The United States of America is the 6th country to host a 2014 West African Ebola virus variant..

v2 01102014 5:51pm AEST

First thing...

CALM DOWN!

This is the first case of Ebola virus infection to arrive in the United States that was not deliberately flown in. Its not the first viral haemorrhagic fever case though (1 case of Marburg virus disease and at least 4 Lassa virus infections and the Reston ebolavirus outbreak among imported animals[3,5]), and none of the earlier infections resulted in secondary transmission among humans; no-one else got infected from by the case.[4]

Countries that have hosted people infected
with the Ebola virus variant causing the
& 2014 West African Ebola virus
disease epidemic.
Click on image to enlarge.

The male is in critical condition.
When he flew from Liberia to the United States (finally arriving in Dallas,Texas). The man was not showing signs of disease when leaving Liberia or on the plane or immediately after arriving.[6]

This means that the man was not infectious - he could not spread it to fellow travellers or airport workers - because it is well known that disease in another does not develop due to virus being shed before disease is obvious in the infected person.

Briefly[1,2]:

• 19th: Departed Liberia, checked and found to be symptom-free
• 20th: Arrived in Dallas, US (connecting flights?)
• 24th: Started to develop symptoms
• 26th: Initially sought care
• 28th: Admitted to hospital in Texas.
• 30th: Texas public health laboratory found Ebola virus this morning of 30th Sept. CDC received samples, tested and confirmed as Ebola virus disease
• Patient is ill and is under intensive care

US family and community contacts (a "handful") are known or being traced and will be under observation/monitoring for 21-days (~21-Oct) for fever. Will any become positive for Ebola virus? Perhaps. I look to Port Harcourt (Nigeria) for some comfort. There were around 60 "high risk" contacts of there and they did not all become ill.

So now we have evidence that supports all those talking heads (me included) who noted that it was possible for sporadic cases of EVD to be imported into countries outside of those in West Africa (Guinea, Liberia, Sierra Leone, Nigeria, Senegal). 

Soon, I very much believe, we will also have evidence that in richer countries with functioning healthcare systems, a good knowledge of what is needed to contain virus infections spread by all possible routes, stocks of the necessary personal protective equipment needed to protect healthcare workers from nosocomial infections and the training to use those stocks...to support that even when such cases arrive, they do not result in outbreaks.

References...

1. https://www.youtube.com/watch?v=6Bxencye1cg&feature=youtu.be
2. http://www.nytimes.com/2014/10/01/health/airline-passenger-with-ebola-is-under-treatment-in-dallas.html?partner=rss&emc=rss&smid=tw-nytimes
3. http://scienceblogs.com/aetiology/2014/08/02/ebola-is-already-in-the-united-states/.
4. http://blogs.scientificamerican.com/molecules-to-medicine/2014/09/30/ebola-in-usno-need-to-panic/?WT.mc_id=SA_sharetool_Twitter
5. http://www.cdc.gov/media/releases/2014/s930-ebola-confirmed-case.html
6. http://news.sciencemag.org/health/2014/09/one-more-ebola-question-dr-frieden-answers-journalists-would-have-first-u-s-case?rss=1

The control gap...

v2 300914

I have a theory.

This theory is meant only to apply to disease outbreak/epidemic/pandemic situations, and then only to those which include fatal cases.

This theory of mine has only emerged since I've been plotting Ebola virus cases numbers from the West African epidemic. I precede the explanation with the caveat that there is very probably already a well developed, well-known actual epidemiology term to describe this theory. But I'm not a trained epidemiologist and this is just a blog, so please forgive me my ignorance.

The theory goes that when a gap grows between the number of new cases being reported and the number of deaths or laboratory confirmations in that population, despite the outbreak having been going for a while, this represents an indication that control of the situation is slipping, or has been lost. 

Mind the gap.

This "control gap" - my term, so don't expect to find it anywhere official or that knows of that which it speaks - can also appear when looking at suspected or probable cases of disease X, and the number of those that have been confirmed by a laboratory test.

Other explanations for the control gap may exist of course; testing may be scaled back deliberately, reporting of deaths may have been deliberately throttled for some political reason. So it may not reflect being "out of control" as much as someone else being "in control".

Probably still more variations that I have not thought of at all.

Ebola virus disease (EVD) in Liberia.

In the graphics below I've used the accumulation of World Health Organization data for Liberia, up to 23-Sept. 

First up - the fold increase in total case numbers (suspect+probable+laboratory confirmed) compared to the fold-increase in the distance between that total and the total number of laboratory confirmed cases alone. This distance, or the "control gap|lab", has widened over time. It has widened because total cases have climbed more steeply than the number given a laboratory confirmed diagnosis of EVD. 

