Doc Gumshoe – COVID-19 Miscellany, May 2020

I decided to add the year to my title in the event that this thing goes on for another full year, and I have to do an update in May 2021.   I pray fervently that such an eventuality will not come to pass, but it’s certainly possible.   Having said that, your obedient servant Doc Gumshoe continues to be an optimist, more or less, and continues on the alert for positive developments and hopeful bits of news.

Well, all I know is what I see on the internet, as Will Rogers would have said if he were around these days.   But here are some topics that Doc Gumshoe has looked at carefully, and which I hope you will think deserving of attention.

The first, and likely most important and most hopeful of these is the emergence of herd immunity.

When, and how, will herd immunity emerge to protect us from the coronavirus?

The “herd” I am referring to here is not cows or sheep, but us – the human population.   The way it works, and the reason it works, is that viruses are not able to survive on their own.   They can exist for a limited time outside of a host.   The duration of that limited time varies among different viruses; in the corona virus (now designated SARS-CoV-2) under normal circumstances it may be as long as 48 hours, but usually much shorter.   It depends, as probably you have heard, on its specific environment; for example, on steel or hard plastic, it might still be present and a possible source of infection 48 hours after it was first deposited there by a cough or a sneeze.   On some other metals, such as copper, not more than about 6 hours.   On paper, cardboard, textiles, and other absorbent surfaces, a considerably shorter time.   Of course, researchers have their ways of keeping the virus alive and active for longer.    

Therefore, in order to survive, a virus needs to penetrate a living being and kidnap the resources it needs to reproduce, which it manages with considerable efficiency.   Multitudes of viral particles can take up residence in a single living cell, appropriate the cell’s own functions, kill the cell, and emerge to invade other cells.   In the case of the novel corona virus, the spikes on the exterior of the virus have the special ability to attach to receptors on the exterior of living cells in the host.   These spikes, by the way, are what give corona viruses their name – they resemble a crown.   

When it penetrates the living cell, the virus is recognized as an invader, and the innate immune system of the living being that the virus has invaded (the host) will produce antibodies, which at the same time can attach to the viral particles and alert the immune system’s defense forces to attack the virus.   The host that the virus has invaded – human or animal – uses its immune response to combat and eliminate the virus.   An all-out war has been declared, and the host is the battlefield.   This is not necessarily agreeable for the host.   We – the human hosts that have been invaded by the virus – develop fevers, inflammation, aches, and other symptoms that we may interpret as signs that we are sick, but are in reality signs that we’re desperately fighting off a severe disease.

But even after the virus’s host wins this war – which we fervently hope the host does win – the antibodies remain, and act as sentries in case the virus should invade again.   It’s not known at this moment what degree of immunity those persons have who have been infected with the evil corona virus and fought off the COVID-19 disease, but what is known about viruses strongly suggests that some immunity will be present in those individuals.   How powerful that immunity will be and how long it will last is a matter of speculation at this time.   

Vaccines are the other pathway to immunity.   At present, more than 100 potential COVID-19 vaccines are in development.   We’ll take a look at a few of the more promising candidates later on in this piece, but despite a certain person’s promise to have 300 million doses of a vaccine available by January of 2021, that timetable seems a stretch.

A vaccine is carefully crafted to produce an immune response without causing the actual disease.   Frequently vaccines do cause some mild symptoms, and the symptoms do vary among the many vaccines.   The smallpox vaccine usually produced a single little pox on the skin at the site of the inoculation.   Many vaccines cause aching arms at the injections site, and mild headaches or a mild  sickish feeling.   (What Doc Gumshoe can state with total conviction is that vaccines do not cause autism.)   

In any case, those mild symptoms are manifestations of an immune reaction, which is what the vaccine is meant to trigger.   The immune reaction essentially means that the vaccinated individual now has a troop of sentinels which are primed to recognize the invasion of the specific pathogens and summon a militia of phagocytes and lymphocytes.   In the case of viruses, the most effective militia are a class of lymphocytes called T-cells, sometimes called natural killer cells, which are highly effective against most viruses.

(Exceptions to this are retroviruses like the human immunodeficiency virus (HIV) that causes AIDS.   These are particularly successful in terms of viral life, because they do not trigger an immune response.   Instead, they take over the host’s immune system, disabling T-cells.   Individuals infected with HIV can live for years without exhibiting any symptoms.   However, during those years they continue to carry and transmit HIV.   This is good for the virus, but catastrophic for the human hosts.)

