AMU Health & Fitness Infectious Diseases Original

COVID-19 Genetics and Statistics: Comparison with Influenza Viruses

By Daniel G. Graetzer, Ph.D.
Faculty Member, School of Health Sciences

The English word “virus” is based on the Latin for “poison,” which originally meant “venom.”  Comparing genetics and statistics of the rapidly mutating coronavirus strain that causes COVID-19 disease versus the several virus types associated with seasonal influenza is like comparing apples to oranges, both are fruits but have different genomes. 

Human infection with COVID-19 is caused by the novel (new) coronavirus SARS-Cov-2, which now unfortunately has several variants. Whereas influenza comes from several virus types with an estimated 30% of flu viruses coming from the coronavirus family. Coronaviruses are typically spherical with extremely large single-stranded RNA genomes – 26,000 to 32,000 bases (RNA “letters”) long – and named for the crown (“corona”) of club-shaped spikes on their surface as seen via electron microscope. 

COVID-19 and influenza are both contagions with key similarities. Both are viruses (not bacteria) that first infect lung tissue. They can be spread by persons who do not know they are infected (asymptomatic carriers); they may cause symptoms ranging from mild to severe and weaken overall immunity enough to increase susceptibility to other invading pathogens. That means these viruses can “opportunistically” infect patients who are otherwise immunocompromised due to diabetes, obesity, chemotherapy, weaker inherited genetics, and can lead to pneumonia and other potentially fatal illnesses. 

The key difference between SARS-Cov-2 and its variants and influenza viruses is SARS-Cov-2 gene strands contain different RNA sequences, which cause them to behave differently. A comparable analogy: Just because humans share about 50% of their genes with bananas does not mean we are functionally “half banana.” 

Influenza viruses are “human viruses,” meaning they are comprised of RNA chains that have theoretically been around long enough to be recognized by the human immune system. Fortunately, that enables at least some immunity each flu season due to previous recovery as a result of direct exposure to similar viruses and/or past vaccines.

SARS-Cov-2 Began as an ‘Animal Virus,’ Meaning it Previously Existed Only in Animals     

SARS-Cov-2 began as an “Animal virus,” meaning it previously existed only in animals and for an unknown length of time. Thus, theoretically it spread only from animal to animal, with no “hidden spreading” of animal-to-human or vice versa. 

The 1918 H1N1 “Spanish flu,” which spread bird-to-human, and the spring 2009 H1N1 “swine flu,” which spread pig-to-human, were able to jump species, which is why public health virologists constantly watch for mutations. Unfortunately, once a previous “animal only” virus mutates enough to be transmitted to people, the human immune system cannot recognize it, much less put up a good fight against it. 

The world was fortunate that 2009 H1N1 swine flu attacked human cells differently than in other pandemics and had RNA strands that mutated relatively slowly and not into forms as lethal as the H1N1 Spanish flu.

Estimating how contagious a pathogen is — called Ro and pronounced “R naught” — reflects the average number of persons who contract it from one single infected person — which then enables the pathogen to continue replicating within secondary cases. They can then further infect third cases who are exposed to the second case, and so forth.  

If Ro is precisely 1.00, each infected person will theoretically transmit it to exactly one new person, indicating a stable “reproduction rate” that is, no decline or outbreak. If Ro is less than 1.00, each infected person will theoretically transmit it to fewer than one other person, indicating the infection rate is declining and hopefully will die out soon. 

If Ro is greater than 1.00, each existing infection will cause more than one new infection and an outbreak may follow if the elevated replication rate continues on and on and on to include anyone within the community who has not yet contracted it or been vaccinated. The higher the Ro, the faster the pathogen is spreading. The statistical Ro estimation assumes that everyone within the community is equally and completely vulnerable to infection, that no one has yet been vaccinated and no one has ever contracted the disease previously. Also, there are no measures in place to control its spread. 

This combination of all conditions is fortunately rare in developed countries in the 21st century, thanks to public health announcements about social distancing, avoiding crowds, wearing face masks, and regular handwashing. Vaccines are the human race’s best defense against potential “slate wipers,” diseases that have the potential to wipe out the human race. Smallpox elimination is modern bioscience’s most notable success against nature. 

Ro of the 1918-1920 “Spanish” H1N1 flu pandemic infected about 500 million people, or about one third of world’s population and one quarter of all Americans. Before it was eliminated, the “Spanish” H1N1 flu killed more than twice as many as were killed in WWI, and lowered life expectancy by about 12 years. Also an H1N1 virus, the 2009 “swine flu” infected 11% to 21% of the global population. Vaccines and antiviral drugs, and adherence to public health measures, made the outbreak much less deadly. 

