Why do we need to go to full-scale military mobilisation to stop Ebola?

I posted last week that we need to move to full-scale military mobilisation if we are going to stop the current Ebola outbreak. After having some discussions about this on HN I thought that I should explain in more detail why we need to use the military and why we need full-scale mobilisation.

Scale of Problem

The problem is far beyond what any non-military organisation can deal with. This recent post from Les Roberts who is leading the WHO response in Freetown, Sierra Leone explains the scale of the problem.

The prediction landscape is looking bad. The official numbers reported are laboratory confirmed cases. Typically, we think people need 7-10ish days to become symptomatic. Typically people have symptoms for 7 days before they get into a health facility. A month ago, it was one day, now it typically takes 4 days from when a patient is sampled to when the patient is told the result of their test (and lots get lost and mislabeled….). Thus, the numbers that you hear about new cases today reflect the transmission dynamics from over 2 weeks ago…..and we thought the doubling time of the outbreak was 30 days, it seems to be less than that here. We knew the ~350 confirmed cases last week were an undercount….we now think there are 7-900 in reality. The need for hospital beds is climbing more than the ability to get them up and running. There might be 200ish ebola treatment beds now countrywide. There are perhaps 600 more in “holding areas.” We have schemes to get 500 or 600 ebola treatment beds up and running over the next 8 weeks. As Foreign Medical Team Coordinator, helping to get these beds up and supported is one of my primary tasks. If there are really 3000 cases this month, and 6000 next month…with all going perfectly on the treatment bed establishment side, we will have 30% of the beds we need next month, slightly worse than the situation now.

Need for effective quarantine

If we are going to get on top of the outbreak we need effective quarantine in the affected areas. Given the geographical scale of the outbreak, the poor infrastructure, and the limited local policing and military forces available, we need to bring in a lot of troops to do this. We also need to provide protection for the healthcare personnel and assist them in getting the sick out of homes and into treatment facilities. Only the military can provide this support.

Need for large numbers of healthcare personnel

We need thousands of doctors and nurses to run the treatment facilities. While we may get enough volunteers, the required numbers could soon exceed the number of volunteers we can recruit. If we run out of volunteers we would need to conscript the needed personnel and doing this would be impossible unless full-scale mobilisation had been authorised.

Toxic politics

Only full-scale mobilisation is going to short-circuit the political games being played. We have seen how hard politically it has been to get even a token number of USA troops deployed to west Africa. To send 40,000 or 80,000 troops and the associated healthcare personnel would be impossible in the current political climate. The only way to get the needed resources on the ground would be to effectively declare Ebola an international emergency and use the war powers available to Obama to do what needs to be done.

My fear is that we are not going to do this until the problem gets so huge that it will be beyond the world’s military to handle. The problem is doubling in size every 20 − 30 days, so each month of delay is making the problem more than twice as big. This is all without considering the risk of an Ebola strain arising that it is more infectious. Time to get serious.

Ebola: What needs to be done right now

I am a scientist with a background in Microbiology and Virology and what is happening (or more importantly what is not happening) with the current Ebola outbreak is very worrying. Rather than just scare my family I thought I should do a write up about what needs to be done.

Figure 1. Scale of the Ebola outbreak October 2014 (source WHO).

Where are we right now?

Ebola is completely out of control and the case numbers are doubling every 20 days or so. It does not look like Ebola had changed (it certainly could), it has just overwhelmed the containment systems we had in place in west Africa. The hospitals in the affected areas have reached (exceed) capacity and are not able to take in any new patients so the virus is running wild (this point seems to have been reached around August). A consequence of this is we really have a very poor idea of the number of cases since no-one is recording the cases that don’t make it to hospital.

What is going to happen?

Ebola is actually a very well studied virus from an epidemiological perspective so we can model its spread quite accurately. Here is what is going to happen according to the CDC.


Figure 2. Estimated impact of delaying intervention* on daily number of Ebola cases, with and without correction for underreporting† — EbolaResponse modeling tool, Liberia, 2014–2015 (source CDC).

* Intervention: Starting on September 23, 2014 (day 181 in model), and for the next 30 days, the percentage of all patients in Ebola treatment units was increased from 10% to 13%. This percentage was again increased on October 23, 2014 (day 211 in model) to 25%, on November 22, 2014 (day 241 in model) to 40%, and finally on December 22, 2014 (day 271 in model) to 70%. Day 1 in model is March 3, 2014. The impact of a delay of starting the increase in interventions was then estimated by twice repeating the above scenario but setting the start day on either October 23, 2014, or November 22, 2014.
† Corrected for potential underreporting by multiplying reported cases by a factor of 2.5 (Table 4).
§ New Ebola patients at peak of each start date. (Note that when the intervention is started on November 22, 2014, the peak is not reached by January 20, 2014, which is the last date included in the model.)

