transmission rate, and England is an open society. There are more variants, some of which are not detected or publicly announced.

Note: The British COVID-19 variant has a higher transmission rate, but the deadly binding sites are still the same.

The mRNA-based COVID-19 Vaccines should be Effective for at least a few seasons.

Different strains of the flu virus mutate over time and replace the older strains of the virus. It’s essential to get a flu shot each year to ensure that your body develops immunity to the most recent virus strains. — WebMD

The human immune system can deal with virus binding sites it has seen before. That’s why Coronavirus usually results in mild cold-like symptoms instead of life-threatening pneumonia.

These Coronaviruses binding sites are the targets of vaccines as well as the targets of our immunity system. Although many pieces of one mutation can change, the critical pieces for spread and infection will remain the same and continue to be recognized by the immune system years exposed earlier.

mRNA COVID-19 based vaccines render COVID-19 deadly binding sites inert in the host. The result is a mild Coronaviruses that passes from immunized person to immunized person, resulting in, at worst, non-deadly cold-like symptoms.

“The SARS-CoV-2 coronavirus is presumably already optimized to affect human beings, and this explains its low evolutionary change,” explains Federico Giorgi, a researcher at Unibo and coordinator of the study. “This means that the treatments we are developing, including a vaccine, might be effective against all the virus strains. — Science Daily, August 2020.

Note: The mRNA-based vaccines are fragile. They can break apart (spoil). They become ineffective at room temperate in seconds. They are shipped cold so that the mRNA vaccines are effective for about two weeks.

Unfortunately, for us (humans), there are other pathways for creating another deadly Coronavirus.

The second and third pathways are zoonotic events that result in a human-deadly Coronavirus strains.

Zoonotic: Pertaining to a zoonosis: a disease that can be transmitted from animals to people or, more specifically, a disease that normally exists in animals but that can infect humans. — MedicineNet.com

The definition is not wrong; zoonosis (plural zoonoses, or zoonotic diseases) has more than one transmission mode. The highest probability occurs with transmission from animal to human, as the above definition states.

Every-time we touch an animal, a bountiful myriad of animal viruses are transmitted. Humans rarely show a symptom from animal contact. The transmission does not mean the virus can affect the human host or survive in the human host.

What is more likely, the cause of deadly zoonotic viruses is the human to animal to human (HAH ) transmission mode. The HAH mode is of lower probability, which is counteracted by the very high probability of human host viability as detected through DNA, RNA, and mRNA analysis.

The reasoning for a HAH viable deadly virus is that the virus started in humans (H), which means it started as a human viable (non-deadly) virus. The virus transmits to an animal species (HA), where it mutated by picking up some of the animal RNA. The mutated virus, which now had some animal RNA, was transmitted to the human species (HAH) in which it was still viable.

The intermediary animal is called an animal reservoir of the virus. The animal species may or may not get sick from being an animal reservoir. The rat and flea were reservoirs (carriers) of the infamous Black Death (bubonic plague) bacteria.

The animal reservoir virus mutates into a deadly human virus as there are many proteins in animals that our immune system has never seen before.

The probability that a deadly Coronavirus strain is created with unknown surface proteins is higher, the higher the density mixture of humans and animals.

Within the last two decades, zoonotic events have resulted in the emergence of three deadly Coronavirus strains where infection can result in life-threatening symptoms.

With new surface proteins not encountered before by our species, the COVID-19 strain causes the immune system to overreact. Overreaction floods your lungs, causing pneumonia, as well as other deadly reactions.

The result is a classification of Coronavirus’s novel strain after its hallmark symptom: Severe Acute Respiratory Syndrome (SARS).

Some past zoonotic events include:

How effective will the forth-coming COVID-19 vaccine be against deadly zoonotic pathway strains of Coronavirus?

A new deadly zootonic (HAH pathway) Coronavirus will have one or more new binding sites.

If a novel strain of a deadly Coronavirus by the HAH pathway appears in the future, then the probability of the current mRNA COVID-19 vaccines being effective is low to not-at-all.

Will there be another pandemic?

What conditions need to change? We are not sure. However, because we keep having pandemics from zoonotic events, we can be confident the critical conditions have NOT changed.

The following may cause the rate of the appearance of pandemics to increase:

Increase of the global human population; Increase in the consumption of animals; Increase in the density (crowding) and/or number of animal meat markets; Deforestation; Climate change.

Correspondingly a decrease in these factors should cause a decrease in the rate of new pandemics.