From a Microbiologist

This is a re-share from Facebook.

Caveats:  Don’t know this person personally, it’s on Facebook, Did check profile and seems to be what he says he is.  This is informational only, not the final word on anything.

Re-shared WITHOUT permission at this time, I will attempt to get permission, but in general if someone has shared it to facebook publicly, it’s generally ok to share informational topics to the general public.

From Pat Fidopiastis on Facebook:

As anxiety levels rise due to COVID19 I just wanted to provide some essential context for some of the more alarming information being put out by officials. I have a Ph.D. in microbiology; I teach advanced courses in virus replication and pathogenesis, so if any of my opinions or facts offend you, spare me your Google Searches, you’re not telling me anything I don’t know. We’re in this together now and we must all see it through. But, we don’t need to endure it with any more added stress from the news headlines than is necessary to achieve the end goal. The situation is fluid, so some data and opinions might change going forward.

“COVID19 is 10X deadlier than the flu”.
There is nowhere near enough data to make this claim. Thus, reported case fatality rates are basically just a guess. Patients that have been tested for COVID19 are disproportionately the sickest patients because so far our limited testing capacity is reserved for them. Also, the COVID19 dataset is much smaller than the influenza dataset; bias is far greater in the much smaller COVID19 data set, especially when the calculations are swayed by numbers taken from groups of disproportionally older people stuck on cruise ships. Thus, I’ll bet my Ph.D. that fatality rates will drop dramatically as the overwhelming majority of mild cases are added to the COVID19 data set. Furthermore, COVID19 and flu viruses both have RNA genomes, however COVID19’s genome is non-segmented, while flu viruses have segmented genomes. The advantage of a segmented genome is that if multiple different flu viruses infect the same cell, they can swap genome pieces and create progeny with incredible variation. This is why our seasonal flu vaccines are usually not a good match to the types of flu viruses that are circulating, and why we are dogged by resistance to our flu drugs. It is also why my colleagues and I live in constant fear that a new variant of the flu will emerge that’s even deadlier than the 1918 strain. In contrast, COVID19 has remained relatively genetically stable and therefore should be an excellent vaccine and drug target, and it will be unlikely to surprise us with huge changes in its infection patterns.

“COVID19 spreads more easily than the flu”
There is not enough data to make this claim. The R0 (i.e. number of people each infected person will infect) reported for COVID19 ranges from 1.4 to 3.9 depending on which of the several published papers on the subject you rely on. Meanwhile the R0 for the 2009 H1N1 flu is about 1.5 and seasonal flu varies from 0.9 to 2.1. So, there is enough overlap in published R0 values to wonder which virus actually spreads easier. COVID19 appears to have entered our population back in mid-January when a traveler from Wuhan flew to Washington. As COVID19 spread freely during that time (prior to quarantines), it would have disproportionally struck down the most vulnerable first. Subsequently, human behaviors and fewer susceptible hosts would slow the spread. The dire models simply assume a constant rate of virus encountering highly susceptible hosts, which is never the case. The rate of COVID19 spread in Italy is truly staggering, but for context, there were well over 400,000 new cases of flu in Italy in a single week in January 2020. As of this writing, even though COVID19 was freely circulating for two months without any response, the United States has just about 28,000 identified COVID19 cases and about 400 deaths. There will no doubt be more cases and deaths. However, by comparison, in just the US alone, there were about 300,000 new flu cases per day, and 200 flu-related deaths per day, since October 2019. Not surprisingly, the need to stockpile ventilators for severe flu cases is an annual problem in the US; it’s not just an issue associated with COVID19. The fear of medical rationing during this COVID19 outbreak was the motivation for the “flatten the curve” mantra, in which doctors hoped to spread out patient loads to conserve resources. This fear continues to motivate the increasingly difficult restrictions we are facing.

“This situation is unprecedented.”
Our reaction to COVID19 is unprecedented for sure. However, the outbreak scenario is not unprecedented. Despite President Obama and the CDC’s efforts, the 2009 H1N1 swine flu infected roughly 60 million US citizens, resulting in about 274,000 serious hospitalizations (the high-end estimate is over 400,000 in the US), hundreds of pediatric deaths in the US, and at least 13,000 total US deaths (the high-end CDC estimate is over 18,000 deaths in the US). As that pandemic burned through the world, does anyone remember the level of fear and anxiety that we’re experiencing now? Clearly, we did not learn anything about pandemic preparedness because there have been between 140,000-800,000 hospitalizations and between 20,000 to 80,000 flu deaths each year in the US since 2009. Based on this year’s flu data, the US had roughly 300,000 new infections per day, and around 200 deaths per day since October 2019. The number of COVID19 deaths in Italy is frightening, but for context, a published paper on flu-related deaths in Italy revealed that between 2013 and 2017 there were a total of 68,000 deaths, with an average of 17,000 flu-related deaths per year in that time frame. We have a flu vaccine and oseltamivir, yet the WHO estimates there are about 500,000 flu deaths world-wide each year. Apparently, we’ve just decided to accept those numbers year after year. Amazingly, the staggering toll that the flu takes on us each year isn’t enough to motivate us to significantly increase funding for vaccine research, purchase more ventilators, or add more hospital beds; it took something “novel” to instill the level of fear that might motivate these improvements going forward.

