Isolation
The Official COVID-19 Pandemic Primer
![PHIL ID #23354 - Transmission electron microscopic image of an isolate from the first U.S. case of COVID-19, formerly known as 2019-nCoV. [1]](https://images.squarespace-cdn.com/content/v1/5e7a6821e4ce7629240016f5/1585163878734-YA2IJYESK1T9W08X9WY0/23354.jpg)
PHIL ID #23354 - Transmission electron microscopic image of an isolate from the first U.S. case of COVID-19, formerly known as 2019-nCoV. [1]
I woke up to the sound of birds singing their morning songs over the backdrop of a silent New York City. This, untimely gift, was an oddly pleasant divergence from the more standard native NY soundtrack of obnoxiously congested traffic & loud people. Needless to say, our newfound serinity is a direct response to the spreading COVID-19 pandemic. The coronavirus novelty introduced itself in late 2019, and has been on a global tour since, if viral infections were rappers, this is literally the Jay-Z of the microbe world, it’s gone several times platinum over now, it’s getting old, but it’s not about to retire. I suppose we should start at the beginning?
It came from where?
Based on the current data released by the Center for Disease Control & World Health Organization, this story begins in late December 2019 within the city of Wuhan, Hubei Province, China, in a patient with a severe pneumonia of an unknown etiology. RT-PCR assay of samples from said patient tissue provided confirmation for a beta-coronavirus infection. Whole-genome analysis further identified the virus as SARS-like, viral isolation tests were carried out on various cell lines affirming cytopathic effects within 96 hours & infections could be neutralized by introducing a previously infected persons serum. By this time, the Wuhan Jinyintan Hospital was buzzing with new cases of the unknown aggressive pneumonia and within short order clusters of infected began to appear in family groups. The epidemic had begun, the 2019 coronavirus novelty introduced itself to the world.
With a population of approximately 58 million, Hubei is home to 4.4% of Chinas population [2], it’scapital and population center is Wuhan, a bustling commercial metropolitan center with a rapidly alternating scenic backdrop. Divided nearly in half by the prominent Yangtze & Han rivers, the city is teaming with industrial activity, busy pedestrian intersections, a state of the art laboratory of optoelectronics, all interwoven by a public transportation system that feeds into the local airport (pertinent details); conversely, it is a traditional and classic chinese landscape peppered with lakes & lush park scenes, sporting endless hills interspersed with marvelous architectural marvels such as Moshan Hill.
It is also home to what Hong Kong English speakers refer to as wet markets, general food & goods markets which often feature a selection of locally sourced fauna offered for fresh slaughter and packaged for consumption, they’ll even cook and prepare on site. Needless to say, these are largely unregulated sites where process and standards are spread pretty damn thin, if ever.
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To be clear, wet markets are not uniquely Chinese (or Asian for that matter), they can be found pretty much world-wide by various names, from the tianguis of Mexico, to the more exotic traders of bush meats in markets and bazaars through out Africa. The lack of overall oversight in proper sanitation and public health concerns at these locations causes for an environment primed for zoonosis. The myriad selection of locally sourced wild animal species interacting closely, shedding viral particles in every fluid & aerosol spread as animals are slaughtered for sale coupled wth the hundreds of thousands of human bodies providing trillions upon trillions of live cells for oppurtunistic virus strains to … well go viral; it’s not surprising that these & similar locations are thought to be the breeding grounds of historic epidemics such as SARS & H5N1 Avian Flu, and bushmeat(s) consumption may be responsible for the spillover that led to HIV. The Huanan Wholesale Seafood Market (wet market), is the current most likely specific origin of SARS-CoV-2.
COVFEFE-19 what?
Expanding on the new terminology added to our life lexicons; COVID-19 is short form for Corona virus disease 2019, which is the phenotypic expression in humans of being infected with SARS-CoV-2, the short form for severe acute respiratory syndrome coronavirus 2 [3]. Classification systems place the SARS-CoV-2 within the Coronaviridae family in the order Nidovirales, along with Arteriviridae and Roniviridae virus families. Another level of sub-division splits the coronaviridae into 4 phylogenetically derived sub-categories, alpha (Alpha-CoV), beta (β-CoVs), gamma (Gamma-CoV) & delta (Delta-CoV) [4]. We know that our novel SARS-Cov-2 is a β-family coronavirus with 96% identity match to BatCov RatG13 [5,6], thus is thought to be propogated by bat reservoir (possibly Rhinolophus affinis, also known as the Intermediate horseshoe bat), with an unidentified host (although there are candidates, such as the Pangolin). At this point, we refer back to wet markets, where species interact in uncontrolled, unsanitary environments and become breeding grounds for spill over between said species. The intermediary is almost surely a resident of the wet market, where frequent contact with humans allowed the virus to use the host as a proxy for infection. Contact tracing and further research within China may reveal more data on the elusive intermediary host.
