Looking at SARS CoV-2

By Chuck | Published Saturday 21-Mar, 2020

Data as of 10 AM 21-March:

Covid 19 CasesCasesDeathsParishes
Louisiana5851629
St. Mary
World286,81611,837
United States19,775276
Italy47,0214,032

Today we will take at look at the SARS CoV 2 virus which is the causative agent of the Covid-19 outbreak. As scientists have more time to study the virus, since it has moved outside of China, information on it is growing.

First off, lets address the conspiracy theorists out there who claim the SARS CoV 2 virus is a product of Chinese or other military labs. Information released yesterday by the Scripps Research Institute shows the virus is of natural origin.

“By comparing the available genome sequence data for known coronavirus strains, we can firmly determine that SARS-CoV-2 originated through natural processes,” said Kristian Andersen, PhD, associate professor of immunology and microbiology at Scripps, and lead author on the paper, “The proximal origin of SARS-CoV-2,” . Anderson, along with coauthors Robert F. Garry, Tulane University; Edward Holmes, University of Sydney; Andrew Rambaut, University of Edinburgh; and W. Ian Lipkin, Columbia University say SARS CoV 2 show no evidence of being created in a laboratory or engineered in any form.

This is a computer generated image of the spike protein that acts as the key to unlock the human ACE2 receptor found on many human pulmonary cells. Courtesy: Cell Magazine

Evidence shows the SARS CoV 2 virus is a mingling in many ways of the SARS CoV virus and the MERS virus. The strongest evidence of natural evolution came from the receptor-binding domain of the SARS CoV 2 virus, which has evolved over time to very selectively bind to the human ACE2 receptor, found on many human cells including those in the respiratory system. The receptor-binding domain is also known as the SARS CoV 2 “spike protein.” The virus binds so well that scientists say it could only be the result of “natural selection.”

As to SARS CoV 2 itself, we are finally seeing some actual photos of the virus. All of the following come from electron microscope imagery:

Image of a single SARS CoV 2 virus from the Smorodintsev Research Institute of Influenza in Russia. Note the bar on the bottom which is equal to 200 nano meters (nm). For reference, there are 1 billion nano meters in one meter.
Transmission electron microscope image of SARS CoV 2 viruses, with their spike proteins, exiting a cell which the virus hijacked to reproduce itself. Courtesy: NIAID-RML
A group of SARS CoV 2 viruses, yellow, cluster on growth medium in this electron microscopic image. Courtesy: NIAID-RML

Thus, SARS-CoV-2 virus belongs to the genera of Beta Coronaviruses, in the order of Nidovirales, family of Coronaviridae and sub-family of Orthocoronavirinae. It is round or elliptical with a diameter of approximately 100 nm.

Here is an amazing graphic of the structure of the SARS CoV 2 virus from a recent article in the Economist.

As we can see, the virus is a very simple design. It is composed of a lipid membrane capsule, which surrounds a nucleocapsid protein that contains the RNA sequence of about 30,000 base pairs. On the outside of the capsule are the spike proteins, which so easily bind to the ACE2 receptors of human cells, especially those in the respiratory system.

It is amazing that something so small, so simple, and non-living, has in a matter of weeks brought the world to its knees. Yet, we are only in the infancy of this outbreak. How long it lasts, and we need to hope it is stretched out over months, and how severe the implications, lay with how well we as citizens can abide by the restrictions put in place.

The future of the outbreak, specifically how bad it gets, is in all of our hands. Hopefully, we have the resolve to recognize the common good above personal need and want and do what is asked. Because barring a vaccine, likely at least a year away, social distancing and isolation is the only answer.

Stay safe and follow the orders of federal, state and local health officials.

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How Much Damage can One Person Do?

By Chuck | Published Thursday 19-Mar, 2020

Here is the data update for Thursday, 19-March.

LocationCasesDeaths Parishes
Louisiana347817
United States9514141
World222,6429,106
Italy31,5062,978
St Mary Parish00

Today we will take a look at South Korea and the story of the now infamous “Patient 31.” As a relatively small country, both in land mass and population, South Korea has led the world in limiting the effects of the Covid-19 outbreak. They did this through a huge testing campaign, tracking of all of those who had been in contact with anyone known to be infected, and strong self-isolation policies to prevent spread. It is the tracking of how many people each infected person came in contact with, which provides the answer to the question posed above: “How much damage can one person do?”