At this point, no one can say with certainty whether individuals who have been infected with SARS-CoV-2 and recovered have immunity to the virus, and if so, how strong that immunity is and how long it will last.   The assumption is that those individuals will have some immunity, and the hope is that the immunity will persist long enough to protect those individuals from infection in at least the near future.   The same hope applies to the effects of a vaccine.   

The hope, essentially, is that enough persons – either because they have had the disease or been vaccinated, or both – will possess a degree of immunity such that the virus cannot spread like wildfire through the population.   The percentage of individuals in the community necessary to provide immunity to the entire herd of humanity is not precisely known, but it is quite high.   The human race was protected from smallpox by herd immunity because almost everybody had been vaccinated against smallpox.   (That herd immunity has vanished at this point, since people are no longer routinely vaccinated against smallpox, but the disease itself has also vanished.)   Up until quite recently, herd immunity kept the measles totally under control, but then a few parents decided that vaccinating their children against the measles violated their principles, with the result that the measles reappeared, and there were even deaths from the measles.

The way herd immunity works is by depriving the pathogen of a site to which it can spread and reproduce.   If in a class of 30 children, all are vaccinated, even if one child gets the measles despite being vaccinated, it doesn’t spread.   (Since no vaccine is 100% effective, some children who have been vaccinated may also get the measles.)      The child recovers; the measles virus expires since it has no place to hide.   But if a sizeable number of children are not vaccinated, the measles will spread.   

In brief: the transmission of a disease, whether bacterial or viral, is in inverse proportion to the percentage of the population that has immunity.   The more people that are immune, the less the disease spreads; the fewer people that are immune, the more the disease spreads.

I deeply hope that herd immunity rises in our country and the world because of the availability of a vaccine and the widespread use of the vaccine, and not because the corona virus itself has infected most of the world’s population.   And I also deeply hope that when this vaccine becomes available, the vaccine deniers don’t try to quash it by manufacturing rumors that the vaccine itself causes some dire disease.   A great deal depends on widespread vaccination – not less than the future of humanity and civilization.   

So, when will a vaccine become generally available?

That depends on whom you ask, and also where you’re asking from.   The White House proclaims that a vaccine will be available to one and all (at least here in the good old USA) by January, 2021.   To that end, a project has been announced whose objective is having 300,000,000 doses – that’s 300 million, by next January.   The project, dubbed Operation Warp Speed, is headed by Moncef Slaouli, who was chairman of vaccines at GlaxoSmithKline.   General Gustave F. Perna, who is in charge of the Army Matériel Command, will be the chief operating officer, tasked with getting those 300 million doses of the hoped-for vaccine manufactured and distributed.

The plan is that the fruit of their labors will be an effective vaccine against SARS-CoV-2 which will be exclusively reserved for Americans.   The plan, according to sources familiar with the plan, is to have 100 million doses available this November and the other 200 million in December and January of next year.   

The project initially focused on 14 candidates selected from the 110 or so possible vaccines that have emerged in the past few months.   That list of 14 was narrowed to eight, chosen in part because they represent different technologies, or platforms, as they are called.   Much of the focus thus far has been on just two technologies.   One constructed with the messenger RNA encoding the corona virus surface proteins that form the spike, or crown.   The other uses an adenovirus (one of the viruses that causes the common cold) to carry a protein that has the capacity to disable the corona virus.   However, other pathways to disable or eliminate the corona virus are being investigated, and the Operation Warp Speed project will consider these as well.

An official speaking for the project made the point that Warp Speed will not consider pushing any potential vaccines made in China or based on Chinese research, such as the inactivated virus vaccine which was recently shown to protect monkeys from the virus.   However, the winning candidate might well be manufactured by a company that is not headquartered in the United States.

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Warp Speed’s plan, based perhaps as much on hope as on careful preparation, is to have all candidate vaccines in human trials by July of this year.   At the same time, the plan is to conduct large-scale investigations of safety in hamsters and monkeys, in order to winnow out any vaccine that produces significant adverse events. 

In the meantime, the National Institutes of Health (NIH) has an initiative called Accelerating COVID-19 Interventions and Vaccines (ACTIV).   It’s relationship with Warp Speed remains unclear.   ACTIV plans to coordinate clinical trial of several COVID-19 vaccines, and is also considering human challenge studies, in which vaccines would be fast-tracked by immunizing healthy subjects (volunteers, of course) and then deliberately infecting them with SARS-CoV-2 or a weakened version of it.   This, I should hardly need to point out, is highly controversial.   However, a phalanx of courageous volunteers has already come forward.