COVID19 is “novel”
This is true. It’s clear from the COVID19 genome sequence that this is indeed a virus that only recently made the jump from an animal host to humans. However, related “mild” coronaviruses infect millions world-wide every year, with significant death rates among the elderly, and comprise a significant proportion (up to 11%) of lower respiratory hospitalizations in the US each year. So, while COVID19 is novel, as a group, coronaviruses are not novel.

“COVID19 remains viable in aerosols and surfaces for hours to days”
There is now published data to support specific claims about how long COVID19 remains viable on surfaces. However, there is a difference between “viability” and ability to cause disease in humans. First, it is important to note that details of the environment matter. To simply say that “COVID19 is viable on surfaces for days” oversimplifies the data. For example, small increases in temperature and humidity seem to dramatically interfere with COVID19 viability on surfaces. In order to conduct these experiments, researchers spray huge numbers of viruses onto a surface under defined environmental conditions, remove samples at regular intervals, and then attempt to resuscitate the viruses under ideal conditions in lab culture. In an actual outbreak scenario, in order for a virus sneezed onto a surface to infect a person, it would not only have to endure the environmental stress, but the potentially weakened (albeit viable) virus would then have to endure the various human immune system defenses in order to cause infection. COVID19 has a flimsy outer coating that is highly vulnerable to damage due to environmental stress. This means that just because a virus on a surface can be resuscitated under ideal conditions in a lab does not mean it is able to cause disease in humans. As with death rates, and other information being disseminated by officials, you’re getting worst case scenarios in order to encourage everyone to stick to the plan. However, even knowing that this is a worst-case scenario, properly wiping down surfaces with a disinfectant and practicing good hygiene should be something we do all the time, not just when we’re frightened during a pandemic.

“COVID19 can spread while you are asymptomatic”
This appears to be true and can complicate efforts to control the spread of COVID19. However, asymptomatic spread is true of many pathogens, which is why we should always be mindful of basic levels of hygiene, not just during a pandemic. For example, my students and I sampled college students for a highly communicable pathogen with a death rate of about 20%, responsible for at least 15,000 deaths annually and billions of dollars in added healthcare costs in the US. We detected asymptomatic carriage in 24% of the healthy population, and the strains were resistant to some of the strongest antibiotics we have. How many of us showing the worst side of humanity by overrunning grocery stores and hoarding food and supplies because of a theoretical COVID19 infection knows whether you’re an asymptomatic carrier of the killer we detected in so many healthy young people? Again, basic hygiene at all times and not just during pandemics is our best weapon.

“Nearly 40% of hospitalized COVID19 patients are aged 20-54”
This statistic is based on a cohort of 508 hospitalized patients, in which 38% (about 200) fell into the 20-54 age range. The vast majority (or likely all) of these individuals will recover but because they require resources, this is still a significant statistic. This information is being emphasized probably in response to images of college-aged Spring Breakers openly flouting the latest quarantine orders. The point is that there is still risk, even if you are younger. However, for context, nearly 500 children died of the flu during the 2018-19 flu season, and there were about 2,500 deaths in the 18-49 age range.

“The virus spreads by aerosols, hand to mouth contact with contaminated saliva, and hand to mouth contact with fecal material”
The virus targets ACE2 receptors, which can be found in the mouth, nose, gut, and lungs, so it has the potential for multiple entry points. Thus, each of these suggested transmission routes is supported. This is a strong reason to rely, first and foremost, on hygiene to inactivate and/or remove viruses on skin and inanimate surfaces to minimize the chances of transmission. Aerosol transmission might be mitigated by practicing “distancing” whenever possible, but this approach is simply not a good long-term solution. Notably, certain human behaviors, such as smoking or vaping, can damage the immune response in the lungs and increase the chance of a more serious COVID19 infection. Thus, countries like China with risk factors such as an aging population, cities with unhealthy air quality, and enormous numbers of smokers, are far more likely to have worse outcomes in this COVID19 pandemic.