The first eleven cases in South Korea were traced back to having come in contact with between two and one hundred people. A lot of exposure and many of those contacted became future cases but nothing out of the ordinary. Then came Patients 12 and 14, a married couple who came in contact with 425 people. The first major community spread. Patient 16 would be in contact with 450 people themselves, becoming the largest spreader of the disease to that point. Patients 17-30 would only be in contact with between 10 and 40 people each before they were isolated.

Then came Patient 31, a 61-year-old woman, who was to become the focus of her own major outbreak. It is not known when the woman was infected. However, we do know that on 2-Jan, she visited the C-Club in Seoul, South Korea, a club purportedly tied to the Shincheonji church. Seoul, a city of just under 10 million is in the northern part of the country. The Shincheonji Church of Jesus is a secretive sect that believes the churches founder Lee Man-hee is the returned Jesus Christ and Lee is the only person who can interpret the secret metaphors of the Bible. It has over 300,00 followers in South Korea.

On 6-Feb, Patient 31 was involved in a motor vehicle accident in the southern city of Daegu after visiting a C-Club there. Daegu is a city of 2.5 million in the North Gyeongsang Province. On 7-Feb, Patient 31 was hospitalized in Saeronan Oriental Medicine Hospital in Daegu. The following day, she traveled home and collected personal belongings before returning to the hospital.

On 9-Feb, Patient 31 left Saeronan Hospital of her own accord and attended two hours of services at Shincheonji Church of Jesus in Daegu, before returning to the hospital. She began running a fever on 10-Feb. On 15-Feb, doctors strongly suggested that she be tested for the SAR CoV-2 virus. She refused, instead taking a taxi from the hospital to the Queen Vell Hotel, where she had lunch with a friend or friends then took at taxi back to the hospital. The next day, she was again advised to be tested for the coronavirus but refused and again traveled from the hospital to two hours of services at Shincheonji Church of Jesus in Daegu. On leaving the services, she traveled to a local clinic where she was tested for SAR CoV-2, before returning to the hospital. At this point, she transferred to Daegu Medical Center where on 17-Feb she was notified she had tested positive, becoming Patient 31 in Korea.

In her wandering travels, Patient 31 came in contact with a known 1,160 persons and untold others. She brought the disease to two hospitals and a clinic, as well as Shincheonji Church of Jesus in Daegu. In the following days, Daegu and the Shincheonji Church of Jesus there would become the nexus for the spread of Covid-19 in South Korea

Courtesy Reuters

The map above shows the impact one person had on the outbreak in South Korea. Daegu is the large blue circle in southern Korea. Seoul with five times the population is one of the small circles in the north. One person can clearly make a difference and have a huge impact on outbreaks. Patient 31 surely did!

Stay safe. Self-isolate and follow the directives of state, local and federal officials.

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Covid-19 Update

By Chuck | Published Wednesday 18-Mar, 2020

Covid-19 Update
3:00 PM 18-MarCasesDeathsParishes
Louisiana257713
St. Mary Parish00 
United States7,324108
Italy35,7132,978
World212,5948,726

Above are the numbers as of mid-afternoon on Wednesday. I will likely be blogging daily during the coming weeks tracking the progress of the outbreak and providing information from verifiable and peer-reviewed data and studies on the outbreak. I am including Italy in the update numbers because they unfortunately are about two weeks ahead of the rest of the western word in this outbreak. They are the best indication of how this will progress and an example of how bad things can get.

All indications are that we are at a critical inflection point in the US outbreak. How well we self-isolate and stay away from gatherings over the next two weeks will determine how devastating this outbreak will become. It seems completely illogical but we want this outbreak to drag on. A longer duration outbreak, with a slower rise in cases over months is far more palatable to the continued nearly vertical slope in the number of confirmed cases. If we do not “flatten the curve,” the number of those critically ill with Covid-19 will outstrip the number of critical care beds in Louisiana and the US as a whole. We could be put in the position Italy now fines itself, where they are literally having to decide who gets ventilators and ICU beds and who does not. Who dies and who does not. As the governor and president have said, how we act as a state and nation in the coming two weeks will determine just how bad things get.