One promising candidate is a vaccine in development by Moderna, Inc (MRNA).   In early trials it was found that the vaccine, mRNA-1273 produced levels of antibodies in trial subjects similar to those found in blood samples from persons who have recovered from COVID-19.   Moderna is planning to start late stage trials in July.

Other efforts to develop a vaccine include the Coronavirus Global Response, organized by the European Commission.   The World Health Organization (WHO) and other groups have formed the Access to COVID-19 Tools Accelerator.   And the Bill and Melinda Gates Foundation is watching about 15 vaccine candidates and will support the most promising among them.   These initiatives aim to achieve equitable worldwide distribution of vaccines when they become available.   Many experts have expressed concern that the Warp Speed plan, which would restrict any resulting vaccines for use in the US only, would deny access to such vaccines to the most vulnerable populations outside the US.  These concerns led more than 140 world leaders to sign an open letter asking governments to consider Covid-19 vaccines to be a “global good” and ensure equal access when the resource does become available.

What is the real fatality rate?

As of today, May 18, when I am writing this, the total number of confirmed cases of COVID-19 on the planet is 4,758,937, with 316,277 fatalities.   These numbers are certainly inaccurate, since every country tracks these numbers somewhat differently.   They are also certain to constitute a considerable undercount, because not every person was tested who had possible COVID-19 symptoms, nor was every person tested who died in the period since COVID-19 emerged.   

Ecuador stands out as a prime example.   Despite its relatively youthful and generally healthy population, Ecuador experienced a high rate of infection and death due to COVID-19, even based on the official confirmed figures.   However, consider this: between March 1st and April 15th, there were 7,600 more deaths in Ecuador than the average number during that span of time in the pre-COVID-19 years.   The number of deaths that the government had officially attributed to the corona virus during that period was 503.   If many or most of those 7,600 excess deaths were due to COVID-19, it would suggest that the actual COVID-19 fatality rate in Ecuador was as much 15 times higher than the official published rate.   (The term “excess deaths” is the epidemiologists’ terminology for the gap between the observed and normal number of deaths; the rest of us probably consider any deaths at all to be in excess of what is desirable.)

In the US, the indications are that in at least nine states the excess fatality rate has been far above normal.   These include California, Colorado, Illinois, Maryland, Massachusetts, New Jersey, New York, Vermont, and Washington.   New York City alone has reported 13,831 confirmed COVID-19 deaths as well as another 5,408 probably related to COVID, but the excess death gap totaled 24,172, suggesting that there may have been nearly 5,300 unreported COVID deaths,       

New York State has so far tested about 7,500 for corona virus antibodies.     Statewide, nearly 1 in 7 tested positive for the antibodies, and in New York City, the number was higher – 1 in 5 New York City residents tested positive for coronavirus antibodies.   Those results suggest that about 2.7 million people in the state of New York have at this point been infected with the corona virus.

When I look at the ratio between confirmed COVID-19 cases and fatalities in various communities in my part of the country, the discrepancies are quite large, and surprising.   For instance, as of May 13th:

 

Where Confirmed

Cases

Fatalities Percent
Putnam County, NY 1,108 7 0.6
Westchester County ,NY 31,611 1,245 3.4
Fairfield County. CT 13,636 1,068 7.8
New Haven, CT 9,570 745 7.8
Hartford, CT 7,732 973 12.5

These differences probably reflect genuine environmental factors that affect infection rates and fatality rates.   Putnam County is a good deal more rural than Westchester County, thus making it easier for people to maintain social distancing.   In Connecticut, Hartford is more congested than New Haven or Fairfield County.   However, it’s also likely that there are differences in the availability of testing between various areas.   

The COVID-19 fatality rate has hit certain populations particularly hard.   For example, in a veteran’s care facility in New Jersey, 72 people died, more than 10% of the residents – not 10% of the confirmed cases, as we were discussing above, but 10% of the entire population of the facility.   Nursing homes and some hospitals have been disproportionately hit, no doubt due to the extreme difficulty (not to say impossibility) of maintaining distancing between persons, as well as the compromised health of the residents.   For example, 70% of the COVID-19 deaths in the state of Connecticut have occurred in nursing homes or senior care facilities.   The town where I live in Fairfield County has reported about 40 COVID-19 fatalities to date, but 38 of these have been in senior assisted living facilities.      

Housing conditions and living arrangements clearly affect the fatality rate, likely due to difficulties in maintaining distancing.   A person living in a multiple-