Archive for category Coronavirus
Dear students of 2035,
Fifteen years ago, possibly before you were born, the world experienced a deadly pandemic with a virus we called “Covid.” You undoubtedly have heard the word, but it’s unlikely you received an explanation of what happened. Those of us born in the 1950’s, heard the words “World War II”, but no one explained that either — a previous generation expects you to know such things by a data download from your mother’s brain directly to your brain at birth. By the way, that method of learning does not exist.
In the last few months of 2019 a virus popped into existence in Wuhan, China. We believe it was a zoonotic infection that jumped from local bats to humans. The virus spread from China to the rest of the world over the course of about six months, despite efforts to stop it.
Many millions of people were infected, and over a million died. In fact, statistics revealed about 3% of the infected died. We faced the daunting task of protecting people from the virus while inventing a vaccine for the seven billion people living on Earth.
As strange as this seems, it took many months for humans to believe a pandemic was attacking. Although scientists warned the public very early in the disaster, the leaders and general public were skeptical of science (not a new phenomenon when bad news is involved).
The recorded history of the 1918 pandemic fell on deaf ears. Years of health department plans to fight a pandemic were discarded in the belief that things would be better 100 years later — we had evolved, our science was better, our drugs were better and our hospitals were better. Lack of a drug against Covid was an inconvenient detail.
Covid spread by the air in tiny particles exhaled or coughed by a victim. Consequently, infectious disease experts told the population in no-uncertain-terms to wear masks, avoid crowded indoor spaces, keep a six foot distance from other people and restrict travel from regions with outbreaks. Well, some listened, many did not. The pandemic simply would not stop given the inconsistent efforts to protect people from spread. We blamed everybody and everything and no one took responsibility.
Older people were very sensitive to the disease. 90% who died were over age 65. Strong isolation measures caused high unemployment in working-age people, and the economy faltered. Many leaders adopted a strategy of reducing health restrictions to allow younger people to work while older people isolated themselves. Older people were cautious, resisting airline travel, cruises, vacations, and restaurant dining — the strategy did not repair the economy or reduce deaths.
An old concept of “herd immunity” was touted by some, although scientists emphasized that seeking such immunity would lead to vastly more deaths. Nevertheless, Sweden championed a laissez-faire strategy causing hundreds of unnecessary deaths, compared to strict measures in neighboring Denmark. The rest of the world was somewhere between.
Governments supported vaccine companies with cash and promises of high profits later. In record time, multiple vaccines were invented and manufactured. However, the task of making enough for seven billion people was a big problem.
As the first experimental vaccines came from the pharmaceutical production lines in late 2020, scientists demanded testing to prove that an effective vaccine would be delivered, one that prevented death from Covid. But politicians just wanted something, anything, jabbed into angry citizens clamoring for “a vaccine.” At the same time, “anti-vaxers” were frightened of the vaccine and refused to take it. As the debate about vaccines flared, people continued to die, hospitals were stressed, and grave diggers worked overtime.
~~ TO BE CONTINUED~~
Imagine the following:
“Sir, this is director Smith, I must inform you we have initiated BIOCON 4. Please confirm.”
The President wiped beads of sweat from his brow. “I confirm BIOCON 4. What is going on?”
Smith stuttered slightly. “Sir, we have reports of numerous virus infections in Laos, at over one hundred dead. Our team will be parachuting to the site as soon as the supersonic transport arrives on scene, probably in a couple of hours.”
The scenario sounds like science fiction — is that because a rapid response is not possible? Would the military fail to respond to DEFCON 1? Unlikely.
In 1962, three years after Alaska became a state, NORAD issued details of the plan to respond to a nuclear missile attack. They were very serious and ready. Included on page 41 of the report was a plan for a biologic warning system – not much happened.
In 2005 President George W. Bush became concerned about viral pandemics, particularly Influenza. His administration issued a call to be prepared — not much happened.
Around 1960 the US military developed the DEFCON (defense readiness condition) strategy to inform the military and the nation about an impending attack.
In the 2010’s several organizations developed bio-threat plans similar to DEFCON, but none at high levels in the government.