For whatever reason(s), laboratory confirmations are not keeping pace with the total case numbers, and they seemed to start slipping at the end of July. 

I suspect a principal reason - and I'm not on the ground of course, so this is all speculation and second-hand knowledge - is that laboratory capacity is overwhelmed. 

Other reasons include that samples might not always be collected or that many recent clinically defined EVD cases are actually due to something clinically similar to EVD, but not an Ebola virus infection. If it were this last one though, the total numbers would be readjusted downwards as new diagnoses were made...if the laboratory has time to make those of course...so I doubt it as a major role.

The control gap|lab
A.) Ebola virus disease case graph for Liberia showing the accumulation of total (suspect+probable+laboratory confirmed) cases (pink line; left y-axis) and deaths (blue line; left y-axis), the laboratory confirmations (green line; left y-axis) and the proportion of fatal cases (right y-axis) at each reporting date (x-axis). The size of the gap between laboratory confirmed cases and total cases is indicated for a range of reporting dates, using a vertical green drop-line.

B.) The drop-lines have been copied and aligned and the amount they have grown has been measured using a scale bar so that the fold-increase can be compared to the first reporting date used, 8-July. The fold-increase value is written at the top of each drop-line. Along the bottom (enclosed within a grey box) are the case numbers at each reporting date examined and the fold-increase (in bold) compared to the 8-July baseline.

Next up -the fold increase in total case numbers (suspect+probable+laboratory confirmed) compared to the fold-increase in the distance between that total and the total number of deaths. The control gap|deaths comparison finds that the deaths and the total cases don't diverge as much as total cases and lab confirmations do. 

The control gap|deaths
A.) Ebola virus disease case graph for Liberia showing the accumulation of total (suspect+probable+laboratory confirmed) cases (pink line; left y-axis) and deaths (blue line; left y-axis), the laboratory confirmations (green line; left y-axis) and the proportion of fatal cases (right y-axis) at each reporting date (x-axis). The size of the gap between laboratory confirmed cases and deaths is indicated for a range of reporting dates, using a vertical blue drop-line.

B.) The drop-lines have been copied and aligned and the amount they have grown has been measured using a scale bar so that the fold-increase can be compared to the first reporting date used, 8-July. The fold-increase value is written at the top of each drop-line. Along the bottom (enclosed within a grey box) are the number of deaths at each reporting date examined and the fold-increase (in bold) compared to the 8-July baseline.

So with that visualization under our belt, there is another, less laborious way to look at this, by graphing the numbers, rather than the gaps.

What we see when we plot the fold-change values against report date is that total cases lost control as we suspected, but deaths are less obviously out of control. From 9-Sept onwards the gap has widened a little more consistently. Before that though the deaths did not dramatically drift away from the rate at which new cases were being added.

I'll graph Sierra Leone, Guinea and Nigeria in the next day or two. Nigeria should serve as an example of how this looks for a country in which EVD is definitely in control. 

Graphing the control gaps

The fifth I give you...[UPDATED]

Senegal. 
According to it's Minister of Health, Awa Marie Coll Seck[1,2], a case of Ebola virus disease (EVD) has been imported from Guinea and it is confirmed by testing at the World Health Organization's collaboration Centre, the Pasteur Institute in Dakar.

Interesting that this occurred one week after Senegal closed its borders (again) with Guinea.[3,4] The infected 21-year old Guinean student travelled on 21-August to Dakar. On the 23rd he presented to a hospital but did not admit to being in contact with known EVD cases; Guinea issued an alert that a person with EVD contact has escaped surveillance 27-Aug; Senegal closed its borders around 22-August.[5,6,7,8].
[WHO Disease Outbreak News places his movements ahead of the closure of the border, arriving in Senegal 20-Aug [8]]

These borders are leaky and so the effect of "closure" essentially hinders aid, trade and economy (all very important to the region, especially right now) but very clearly does may not stop the spread of human hosts-as we have seen here. 

Humans are the variable in outbreaks. 

They behave differently each time. 

They respond differently each time. 

This is why no two outbreaks are identical. 

It's why you're a mug to assume this outbreak will be like the last outbreak.

While it looks like this is now a case study in why closing a border is ineffective, I maintain a position that border closures can't contain infectious disease. And please, do not point me to "temperature measurement" as a way to ensure capture of infected individuals. You could easily be harbouring an infection that does not yet express the symptom of fever. 

Click on image to enlarge. 
Graphic lifted from a great CNN video narrated by
Dr Sanjay Gupta. The video describes an example of
contact tracing and its importance to the fight
to contain EVD.[2] 

The contact tracing starts in Senegal now. A 42-day clock starts for the country and a signs and symptoms watch continues on all this case's contacts for 21-days.