“The pandemic will last 18 months or longer”
This is possible, but I doubt it. The dire mathematical models that are driving our response to the virus are based on extreme worst-case scenarios in order to force compliance and hopefully end this pandemic as quickly as possible. Still, rather than fret over worst-case models, it is more useful from a “sanity” perspective to look at outcomes in countries that are more like the United States. The first COVID19 case was confirmed in S. Korea on Jan 20, and as of this writing, the number of new cases slowed from nearly 1000 at its peak to about 70. Importantly, according to a recent news report,“S. Korea is experiencing these dramatic drops without locking down entire cities or taking some of the other authoritarian measures used by China to bring down its number of cases.” Apparently, the key to S. Korea’s positive outcome has been expanded testing to quickly identify new cases. To counter balance the dire predictions about the disease, there are equally dire predictions about the long-term effects of quarantines. Here’s a sample of some of the recent headlines: “Domestic violence calls increase as people shelter in place during COVID-19 outbreak”. “Job losses could quickly soar into the millions as coronavirus craters U.S. economy.” “Gun sales surge as coronavirus pandemic spreads.” “Covid-19 positive patient jumps to death in Delhi”. “The threat of quarantine looming over sick workers and school closures threatening food access and child-care shortfalls”, “The lack of paid sick leave for tens of millions of workers could be catastrophic for low-income families“, “The Economic Impact Of COVID-19 Will Hit Minorities The Hardest”. Another thing that fear will do is drive more people to go to the hospital with even the slightest symptoms, which the vast majority would not do during a normal flu season. This not only increases the spread of the virus, it will overrun hospitals, just as it drove people to selfishly wipe out supplies at stores.

The question that we have to ask ourselves is how did we get to a place where epidemic preparedness is an after-thought, yet there’s always money for massive increases in military spending? Why is it that public health officials are contacting me and my colleagues for molecular biology supplies to conduct COVID19 testing, and asking us to step in as volunteers in the event that case-loads get overwhelming? It is a constant struggle to get average citizens to stay focused on outbreak preparedness beyond each sensational news cycle. Who even thinks about Zika virus anymore? What do all of us need to do every day, not just during a pandemic, to limit the frequency of severity of disease spread? Why was it so hard for the wealthiest country in the world to rapidly mobilize our resources to develop test kits to quickly identify and quarantine people infected with the disease? I taught my 9 and 12-year old children to conduct PCR-based COVID19 testing, so it’s not an issue of technical difficulties, it’s just a matter of properly funding the problem in order to scale up resources. Decision makers in our government deemed this preparedness approach too expensive; they are all quickly learning that the costs of our current unsustainable response will be devastating. In the end, our lack of preparedness has resulted in decision-making based on limited data, painting a picture of extreme worst-case scenarios. In turn, once we move past COVID19, we’ll no doubt end up dealing with the fallout from decisions that were just as bad as the problem we were trying to solve.

One thought on “From a Microbiologist

  1. An additional comment from the author to another questioning his work (formatting mine):

    From Pat Fidopiastis to Clay J.: You’re right, none of us knows where this is heading. So, if we’re all “sheltering at home” and clearing store shelves of Purell, what good does it do to let the doomsday mathematical modelers, that don’t even work with these microbes, dominate the narrative?

    Would they like us to go from “sheltering at home” to “sheltering under our bed, curled up in the fetal position?”

    That’s my main angle in writing the letter. It’s weird to me that we barely shrug at the CDC statistic that between Oct 1, 2019 and the present, there were between 24,000 and 62,000 flu-related deaths. One person commented that I should stop comparing COVID19 to the “vanilla flu”.

    Ignoring tens of thousands of flu dead makes me wonder what a person’s motivation is when they get angry at me for bringing that up. One person argued that I seem to miss the point that it’s the rate that we need to worry about. I understand the importance of rate on the health care infrastructure, and I sympathize with the health care providers in NYC and other hard-hit places. However, as a doctor, would you be willing to tell the loved ones of those 24,000+ dead people that we’re sorry for your loss, but at least the rate at which your loved one suffered and died of the flu was scattered over a few more months than those that suffered and died of COVID19?

    When this is over and the fog clears, I’ll be able to compare these viruses on additional levels. In the mean- time, I’m doing my part by working out a backup RNA extraction/qRT PCR protocol for COVID19 detection for my county Public Health department. To your last question, in a perfect world, the most powerful country in the world should have been able to immediately cease commercial flights in and out of the US, and rapidly scale up testing to identify and quarantine infected individuals. Given that we missed the boat on early intervention, I wouldn’t second guess our current policy.


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