>> BIOCON <<
The DEFCON system appears to have survived where biologic emergency plans have failed. It is logical to have a similar system for pandemics or bio-terrorism. Below is such a readiness scheme.
|BIOCON 1||Infection spreading in the US||Shelter at home. Institute financial stabilization measures. Delivery vehicles and drivers to wear PPE.|
|BIOCON 2||Outbreak involves multiple countries||Close borders. Make 300 million test kits and distribute. Notify hospitals to prepare for pandemic cases. Open reserve ICU beds.|
|BIOCON 3||Outbreak spreads over over 50 miles||Distribute stockpiled PPE, ventilators and medications as appropriate. Make at least 1 million test kits and distribute to states.|
|BIOCON 4||Outbreak involves over100 people||Obtain DNA sequence. Start vaccine production. Notify all Dept. of Health each State. Start vaccinations if available. Manufacture test kits.|
|BIOCON 5||Limited outbreak in foreign country||Send team to investigate. Stop all travel from that country. Quarantine all travelers who otherwise arrive from region.|
China has run the gauntlet with the novel Coronavirus. They do not report any new cases now and the population is cautiously and gradually returning to normal activity. China has reported on the number of cases and deaths despite very difficult times. One problem they have had as will other countries is how to report deaths that did not happen in a hospital or without testing to verify the presence of COVID-19.
The main question currently in the United states is when will the population be free from restrictions to stay at home? As mentioned in the previous post the experience from china gives some clues. The following are two graphs; the first shows an overview of number of new cases over time (left axis) and the number of deaths (right axis). The data becomes erratic at the peak of the curve when the hospitals and healthcare workers were overwhelmed. The bell-shaped red is a fairly good fit to the number of new cases. The yellow curve is from a similar effort at fitting a curve (see below) to the numbers of deaths per day.
The disease started sometime at the end of December 2019 and spread. Millions of people were confined to their residences finally leading to no new cases about 2 months later. The peak of cases happened around February 8 while the peak of deaths was about 1 week later. The deaths subsided about 2 weeks after the peak, marking continued hospital overload and a reservoir of virus that could escape and threaten the population again.
China has been criticized for the reporting of deaths, and the irregularities are easy to see around the peak of deaths probably related to a saturation of the health care system. Patients likely died at home since admission to hospitals was not possible and furthermore an exact diagnosis based on PCR testing was lacking. Nevertheless, the picture is sufficiently clear to be a guide for other countries regarding what to expect.
In a region such a one of the States in the US several milestones should be reached before social distancing is eased:
- No new cases in a State
- Borders to the State remain closed if adjacent states still have active cases (people could leave states but would likely need 2 weeks of quarantine if they return).
- Hospitals only have a few remaining cases of COVID-19 patients and have the staffing to receive emergencies if needed (this could take about 2 weeks from the last new case).
- The State Health department has the capacity to rapidly trace any new cases and institute strict quarantine.
- Adequate and rapid viral testing is available to the health department and physicians.
Social distancing allowed many persons to avoid infection, associated illness and death. A resurgence of COVID-19 is easily possible in the populations of uninfected individuals.
Healthcare workers and any other workers who have survived the illness could return to work at any time, even now. They are at very low risk due to the immunity developed to clear the virus from their bodies. At some point, a test for immune status based on antibodies present in the blood would be helpful because a large number of persons were probably infected and not diagnosed at the time with PCR testing (the mouth or nose swab). Persons with adequate antibodies also could safely return to work now.
So what does the crystal ball suggest: many people will be returning to work toward the end of April, 2020. There will be states that lag because the virus started in those states later — that’s going to be a difficult pill to swallow. Predictions about what will happen are subject to lots of unknowns. With time, the end-game will be more clear.
At the height of the novel Coronavirus infection the transmission rate is about one to three. Meaning that one person infects three. When that rate drops from three to less than one then the virus is losing ground and will fade away. When no new cases happen then the virus has no way to reproduce and is gone (yea!).
An individual who contracts the virus (sorry) the illness lasts about two weeks. A small percent (less than 2%) may die. The good news is that surviving the virus means the body fought it off leaving lots of antibodies floating around in the blood to prevent reinfection with the same virus (at least for several years).
The initial fear was that the virus might mutate (change it’s structure) quickly so that a person’s antibodies would not be effective for very long. Fortunately for humans, the little devil does not seem to mutate quickly (needs more observation to be sure). Surviving persons cut the transmission rate since they don’t catch the virus.