The graph above says it all. If by self-isolating someone prevents one case of Covid-19 today, it will prevent 2,200 new cases in next 30 days. If we say “oh its not that bad” and wait a week before preventing that one case, we only prevent 500 new cases. A difference of say 700 cases. That is how fast this virus spreads!

We are all seeing the number of cases climb exponentially in Louisiana and across the US and world. But even those numbers are somewhat deceiving. Let’s look at Louisiana. We now have 257 confirmed cases. That is based on just under 600 people being tested in Louisiana. There are over 4 million people in Louisiana. Of those positive tests, 40% are in people under the age of 50. They were tested because they either were exposed or had symptoms. But, in that age demographic, most healthy people do not have serious symptoms from the virus and may not even know they have it. So imagine the number of people who likely have the virus in that age group but have no idea or are just treating their illness as a cold or the flu. Each person out there infected, unknowingly, will lead to 2200 new cases in 30 days. The impact is staggering.

We must also remember that Covid-19 has an incubation period of somewhere between 5 and 14 days. That means it could be a week or more between when you are infected and begin to show symptoms. But by the second or third day, your body begins to shed the virus to your surroundings. All the while, you are spreading the disease and do not even know it. And once you see the onset of symptoms, they will initially resemble a run of the mill upper respiratory infection possibly leading to even more people becoming infected pending testing. The bottom line is that those who acquire the virus are likely to spread it for up to 10 days before they are aware they are a threat. This is why Governor Edwards said today we must all assume we have the virus and do not know it, if we are to flatten the curve.

The graphic above is from the World Health Organization and shows the symptoms associated with Covid-19. For the most part, they are the same as any upper respiratory infection, bronchitis or pneumonia. If you have any of these symptoms, contact your health care provider, If you do not have a doctor, call 211 in Louisiana for a referral. Only be identifying and isolating those with the virus will we ever slow its growth.

I will close with another great graphic countering the sentiment still seen online that Covid-19 is no different than seasonal flu outbreaks.

This graphic clearly demonstrates the Covid-19 outbreak is twice as contagious as the flu, has an incubation period up to four times longer, is nine times more likely to lead to hospitalization and is up to 34 times more deadly. This is far worse than the seasonal flu! And by the way, the seasonal flu will affect 30 million in the US this year and kill around 20,000. And we have a vaccine for it.

Finally, there are stories all over the internet that ibuprofen may make a Covid-19 infection worse. This is baseless. The World Health Organization and US Centers for Disease Control and Prevention both said today that there is no scientific basis for this claim and ibuprofen is a perfectly reasonable alternative to acetaminophen, especially for those who cannot use Tylenol and other acetaminophen products.

Until next time, stay safe and flatten the curve by following the recommendations of state and federal officials.

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A Different Threat

By Chuck | Published Monday 16-Mar, 2020

We are still months away from the hurricane season, yet dark clouds are still approaching rapidly. Just as I have used CajunWx to keep friends and family informed about happenings in the Gulf and tropics, I felt it might be a good idea to also discuss the coronavirus crisis. As with tropical weather, I do not portend to be an expert in virology or infectious diseases. That said a decade of emergency room and trauma nursing along with lifelong studies do make it possible for me to wade through the ocean of scientific papers pouring in on the coronavirus and decern trends in the information.

Probably the best place to start is the name, or rather names, of this outbreak. I say this after watching a trained doctor on one of the networks leave all viewers more confused than when they started. The common name of “coronavirus” stems from the fact that the virus which causes the current outbreak comes from the family called coronaviridae, Latin for coronavirus. The specific name of the virus is SARS CoV-2 which basically means it is “Severe Acute Respiratory Syndrome Coronavirus #2.” While it is closely related to the SARS CoV virus which caused the outbreak that infected 8,098 people in 2002, killing 774, the current outbreak involves a “novel” or new virus. Thus the new name. Finally, we also name major outbreaks of infectious disease. In this case, the disease outbreak is known as Covid-19, the coronavirus outbreak originating in 2019.

