Lake Erie HABs

Jeff Reutter of the Ohio Sea Grant, gave a nice talk this week on the causes of Lake Erie’s Harmful Algal Blooms (HABs), including last weekend’s incident that affected Toledo’s water supply. He’s been focused on this and other issues for four decades and gives great talks.

Ebola epidemiology data scraper

Note: The following post is current as of WHO report of 09-18-14, which includes data to 09-14-14. [I’ve altered this code a number of times because of the nearly constantly changing format and location of the WHO data.]

I wanted to find certain statistics for the West African Ebolavirus (EBV) outbreak from its inception, e.g. recent case and death rates. By “recent” I mean at WHO GAR reporting intervals, typically a few days. But the sites where I’d expect to find such (WHO, CDC etc) didn’t have them, at least in a synthesized form. So, I wrote an R script to scrape, compile, rearrange, and plot the data, for any country or all together, as taken from two sources. Starting with the WHO July 1 GAR report, tables of new and cumulative cases and deaths, categorized by degree of certainty, for each of the three countries in the outbreak, are given. Wikipedia has a less detailed table for all dates from March 25 on. I used it to obtain total cases and deaths up to July 1.

Below are graphs of the recent, per-day (1) case rates, and (2) death rates, from March 22. Each shows the raw data (thinner line), and a loess-fitted trend (thicker line). Note that reporting issues are partly, perhaps largely, responsible for extreme fluctuations in the raw data.

Ebola case recent rates 2q
Ebola death recent rates 2q

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Ebola references (updated)

This is an abbreviated list of freely accessible, Ebola-related articles. Some are specific to the current outbreak, others are more general, some traditional science articles and others good online articles. [There are also a couple of useful links in the article below.] There will likely be a large number of articles emerging, potentially very large, given the nature of the situation.

1. Scientific literature and reports:
Atherstone et al., 2014. Ebola risk assessment in the pig value chain in Uganda (a good article, much more comprehensive than the title would indicate!)

Baize et al, 2014. Emergence of Zaire Ebola Virus Disease in Guinea-Preliminary Report

Bausch et al., 2014. Outbreak of Ebola Virus Disease in Guinea: Where Ecology Meets Economy.

CDC Mortality and Morbidity Weekly Reports, 2014. Ebola Viral Disease Outbreak — West Africa.

Dudas and Rambaugh, 2014. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak.

Feldman et al, 2003. Ebola virus: from discovery to vaccine.

Gatherer, 2014, (in press). The 2014 Ebola virus disease outbreak in west Africa

Legrand et al., E&I, 2007. Understanding the dynamics of Ebola epidemics.

Leroy et al., 2001. Early immune responses accompanying human asymptomatic Ebola infections

Muyembe et al., 2012. Ebola virus outbreaks in Africa: Past and present

Vanessa and Matthias, 2012. Infection Control During Filoviral Hemorrhagic Fever Outbreaks

2. Web pages:
WHO, 2014. Ebola virus disease, West Africa – update 10 July 2014

WHO, 2014. EBV FAQ

Laden, G., 2014. Ebola Outbreak in West Africa: Some basic information (Updated)

Black, 2014, on-site reporting (doctor with DWB, on scene in Sierra Leone), In the Shadow of Ebola and The First 24 Hour Shift

Poon, 2014, WUNC Radio. Ebola 101: The Facts Behind A Frightening Virus.

Ebola update

The West Africa Ebola epidemic is not waning. The latest (July 6) numbers from the WHO show that about 5.6% of the total cases (including probable and suspect cases), and 4.6% of the deaths, originated just in the four days from July 3 to July 6, inclusive. The minimum mortality rates are 350/626 (56%) for confirmed cases, and 543/894 (61%) when also including probable and suspect cases. The epidemic appears to be moving out of Guinea, and into Liberia and Sierra Leone, based on the recently reported cases. The WHO Ebola FAQ is here if you want to learn more about it, but on the outbreak itself there appears to be a serious dearth of reliable information.

  Country  Date   Type New* Confirmed Probable Suspect Total
1  Guinea 07_08  Cases    0       294       96      18   408
2 Liberia 07_08  Cases   16        63       30      38   131
3    S.L. 07_08  Cases   34       269       34       2   305
4   Total 07_08  Cases   50       626      160      58   844
5  Guinea 07_08 Deaths    2       195       96      16   307
6 Liberia 07_08 Deaths    9        41       28      15    84
7    S.L. 07_08 Deaths   14       114       11       2   127
8   Total 07_08 Deaths   25       350      135      33   518
#  *New cases (reported since 07_03) are neither classified nor included in Total

Updated values as of 7-10-14:

  Country  Date   Type New* Confirmed Probable Suspect Total
1  Guinea 07_10  Cases    1       296       96      17   409
2 Liberia 07_10  Cases   11        70       32      40   142
3    S.L. 07_10  Cases   32       298       34       5   337
4   Total 07_10  Cases   44       664      162      62   888
5  Guinea 07_10 Deaths    2       197       96      16   309
6 Liberia 07_10 Deaths    4        44       28      16    88
7    S.L. 07_10 Deaths   15       127       11       4   142
8   Total 07_10 Deaths   21       368      135      36   539
#   *New cases (reported since 07_08) are neither classified nor included in Total

1. New articles, both good, on Doctors Without Borders and The Economist web sites.

2. The Wikipedia page on the topic contains a summary table of the weekly course of reported cases and deaths since March.