The only thing missing from this modelling is the “do nothing” option since the CDC has assumed that we will start doing something by November 22nd (unlikely). They have also been too scared to model past January 2015.

This modelling also assumes that the virus does not become better adapted to spread in humans which could, and may even be likely, to happen. The most probable adaption would not be for Ebola to become airborne (this is only slightly less likely than pigs becoming airborne), but for the virus to slow down in the speed in which it kills people so they stay infectious for a longer period of time. A strain could arise that takes a month to kill you (rather than a week) and where you are asymptomatic, but infectious, for a couple of weeks. Such a strain would allow each patient to infect many more people before they died or recovered. One of the reasons that Ebola has not caused major outbreaks in the past is that it kills so rapidly that there is little time for each patient to infect new people. The selection pressure on Ebola to slow the speed in which it kills is extremely strong and the more people infected the more likely it becomes that such a mutation will occur.

Why did this Ebola outbreak get so bad?

This is a good question as it is not the first Ebola outbreak. The best explanation I have seen is from the discoverer of Ebola, Professor Piot, as quoted in De Spiegel.

SPIEGEL: Why did WHO react so late?

Piot: On the one hand, it was because their African regional office isn’t staffed with the most capable people but with political appointees. And the headquarters in Geneva suffered large budget cuts that had been agreed to by member states. The department for hemorrhagic fever and the one responsible for the management of epidemic emergencies were hit hard. But since August, WHO has regained a leadership role.

What do we need to do to stop Ebola?

We need to get the R0 below 1. This means each infected person needs to infects less than one new person. Right now the R0 is somewhere between 2 and 10 (i.e. each infected person is infecting between 2 to 10 new people). To get the R0 of Ebola below 1 we need to move at least 70% of infected people into properly functioning infection control hospitals. Sounds easy doesn’t it?

How do we actually do this?

This outbreak is now beyond the ability of the governments in the affected areas, the WHO, or any NGO to bring under control (the head of MSF has stated that the outbreak is now beyond their ability to deal with). There is only one option left which is full-scale military mobilisation. In practicable terms this is what needs to happen:

  • The UN Security Council needs to authorise the use of all available resources to control and contain the outbreak in the affected countries and surrounding regions including the use of international military force. This needs to be done as soon as possible (days not weeks).
  • Those countries with the ability to do this (the USA mostly) need to move to full-scale military mobilisation (i.e. war level)*. This may require conscription of the required healthcare workers, but if we are lucky and act soon we might be able to get by with just volunteers.
  • Start an outside-in Ebola containment/infection control process in the region. This will require putting large numbers of troops and medical personnel on the ground in the surrounding countries and then moving into the worst affected areas as more hospitalisation capacity is brought online. The key is to fight Ebola where it can be controlled so that it does not spread further and not waste our resources fighting it in those areas where we can’t get the R0 below 1 (i.e. where we can’t achieve the required 70% hospitalisation rate).

*Why do we need mobilisation? In theory we don’t, but politics in the USA is so toxic that unless this is treated as war it won’t be possible to get the required resource on the ground quickly enough. An example of this is the 3000 troops announced a couple of weeks back that were going to be sent to Liberia to help have still not left as they are being held up by congress as politics is played.

What do I think will actually happen?

A lot of dithering and token efforts from the UN and the rest of the world until January 2015 when wholesale panic sets in and we then move to full-scale mobilisation. If we are lucky the virus won’t have mutated and will only destroy west Africa. By the end of 2015 a 100 million people could be dead and the world in a massive recession as international trade grinds to a halt. Of course I could be wrong (I certainly hope I am), but based on what I know and what I see happening (or more importantly not happening) I am not that hopeful. Time to get serious.

Install R on CentOS 5 x64 using yum

I recently had the fun of installing R on my development box. While you can install from source I wanted to be able to install using yum. R is not in the standard packages, but it is in the epel repository (Extra Packages for Enterprise Linux 5 – x86_64).

Steps for Installing R
1. Make sure that you have epel in your yum repositories (use yum listrepo to check). If not add epel to your yum repos (see here for instructions how to do this).
2. Install R and dependencies using yum install R-core R-2*
3. Enter R (just type R) and update all the default package using update.packages(). You will need to choose the nearest mirror to you.
4. Install the packages you need using install.packages(“package_name”, dependencies = TRUE)
5. Quit R using q()

Hope this saves someone a little time.

If you are behind a proxy server then use the following (change for your proxy setting) after starting R
You can check if correct by
then update by