So now that we know the names associated with the outbreak, let’s begin with what a virus actually is. At its simplest, a virus is a non-living particle, which carries DNA or RNA, and must hijack a living cell to make it do the work of reproduction. The structure of a virus is quite simple, with most having only three components: The first is a strand of either DNA or RNA which holds the code for reproducing the virus. The second is a protein shell or capsule which surrounds the genetic material and protects it. Finally, on the surface of the capsule will be a number of receptors which allow the virus to bond to living cells. There is no metabolism or life, just the ability to reprogram a cell. This means you cannot truly ever “kill” a virus, as it was never alive. You can though render it safe by a number of means. Heat, disinfectants and such work well as does just common soap.

A representation of SARS CoV-2

The SARS CoV-2 virus would look something like the image above if we were able to take a look at it. But that would take a specialized piece of equipment known as an electron microscope. The SAR CoV-2 virus is about 120 nanometers across. As there 1000 nanometers in a micron, we can see that the virus is quite small. The spikes that cover the surface of the virus are its key to entering the body. Those spikes work like a key when they find a cell in the body with an ACE2 receptor. ACE2 stands for the angiotensin-converting enzyme-2 but don’t worry about what that is, just that the majority of the cells in the human respiratory tract have such receptors.

The diagram above from The Economist shows how the virus uses the ACE-2 receptors to enter into human cells and take over the cell machinery to make it produce thousands and thousands of copies of the virus until the cell literally bursts to spread the new viruses through the body. Each new virus particle then attempts to hijack another cell and the process continues until the body builds a sufficient immune response to fight off the assault.

How easily is Sars CoV-2 transmitted? To determine this, scientists use a mathematical calculation known as R0 or R naught. R0 basically measures how many people will be infected by a single infected person. If the R0 for an infectious agent is less than one, then the disease is likely not to spread and eventually die out. If the R0 is equal to one, the one new infection will occur for each old one. Such diseases will stay alive and stable but will not become an epidemic. When R0 is greater than one, we have the potential for an epidemic.

So how does SARS CoV-2 stack up? The R0 for the MERS outbreak was less than one. The flu has an R0 of 1.3, around that of the common cold. The ebola virus has an R0 of 2.0, mumps an R0 of 4.7, and smallpox an R0 of 7.0. The R0 based on numbers from China for the SAR CoV-2 virus was set at 2.2, meaning every infected person passes the disease on to another 2.2 people. As we get more data out of Europe, it appears the SARS CoV-2 R0 may be closer to 2.7 to 3.0. Only time and more data will tell.

Another item related to the R0 concept of disease transmission is that it only relates to those who have no natural immunity for the infectious agent. In other words, even though the R0 for the flu is 1.3, major outbreaks are rare because of both natural immunity from previous exposure and the widespread use of a vaccine. However, in 1918 the world saw an outbreak of the H1N1 flu variant, at the time a novel strain which had never been seen before by man. The R0 of the Spanish Flu as it was called, was around 2.1, but due to the lack of natural immunity and the war-ravaged state of the world, it claimed over 20 million lives. Therein lies the rub with SARS CoV-2, it has a relatively high R0 of say 2.2 – 3.0, and the world population has no natural immunity. We also lack a vaccine, with the nearest likely a year off, or any drugs which effectively fight the disease process. The state of mankind’s health and medical technology are far beyond 1918 but this outbreak will likely continue to grow unchecked without strict isolation procedures. Basically, we are just beginning to see the ravaging effects of SARS CoV-2 and will be living with it for months to over a year. Current estimates by the CDC say 30-90 million Americans could be infected before we are done!

But how deadly is the Covid-19 outbreak? Some articles on the internet would have you believe it is less deadly than the seasonal flu. They are wrong. Covid-19 tends to kill about 3.5% of those who are infected. The seasonal flu, on the other hand, has a mortality rate of just 0.1%. And once again the Covid-19 death rate is based mostly on data out of China, while the data out of Europe is showing that 3.5% may be too low. So the Covid-19 outbreak is far more deadly than the seasonal flu. It is also worth noting that even with a vaccine and natural immunity, over 34 million will be infected and 20,000 die this year from the seasonal flu in the United States alone. Add in a multiplier of 35, the difference between 3.5% and 0.1%, and Covid-19 could claim up to 700,000 lives before it is done.

