MAP and Stats: track the spread of Coronoavirus

8 Comments

1. JustaSinner says:

   31 January 2020 at 11:27 AM

   Who is the patron Saint of Epidemiologists? Maybe we lay people can take a hand at this and ask Bishop Sheen to intercede on humanity’s behalf and head this pandemic off.

   [A strong contender would be St. Aloysius Gonzaga, who cared for the contagiously ill in the 1591 Plague in Rome, caught it, and died from it.]

   
2. chantgirl says:

   31 January 2020 at 1:09 PM

   There is a video on Liveleak.com entitled “Coronavirus Wuhan” which purports to show the chaotic scene inside a health center in Wuhan. I won’t link to it here because Liveleaks has a ton of smut on it, due to it being a pretty open platform that people can upload to. However, people in China are having a difficult time posting anything about the virus without it being censored, so a platform like Liveleak may be one of the few places they could post.

   The video shows what looks like a minimum of 150 people on the floor of a Chinese treatment center while medical personnel walk around in white coats observing them. The poor people are writhing around, having severe spasms, screaming, while the medical personnel do nothing but watch them. IF the video is authentic, it appears that this virus does more than cause pneumonia. IF authentic, it appears to show that the virus attacks the central nervous system as well.

   IF the video was authentic, we need to be praying and fasting for these people in a SERIOUS way. They appear to be suffering severely, with no priests to give them the sacraments. It is horrific.

   Again, PLEASE only search out the video if you can avoid looking at the smut ads on the page.

   Fr. Z, I understand if you don’t post this comment. I just think that people need as much information as possible to be prepared for the possibility of what their families could be facing.
3. The Masked Chicken says:

   31 January 2020 at 2:19 PM

   Since I’m writing some papers in mathematical epidemiology at the moment (including one on the 1962 Laughter Epidemic in Tanganyika), I thought I would explain a few terms that might crop up in the news, if anyone is interested.

   1. Ro. The most important number in disease spread is the Ro (pronounced, R-naught), which is the Basic Reproduction Number. It measures, on average, the number of persons an infected person will infect. If Ro is less than 1, the disease will die out, naturally. If Ro is greater than 1 (i.e., an infected person infects one or more subsequent people), the disease, without intervention, will likely go either endemic or epidemic.

   The Ro for the Coronavirus has been estimated between 2- 5 (lower by Western experts, higher by Chinese experts). This does NOT mean the world is doomed. The Ro is an average number, based on the idea of what is called the Law of Mass Action, which, basically, assumes uniform random contact between people, but it is known that there is a difference between the ability of, say, a mayor, who comes in contact with tens or hundreds of people a day, to spread the infection and that of a 90 year old house-bound grandmother. The mayor is said to be a Superspreader. So, the idea that every infected person will infect between 2 – 5 people has to be taken with a grain of salt. As more information becomes available, the Ro usually gets smaller. Determining the Ro in real-time with constantly developing data is not only an art, but there is, in fact, no established method to do so. There are several methods in the literature and they all depend on the data available.

   A Harvard epidemiologist, Dr. Eric Feigl-Ding, wrote an alarmist Twitter post that went viral shouting, “HOLY MOTHER OF G*D – the new coronavirus is a 3.8!!! How bad is that reproductive R0 value? It is thermonuclear pandemic level bad – never seen an actual virality coefficient outside of Twitter in my entire career. I’m not exaggerating…”

   In my opinion, he should study the literature a little more. SARS (another coronavirus) has an Ro of 2 – 5, but it did not go pandemic.

   2. Herd Immunity. If a large enough segment of the susceptible population is either vaccinated or recover from the disease (thereby, having immunity, at least temporarily), they will act as blockers in the infection network, cutting off contact between infected and susceptible people (think, Star Trek, The Original Series, episode, That Which Survives, where Kirk blocks Losira’s touch for Sulu, etc). This will cause the infection to die out. Herd Immunity is, nowadays, gotten through mass vaccination. The Herd Immunity Threshold (HIT) depends on the Ro. Here is a chart, from Wikipedia (I don’t know if this will format, properly):

   Disease Transmission R0 HIT
   Measles Airborne 12–18 92–95%
   Pertussi. Airborne droplet 12–17 92–94%
   Diphtheria Saliva 6–7 83–86%
   Rubella Airborne droplet 5–7 80–86%
   Mumps Airborne droplet 4–7 75–86%
   SARS 2–5 50–80%
   Ebola Bodily fluids 1.5–2.5 33–60%
   Influenza Airborne droplet 1.5–1.8 33–44%

   We, usually, think of infected people being quarantined, but herd immunity is, in effect, a form of quarantining well people from the sick people. If enough people survive this particular coronavirus, it will, eventually, die out due to herd immunity, whether or not a vaccine can be developed, soon.