The overall Ro for COVID-19 has been estimated by various research groups to have a median of about 5.7 in mid-to late-2020. A 5.7 Ro indicates that one person with COVID-19 is transmitting it to nearly six other people, with each person then going on to infect others at the same rate. 

Infection Rates Vary Widely within Various Areas of the U.S. and the World

Infection rates vary widely within various areas of the U.S. and the world. College towns tend to exhibit the highest spikes. Statistically, an Ro of 5.7 will require at least 82% of a community to be immune to current variants of COVID-19 to achieve herd immunity. Herd immunity is achieved through protective antibodies from a combination of vaccination, exposure to the virus, and blood transfusion from a previous COVID-19 patient who is now virus-free. Ro thus indicates the herd immunity threshold, which estimates level of immunization needed to reverse the outbreak.

Another important statistic is “doubling time.” That is calculated by the number of positive coronavirus tests, hospitalizations, and deaths. The shorter the doubling time, the faster the pathogen is spreading.

One leading theory is that a mutated coronavirus strain jumped from an animal to humans due to selection pressure sometime in late 2019. Then, within just a few weeks, it was able to jump from human to human, while at the same time becoming especially virulent, that is increasingly rapid and dangerous to human lung tissue.

Sickness and death rates in past pandemics have shown that immediate lockdowns can greatly reduce community spread. That was proven during the Spanish flu when certain U.S. cities were reluctant to shut down public events and those communities were the hardest hit.

Henry VIII, for one, was paranoid about another “Black Death,” a huge wave of bubonic plague from 1346 to 1353 that wiped out an estimated 60% of the world population and killed over 20 million in Europe alone. History has repeatedly shown that social isolation buys time until nature runs its course.

Vaccination Is a Sensitive Issue for Many due to Religious Convictions and Other Beliefs

Realizing vaccination is a sensitive issue for many due to religious convictions and other beliefs that proscribe vaccination. In no way wanting to discredit or minimize apprehension toward vaccination in general, I offer the following:

1. To my knowledge, no pharmaceutical company — Johnson & Johnson, Pfizer, Moderna, AstraZeneca — currently utilizes stem cell tissue from recent human fetuses in vaccine production. That said, it is common to use “immortalized” cell lines, which can be propagated indefinitely from a variety of previous tissue sources, for testing as a quality control measure, but not for production. Data showing efficacy of a specific vaccine on established human cell lines is most often required prior to FDA approval to inoculate living humans in clinical trials. It’s my understanding that some foreign companies have possibly found a way to avoid the use of human cells lines in testing. But I do not believe this technology will be available in the U.S. until sometime after 2021.

2. Putting virus genetics and statistics in perspective, there are probably several million virus types in nature that virologists have not yet identified, any of which could become pandemics. To my knowledge, public health agencies and governments in the U.S. and elsewhere are not treating COVID-19 any differently than past pandemics, including polio and measles. Also, there is no credible evidence that anything underhanded or conspiratorial is going on. To me, vaccination as a precaution similar to wearing seat belts, they save lives.

The unfortunate reality is that outbreaks such as COVID-19 can come upon us almost as suddenly as an automobile accident. Auto accidents will continue to occur in a similar manner as viral infections, at least until herd immunity occurs perhaps through universal use of self-driving vehicles, which many take several decades if ever to happen.

News reports that a vaccine has over 90% efficacy are certainly encouraging. But this applies to effectiveness against the original COVID-19 strain and a few current variants only. There is no guarantee on future variants with larger mutations. Coronaviruses have the potential to mutate very rapidly. Current COVID-19 variants can largely be stopped now, but these early vaccines will lose their effectiveness if mutations continue. If there is no community spread, there will be no further mutations.

3. I have tremendous confidence in the 90% efficacy rate of the several vaccines now available. Optimal vaccine strength for effectiveness and safety is ideally determined via trial and error on animals. The goal is to determine the minimal dosage needed to defeat the microbe while preventing “collateral damage.”

4. The “mark of the beast” mentioned repeatedly in the Bible (Revelation 13:16-18, 14:9-11, 16:2, 19:20, 20:4) refers to a mindset, certainly not a liquid vaccine. Romans 14:7 says “None of us liveth to himself and no man dieth to himself” indicates to me personally that I have a responsibility to protect others — regardless whether I need or want to get vaccinated for myself. Thus, I will get vaccinated as soon as I am eligible out of regard for my community.

Daniel G. Graetzer, Ph.D., is a faculty member in the School of Health Sciences and enjoys giving students the latest statistics when instructing SPHS500 Statistics for Sports and Health Sciences. Daniel also teaches a variety of mathematical sciences courses for Global University, including Statistical Techniques, Business Mathematics, Mathematics for Liberal Arts, and College Algebra.

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