The Spread (how sh*t got real)
Wuhan, is a city of approximately 10 million people, with 4.4 million concentrated in the metro area, interwoven by extensive public transportation systems linking destinations for traveling pedestrians, and a busy airport (WUH), much like many other modern cities. From a purely mathematical perspective, China & America are roughly the same size in area [8], however China has a population of about 1.3 billion compared to Americas at just over 300 million, accordingly the populaton density in China (389 people/m^2) is 4 times that of Americas. This lends itself as an incentive to the propagation of a viral pathogen whose primary transmission route is via exchange of respiratory droplets, an event whose likeliness increases with population density. Insert the R0 value of any virus, it’s reproductivity rate, which in the case of SARS-CoV-2 is between 2 and 2.5, those infected left unhindered will go on to infect 2 or more other individuals. This cycle continues on, if left unhindered, and by the time scientists identified the strain of coronavirus they were dealing with was SARS-like, healthcare systems across China had already begun to deteriorate with overloaded capacity. Wuhans commercial status & central location in Hubei makes it a transportation hub, and the infrastructure which facilitated the rapid increase of blast radius. SARS-CoV-2 at this point, accomplished person to person & community spread within Chinas borders; and the route outside of China and into the greater world…was as simple as… a scheduled flight. Based on data aggregated in flightradar24, there are daily direct flights from Wuhan (WUH) to airports as remote as JFK in NY or ANC in Alaska, and ofcourse, travellers interacting with other travellers, only act as a multiplicative factor in increasing the speed of spread. Consider that, in the height of this pandemic itself, there are about 200,000 flights travelling across the world on any day, when we aren’t all scared shitless, there are several more more. Viruses can indeed, tour the planet, in record time.
Daily Flights Tracked
during the pandemic
Our small world is well interconnected. And this is the answer to Cardi B’s relevant question of, “how did it get all the way from Wuhan across the world?” (paraphrased)
Who should be scared shitless?
Thus far, physical expression of infection have varied on a spectrum, on the lower end reports of fever, dry cough, shortness of breath, lathargy, but on the more severe end, aggressive pneumonia and respiratory symptoms that may escalate to death. By far, most cases recover, however it has been observed that the elderly population, and those with pre-existing conditions and/or immunodepression are at increased risk for severe responses and death. So, only the elderly should be scared shitless… right? (wrong, cont.)
It is still very early in this pandemic, and there have been several outlying examples of younger people dying, who otherwise have no pre-conditions or underlying disorder. An even more concerning phenomena, comes from research in Iceland, who taking advantage of their small population have pumped their rate of COVID-19 testing up to one of the best rates in the world (per capita), testing nearly 10,000 people so far, have discovered that around 50% of those infected, were asymptomatic (showing no symptoms, but still actively infecting others) [9]. This creates a sinister condition where the young, are transmitting the infection to the elderly, our parents, our grandparents, our professors are all at heightened risk, and a simple care filled interaction after a night out with the boys, can literally be the kiss of death.
Compounding onto this problem, possibly in the worse way, is human ignorance;
Inability to coordinate on a wide scale
The need to blame rather than resolve the issue at hand.
Our president is an idiot.
Anti Scientific cults, and a general anti-scientific culture across the board,
Internet conspiracy theorists and couch crust are all over it.
American racism
American stupidity
In Florida where they continued on with spring break festivities at densely packed beaches despite the growing active cases all over the country, only to; within the incubation period, disperse and act as super spreaders, on the routes to and from spring break locations, infecting hundreds, and by way of those hundreds, thousands. Florida now is a growing epicenter.
In New Orleans, LA, in the middle of a global pandemic, Mardi Gras was allowed to continue on, yes, Mardi Gras, a free part full of sloppy drunk people nearly naked in the streets exchanging beads they’ve draped in strange areas. New Orleans is now a growing epicenter, and the largest growth rate.
Ignorance is ubiquitous. Texas, Virginia, Illinois, Michigan, we have a long road in front of us.
New York, my lovely home, is being hit pretty hard, which to some degree is expected, we have all the signature attributes to propogate a highly contagious pathogen around quickly. Beefed up infrastructure, public transportation connecting this distant portion of the state, to the next, millions upon millions of people within close proximity of each other. In a year, the new york MTA transports 1,762,565,419 people [10], on an average weekday, about 500 million people move back and forth on trains (not individual people, round trips, etc). We have, not one, or two, but several airports, with JFK taking flights from WUH, for example. We are the hottest hotspot in the country, and expanding, we’ve taken the whole tri-state with us. Governor Andrew Cuomo, has become our national hero, using science and data to drive his decisions, in place of our impotent president.
To the sub-topic point, if you live on the planet Earth, and register as a human, you should have a healthy amount of fear, this is a modern viral spill-over event, and based on trends, it will be ugly before it gets remotely stomachable. The common cold, for example, is a type of coronavirus that spilled-over a very long time ago, perhaps previous to modern humans in evolutionary histry, and is now, a very mild annoyance, rarely escalating to death. Before the common cold became “common”, it probably ripped through populations violently as well. If we were quick to isolate this virus, and let it burn out in place, we may have been able to avoid what will now most likely be, a new human disease we just have to deal with.
If you are an American, you should be scared shitless, from a top-level perspective, we are failing miserably, and this isn’t something you can “just fix”, this is a deep tissue American cultural cancer that’s been metastasizing for decades. Despite the pandemic being registered in each of the 50 states, military sea vessels dispatched to americas busiest ports to amplify capacity in a buckling health care system, and a death toll of over 2000 Americans and rising (today, +11%), our president is making plans to lift lockdowns to “spin up the economy”. Despite the local lock downs our governors have implemented statewide, the president wants to “quarantine” the tri-state, most likely giving him brain space to relax lock downs in other parts of the nation. This, is a royally bad idea, the incubation period of this virus (again) is up to 2 weeks, the number of asymptomatics in the population is unknown as we haven’t ramped up testing to any usable degree nationally. We simply don’t know where this where this virus is, who is holding symptoms, or who is transmitting and not showing any clinical symptoms. Given it’s mature ability to move quickly, we should ASSUME, it has seeded itself in all locales, and shut down to ride out the next cycles of incubation and presentation.
The Numbers
Global Tally of cases.
Global Tally of deaths, and deaths per 100 cases.
Data Source: John Hopkins U. / WHO
Citations
COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives
China vs. USA (Area)