Saturday, January 25, 2020

"The Unforgiving Math That Stops Epidemics"

We've added China's Global Times' real-time update site to the blogroll at right: Coronavirus Updates.
Here are four hours of the latest timestamps (Beijing time):
9:07pm Jan 25 Beijing will suspend all tour group businesses, including outbound tours, starting Monday.

8:00 pm Jan 25 5 new cases of Wuhan Coronavirus infection confirmed in Beijing. Two had no history of exposure in Hubei Province.

7:35 pm Jan 25 Central Politburo of Communist Party of China sets up Party-leading working group to deal with Wuhan Coronavirus.

6:28 pm Jan 25 Northwest China's Qinghai and Northeast China's Jilin raised their public health emergency response to level I to curb Wuhan Coronavirus.

6:03 pm Jan 25 Northwest China's Shaanxi raised its public emergency response to highest level on Sat afternoon, the 26th province to do so in the country.

5:52 pm Jan 25 A latest research from Peking University suggests that the intermediate host of the Wuhan Coronavirus may be mink. And the virus may have an infection similar to that of SARS: The Beijing News

5:47 pm Jan 25 Northwest China's Qinghai Province confirmed its first case of Wuhan Coronavirus infection. The patient is in stable condition.

5:40 pm Jan 25 Chinese health authorities announced that at least 1, 355 confirmed cases of pneumonia caused by the novel coronavirus had been reported in the country as of 5:40 pm on Sat. The pneumonia situation had resulted in 41 deaths.

5:35 pm Jan 25 Northwest China’s Qinghai Province confirmed its first case of Wuhan Coronavirus infection. The patient is in stable condition.

5:28 pm Jan 25 Fever clinics in all Wuhan hospitals will accept patients for 24 hours starting Sunday.

5:20 pm Jan 25 Wuhan to build a second special hospital with 1,300 beds within half a month for people infected with novel coronavirus
And a repost from October 2017:
Coincidentally with the news of the plague epidemic in the post immediately below, Quanta Magazine is leading off their current issue with the headline story.

From what I understand, the plague vaccine is not as effective as some other disease vaccines, for example polio, a focus of the Bill and Melinda Gates Foundation, which Mr. Gates this week said should be eradicated by the end of this year rather than the 2018 target the Foundation was using as recently as June.

Back to the plague, according to the Centers for Disease Control the efficacy of the vaccine is in question because of the lack of follow-up studies, so treatment with hard core antibiotics such as Cipro or Levaquin is probably the best bet in plague affected areas. Oddly enough one of my MD's is one of the go-to guys for tropical and infectious diseases, ebola etc. but I couldn't reach him before posting this piece.
Anyhoo, on to the big brains at Quanta:

If you didn't get a flu shot, you are endangering more than just your own health. Calculations of herd immunity against common diseases don't make exceptions.
As the annual flu season approaches, medical professionals are again encouraging people to get flu shots. Perhaps you are among those who rationalize skipping the shot on the grounds that “I never get the flu” or “if I get sick, I get sick” or “I’m healthy, so I’ll get over it.” What you might not realize is that these vaccination campaigns for flu and other diseases are about much more than your health. They’re about achieving a collective resistance to disease that goes beyond individual well-being — and that is governed by mathematical principles unforgiving of unwise individual choices.

When talking about vaccination and disease control, health authorities often invoke “herd immunity.” This term refers to the level of immunity in a population that’s needed to prevent an outbreak from happening. Low levels of herd immunity are often associated with epidemics, such as the measles outbreak in 2014-2015 that was traced to exposures at Disneyland in California. A study investigating cases from that outbreak demonstrated that measles vaccination rates in the exposed population may have been as low as 50 percent. This number was far below the threshold needed for herd immunity to measles, and it put the population at risk of disease.

The necessary level of immunity in the population isn’t the same for every disease. For measles, a very high level of immunity needs to be maintained to prevent its transmission because the measles virus is possibly the most contagious known organism. If people infected with measles enter a population with no existing immunity to it, they will on average each infect 12 to 18 others. Each of those infections will in turn cause 12 to 18 more, and so on until the number of individuals who are susceptible to the virus but haven’t caught it yet is down to almost zero. The number of people infected by each contagious individual is known as the “basic reproduction number” of a particular microbe (abbreviated R0), and it varies widely among germs. The calculated R0 of the West African Ebola outbreak was found to be around 2 in a 2014 publication, similar to the R0 computed for the 1918 influenza pandemic based on historical data.

If the Ebola virus’s R0 sounds surprisingly low to you, that’s probably because you have been misled by the often hysterical reporting about the disease. The reality is that the virus is highly infectious only in the late stages of the disease, when people are extremely ill with it. The ones most likely to be infected by an Ebola patient are caregivers, doctors, nurses and burial workers — because they are the ones most likely to be present when the patients are “hottest” and most likely to transmit the disease. The scenario of an infectious Ebola patient boarding an aircraft and passing on the disease to other passengers is extremely unlikely because an infectious patient would be too sick to fly. In fact, we know of cases of travelers who were incubating Ebola virus while flying, and they produced no secondary cases during those flights.

Note that the R0 isn’t related to how severe an infection is, but to how efficiently it spreads. Ebola killed about 40 percent of those infected in West Africa, while the 1918 influenza epidemic had a case-fatality rate of about 2.5 percent. In contrast, polio and smallpox historically spread to about 5 to 7 people each, which puts them in the same range as the modern-day HIV virus and pertussis (the bacterium that causes whooping cough).

Determining the R0 of a particular microbe is a matter of more than academic interest. If you know how many secondary cases to expect from each infected person, you can figure out the level of herd immunity needed in the population to keep the microbe from spreading. This is calculated by taking the reciprocal of R0 and subtracting it from 1. For measles, with an R0 of 12 to 18, you need somewhere between 92 percent (1 – 1/12) and 95 percent (1 – 1/18) of the population to have effective immunity to keep the virus from spreading. For flu, it’s much lower — only around 50 percent. And yet we rarely attain even that level of immunity with vaccination....