That brings us back to the original question: exactly when will the pandemic end? We can only guess because the answer is up to the virus and how well people avoid each other. Effective drugs against this virus or immunizations are simply not available now and almost certainly will not be available for at least a year (perhaps in 2021).
Did you say guess? Yes. So let’s make an educated guess. China was a huge experiment. In that country the virus went away (with great effort) in about sixty days. That’s roughly what to expect in the United States.
The Chinese experience revealed the course of the virus followed a ubiquitous mathematical progression called a Gaussian curve, otherwise known as the “bell-shaped curve”. The number of new cases goes up, hits a peak and then declines. The mathematical equation for the Gaussian curve is a little complicated:
y = a * exp( 0 – (x – b)^2 / (2 * c^2))
where y it the number of cases on the vertical axis
x is the day on the horizontal axis (1,2,3,4,5…)
a is the height of the peak
b is the day where the peak happens
c is the width of the bell.
Once some of the actual data is known (e.g. the numbers of new cases) a curve fitting program can figure out a,b and c. Here is an example for the State of Colorado in the United States at the time this post was written: (see updated graphs at end of post)
In the graph the blue dots are the number of new cases each day and the red line is the Gaussian curve fitted to the available data. The best “guess” is that new cases will stop at the end of April where the red curve hits zero. Of course, the medical havoc from the virus in those final few people infected would last for another two weeks. The peak of new cases happens at about April 5th. Unfortunately, the peak of deaths occurs about a week after the peak of new cases.
The end of new cases for the United States overall is more complicated than China since the virus started in the various states at different times. The sum of all the bell-shaped curves from each State may create a US curve that shows several small delayed peaks or just a skewed curve with a longer tail on the right side — time will tell.
Once the virus has subsided in one area it is possible a flare-up could happen due to travel of infected persons into an area that had many non-infected people. If that happens, the State health department should quickly quarantine the area — another mini bell-shaped curve will happen in that area.
Whether the virus will come back later this year or next year or never is unknown. If it does, many people will be immune and laboratories may have a greater ability to test for it. Hopefully pharmaceutical companies will manufacture an immunization. Is this the last pandemic? NO. We must do a better job of preparation and acting on the warning signs. Will humans remember this lesson? (no answer).
Updated graph of cases per day in Colorado, USA as of 4-14-2020
Update for Colorado, USA as of 4-21-20
Observation: as more testing is done more asymptomatic cases are being found. This has the effect of hiding stay-at-home measures with an artifactual bump in numbers if new cases. The aberration should be less with time and with lower number of cases. At this point many analysts believe the rate of hospitalizations may be the best indicator of disease activity. Steve Goodman, Stanford Professor of Epidemiology & Medicine, gave an interview to KPIX, a local TV station 3/25/2020, supporting the importance of hospitalization data:
A graph of current COVID-19 cases is below and now includes hospitalizations (and a 4-point smoothing curve).
Update for Colorado, USA as of 5-1-2020
Today the state will begin to allow some workers to return to work and stores to offer limited (curbside) service. The new case and new hospitalization data have reached a variable level that is much lower than most models (without stay-at-home orders) predicted. The stay-at-home strategy appears to have reached the goal of “flattening” the curve. Unfortunately, restrictions of movement are being lessened while the virus is still at peak activity. An additional concern both nationally and in Colorado is the late reporting of cases which has muddied the waters.
Some modeling experts predict a resurgence is in the offing. Below is the latest graph without the Gaussian prediction for new cases and with the use of a 7-day smoothing (necessary due to the erratic reporting). The “dump” of “unreported” deaths confuses the overall picture — such deaths probably happened over several weeks, not on one day.
The success of stopping the virus in New Zealand, Australia, Vietnam and China was due to forceful stay-at-home orders. In Colorado and the US as a whole, such force of law and will is lacking and stems from a huge concern about economics. The sentiment among retired people is to stay-at-home to minimize risk; consequently, many new deaths will likely be in members of the workforce.
At the start of this post the “assumption” was the US would try to stop the virus. That made predicting an “end” a reasonable endeavor — now that is no longer the case and some time will need to pass for a new pattern to emerge. Only when hospitalizations are near zero will we feel Colorado is close to the end of the pandemic.