   3. SEIR Model of Infection. In studying the spread of a disease, it is common to split the population into groups or “compartments”. S stands for those who are Susceptible; E stands for those who have been Exposed, but are not yet showing symptoms; I stands for the Infected and showing symptoms; R stands for those who have Recovered (or died). Knowing such things as the incubation period, the infection period, the total population, and the age and travel patterns of people, it is possible to develop a model of the rise and fall of the disease.

   4. Droplet transmission. The flu and many viral infections (including the Coronavirus) are spread by sneezing, coughing, etc. Why is the flu worse during winter months? We used to think that it was because people were indoors, together, but we now know that that is not the case. We now believe that the cause is the lack of moisture in the air during winter. In the summer months, in the moist air, the virus particles will get attached to water droplets that fall to the ground, but in the dry air during winter, the particles stay suspended in the air for a much longer period. So, one thing that can help prevent droplet infection is to humidify the air.

   5. Zoonosis. This is the jumping of a virus from one species to another. China has a large number of small farms and markets where viruses of animal species can mutate and, occasionally, jump the genome. Once the virus jumps to humans, it usually mutates to become easier to jump from human to human. Coronavirus is slowly taking that pathway.

   For people who have the inclination to read about epidemiology, I highly recommend the site, Springer Link. Because of the high cost of journal subscription, these days, many academic publishing companies have come under fire by scholars. Springer threw a bone to scholars by putting 10,000 of its books and articles on-line for free download. There are several very good books on epidemiology available for free download, including those by Fred Brauer and Maria Martcheva, which survey the mathematical techniques, and the Handbook of Epidemiology, by Wolfgang Ahrens.

   Originally, the Coronavirus was isolated to China and all of the deaths, so far, have been among Chinese citizens. In the early days, a quarantine of Chinese nationals would have halted the disease spread, but because of the variability in incubation period (2 days to 2 weeks), once at least a small population of non-Chinese people become infected, any efforts at quarantine will become ineffective. This is not, however, like the days of the Plague. We understand patterns of disease transmission and have a speed of communication that earlier generations could only dream of. Coronavirus (2019 n-CoV) has a kill rate of only 1 -2 %, so I don’t expect people to be dropping in the streets. It may be a bumpy ride for the next month or so, however.

   The Chicken
4. acardnal says:

   31 January 2020 at 2:27 PM

   There is also a lot of disinformation and misinformation out there on the internet about coronavirus. Facebook took a site down for this very reason or will label them as false. Beware.
5. chantgirl says:

   31 January 2020 at 3:05 PM

   acardnal- Agreed. In the age of the internet, it has become very difficult to decipher fact from fiction. However, for China to quarantine as many people as the population of England, I have to wonder how much worse the outbreak is there than the Party is portraying?
6. Irish Timothy says:

   31 January 2020 at 7:55 PM

   I’m saying a Novena to Our Lady for an end to this virus. I’ll keep praying for those that are sick from this and for the souls of those that have died from it when I pray the rosary each day. That’s what I/we can do. Like anything else in life….it comes down to trust in Our Lady and trust in God.
7. ChrisP says:

   1 February 2020 at 2:53 AM

   A thought: given the spread of the coronavirus and the shut down of transport facilities, what possibility this might affect the Great Global Education thingymajig that PF has called for May? It does start on May 14, one day after the 13th……….
8. Semper Gumby says:

   1 February 2020 at 1:23 PM

   chantgirl: Good question.

   First, acardnal, Masked Chicken and TonyO et al have good points in their comments in this post and others the last several days.

   There is precedent for the Chinese Communists to underreport, such as a few years ago with SARS.

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