Put in the above context and taking into consideration the ease with which Covid-19 spreads and its high mortality rate, along with what is happening in Europe, which is a mere two-weeks further along in this than us, and we are likely in for a long haul. Further restrictions, including the suspension of flights and even travel, are possible if not probable. This is also not something which will play out in weeks but rather months. The world is facing a crisis, unlike anything it has seen in over 100 years. Yes, it is scary. But the more we learn about the science of SARS CoV-2 and Covid-19, the easier it is for us to accept the restrictions which are likely to come. I will follow up in the coming days and weeks as number change and we gain more clarity. For now, listen to government officials. Isolate as much as you can and pray something slows this deadly juggernaught!

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It’s That Time of Year Again!

By Chuck | Published Monday 21-May, 2018

While we have not yet reached June 1 and the official start of the 2018 Atlantic Hurricane Season, it looks like nature may be poised to jump the gun by a few days. Models have been hinting for about a week that something might try to form near the Yucatan Peninsula and move into the Gulf of Mexico late this week into the Memorial Day Weekend. The most consistent indicator of a developing system has been the European Model, which also happens to be arguably the best model for tropical systems. The US based GFS model has also hinted at a developing system but had a tougher job nailing down what it might do. Things have become a bit clearer over the weekend though as we now have several models pointing to development in the central to eastern Gulf by mid- to late week and some sort of system moving inland over the Memorial Day weekend.

The European ECMWF Model is still the most solid, showing a 996 mb system with winds near 40 knots approaching the Louisiana coast mid-weekend. There are a couple items of interest in this image of the 0000 UTC run of the Euro. The familiar bulls-eye of a surface low centered just about due south of Atchafalaya Bay is pretty obvious. But note the rain pattern. The heaviest rains early Sunday morning would be from the mouth of the Mississippi River to the north shore of Lake Pontchartrain, as well as over much of Florida. This is due to the fact that the system will likely not become very organized until it nears the coast, where waters are much warmer. Until then it is just a disorganized low with lots of rain mostly on the east side and with much less to the west.

If we move ahead with the Euro, we see that early Monday morning, the system is a little better organized, even with its proximity to land, showing a more concentric pattern, lower pressure of 994 mb, and winds over 40 knots. By early Tuesday morning, the system is now near Lake Charles with a central pressure of 993 mb and winds still near 40 knots. It is only on Tuesday, image to left, that the rain from the system separates from the moisture plume over Florida. It is this quirk, a sort of double system which seems to be giving the GFS  problems. However, as of this morning, the Canadian “CFS”  and the US Navy “NAVGEM” models. are both showing a similar system, though those models lie a bit east of the Euro, from the mouth of the Mississippi to the Mississippi Gulf Coast. But all then move it westward along the coast through early next week.

So what does all this mean? Keep a close eye on the weather as the week progresses and you make plans for the weekend, especially Sunday. It is still way to early to know if or where a system may form. Regardless, there is a strong likelihood that the Northern Gulf Coast and Florida will very likely get some rain and wind for the second half of the Memorial Day Weekend into early next week. As the system is projected to be a slow mover to the west, there will likely be heavy rainfall in certain areas, along with gusty winds and heavy thunderstorms in the impacted parts of the coastline. As with most early season systems, it is the rainfall which is likely to be the biggest problem. Also, expect these landfall projections to change as the week progresses. Everywhere, from Key West to the coastal bend of Texas could see some impacts from whatever forms. For the moment we are sort of in the center of things is about all we can say for now.

Finally, the way this system is projected to develop: that being a disorganized system which gets stronger as it approaches the coast is also what most of the major hurricane prognosticators are projecting for this hurricane season. We will likely see fewer storms form way out in the Atlantic and track for days across the ocean. This is due to cooler waters in the eastern and central Atlantic. However, waters in the Gulf, northwestern Caribbean and along the Atlantic seaboard are projected to be warmer than normal. So we may see more homegrown systems in the Gulf, NW Caribbean and western Atlantic. That may keep overall numbers down, but mean more system which do form impact the US. Time will tell? For now all eyes to the Gulf this week as we see what plays out. I will update mid-week or sooner as conditions warrant.

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