The filovirus tree has been shooting wildly

While there are not a lot of new branches, there are many, many new leaves on this growing tree. That is overwhelmingly due to the fantastic work of Dr Pardis Sabeti, and Stephen Gire at the Sabeti lab, Harvard University, and their many collaborators. 

It sounds like even more sequences will be coming out in the future. This group is the face of the molecular epidemiology of history's largest Ebola virus disease epidemic in Sierra Leone. If a team of scientists could be said to embody an aspect of an epidemic, it has been these guys and their virus characterization. Hugely impressive stuff.

I only wish we could see more Guinean and Liberian sequences - they are both hugely under-represented in this tree of complete genomes downloaded from GenBank a week or so ago.

Click on tree to enlarge even further.
Coloured boxes surround those sequences generated during the
2014 EVD epidemic. Orange boxes point out the nearest neighbours
and the year from which the sample that was sequenced, originated.
The West African Ebola virus Makona variant has been
traced back to sharing an ancestor in common with a 2007
variant in 2004.

References

1. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC.
   Science. 2014 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28.

Mali makes it 6 countries in the West African Ebola virus disease epidemic

v2 251014

The 6th country in the West African outbreak to host a case of Ebola virus disease (EVD) in 2014, is Mali.

The case was a 2-year old girl who was symptomatic while still in Guinea.

She travelled with her grandmother >1,000km by public transport to Bamako (Capital city of Mali), setting out 19-Oct. WHO are treating the situation as an emergency; there were multiple opportunities for exposure. The case's mother may have died of EVD in Guinea and her grandmother may have travelled from Mali to Guinea to attend the funeral.

The case had contact with health services in Kayes, western Mali, on 20-Oct. She was referred and admitted to a paediatric ward of Fousseyni Daou Hospital 21-Oct with a fever of 39’C, cough, bleeding from nose and blood in her stool). Tests were negative for malaria but positive for typhoid fever. Pain relief was given but there was no improvement. 

Further tests confirmed EBOV 23-Oct at the SEREFO (Center for TB and AIDS Research) laboratory in Mali.

Samples are being sent to a WHO-approved laboratory for confirmation.

The girl has since died.[2]

The 2014 West African epidemic and Central African outbreak of EVD.
Click on image to enlarge. Feel free to use and share this map
(please attribute to this blog).
NB: Nigeria (19-Oct) and Senegal (17-Oct) were declared EVD free.

References..

1. http://www.who.int/mediacentre/news/ebola/24-october-2014/en/
2. http://www.bbc.co.uk/news/world-africa-29755443

Update on Ebola virus disease (EVD) case accumulation chart with new WHO African Regional Office data...[UPDATED].

UPDATED with 2 Sierra Leone probable deaths.
Click on image to enlarge

Not much of a change to be seen with the data from WHO following that from UNICEF yesterday.

No Species Zaire ebolavirus cases have been confirmed in Sierra Leone nor any in Mali (6 suspected cases however; 2 other samples tested negative) or elsewhere. 

Click on image to enlarge.
Maps purchased from maptorian and adapted by VDU

EVD cases are still restricted to Guinea and Liberia and all cases remain linked to infections in Guinea. 

As I understood the recent WHO virtual press conference, because the index case was known, the transmission chain of contacts is mostly already under observation. While Ebola virus disease (EVD) has a grisly progression, once experts are in place to help track, test and educate, with the help of local and international governments, the spread of EVD can be contained. 

But it will still take time to be sure the outbreak has been contained; 2 full incubation periods worth of time.[3] As the maximum incubation period is 21-days (2-21 days being the full range), you start to see why the WHO speaks in terms of "months" [2,3] before the outbreak can be considered over. And that clock starts sometime around the end of the last case's disease onset I'd guess.

“We fully expect to be engaged in this outbreak for another two, three, four months”

Dr Kenji Fukuda, WHO[3]

So as the outbreak comes under control, as seems to be the case, we should pay attention to when new cases stop appearing. Then it becomes about waiting until everyone can safely say there are no new cases.

The most recent case had an onset of illness on 08-April-2014.

Sources...

1. WHO-AFRO Ebola virus disease, West Africa (Situation as of 10 April 2014)http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4093-ebola-virus-disease-west-africa-10-april-2014.html
2. Ebola expected to terrorise West Africa for ‘months’–WHO - Euronewshttp://www.euronews.com/2014/04/09/ebola-expected-to-terrorise-west-africa-for-months-who/
3. Officials Say Ebola Outbreak Could Last Months - Timehttp://time.com/54299/officials-say-ebola-outbreak-could-last-months/

Update on Ebola virus disease (EVD) case accumulation chart with new UNICEF data...

Click on chart to enlarge.

Thanks to a UNICEF Australia's update I've added a few cases to the produce a new chart; I expect we'll see some WHO numbers soon, and I'll update if there are any differences.

Check the version number in the bottom left hand corner - it defines whether it is the only chart of the day from VDU, or one of several.

The new version shows the proportion of fatal cases holding fairly steady at ~60% of all cases. This calculation includes those cases that also that look like EVD but have not been laboratory confirmed as EVD, as well as those that have been confirmed.

As I went into yesterday, these are very volatile numbers, so regard this chart for its trends only.

Sources...

1. UNICEF Australia's PDF of numbers from ~3-hours ago
   http://ow.ly/d/24bM