References...

1. http://in.reuters.com/article/2014/08/29/us-health-ebola-senegal-idINKBN0GT1CD20140829?feedType=RSS&feedName=health&utm_source=dlvr.it&utm_medium=twitter&dlvrit=309303
2. http://edition.cnn.com/2014/08/29/health/ebola-outbreak-senegal/
3. http://www.washingtonpost.com/news/world/wp/2014/08/29/the-ebola-virus-has-spread-to-senegal-as-the-deadliest-outbreak-in-history-gets-worse/
4. http://www.washingtonpost.com/world/africa/alarm-grows-as-ebola-outbreak-spurs-more-flight-cancellations-border-closures/2014/08/25/87e6d020-2c66-11e4-994d-202962a9150c_story.html
5. http://www.bbc.com/news/world-africa-28893835
6. http://fox59.com/2014/08/22/senegal-closes-its-borders-with-guinea-over-ebola-fears/
7. https://www.internationalsos.com/ebola/index.cfm?content_id=434&language_id=ENG
8. 
   

Ebola West Africa numbers in context...[AMENDED]

A quick glance at how the suspect, probable and laboratory confirmed (susp/prob/conf) cases of Ebola virus disease (EVD) stack up in the 3 countries with local spread of Zaire ebolavirus.

Please note that I have separated Guinea-2014, Sierra Leone-2014 and Liberia 2014 only to highlight that each country in the single "West Africa" outbreak (involving a single viral variant as far as we know) has greater case numbers than those found in many of the earlier outbreaks.

I have not yet listed the case imported to Nigeria here.

Click on chart to enlarge.

Ebola virus disease (EVD) West Africa update for 02-May, WHO-AFRO update...

Click on image to enlarge.

Thankfully the latest World Health Organisation update includes figures for Liberia. The last West Africa update did not, so I didn't post a chart.

Summary..

Total suspected/probable/confirmed cases: 244
Total suspected/probable/confirmed deaths: 162 (66.4%)
Total lab confirmations: 133 (54.5% of 227)

These figures are very important for two reasons...

Firstly they show a drop in suspect/probable cases after data scrubbing by the Liberian Ministry of Health and Social Welfare. This reinforces that the outbreak is being well controlled.;The date of isolation of the most recent confirmed cases is 30-April from Conakry and Guekedou (Guinea).

Secondly there has been a concomitant rise in the proportion of fatal cases of EVD due toZaire ebolavirus (see the percentages above the orange line in the chart). This is not because the numbers have jumped, it's because the denominator has shrunk for the relevant calculation:

No. EVD fatalities/No. total susp/prob/conf cases.

We've known this rise in proportion was coming because it was highly likely that case numbers would change as the dust settles and the susp/prob EVD patient numbers get discarded because they are found to be infected by something else; clinically similar disease, but not because of infection with Zaire ebolavirus. I've written about it previously if you'd like some background.

With the use of more antibody testing, the numbers will continue to change, as they always do in outbreaks.

This will be my last update on this outbreak linked to the WHO-AFRO announcements unless anything major happens.

A reminder - the chart above is made for general interest. It may be that I have misinterpreted the language in the report (sometimes a little tricky to wade through these reports) but the trends should still be informative even if a number or data point is out of place.


Sources...

1. http://www.who.int/csr/don/don_updates/en/
2. http://reliefweb.int/report/liberia/unicef-liberia-ebola-virus-disease-sitrep-20-2-may-2014
3. http://virologydownunder.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html

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

Ebola virus disease (EVD) outbreak in West Africa: chart of cases to 04-Apr

Data are based on WHO DONs, French Embassy Conakry
 figures and WHO Tweeted information.
Click on image to enlarge.

The Ebola virus disease (EVD) case chart adjacent is based on the latest Disease Outbreak News (DON) from the World Health Organization (WHO) posted at the Global Alert and Response (GAR) site [1] and at the African Regional Office (WHO-AFRO) [2].

There are roughly 163 suspected, probable and laboratory-confirmed cases including 95 deaths (58.3% proportion of fatal cases) for which only 56 (34.4%) have been confirmed by laboratory tetsing.

I'm also maintaining a curated Storify timeline here which lists some key Tweets and links on this outbreak. 

A few things to note about the chart and the outbreak:

1. The susp/prob/conf (shorthand I use on Twitter) numbers change - the 1st 2 numbers can go down as well as up as cases that cannot be laboratory confirmed as due to EVD are discarded from the tally. Other diseases with similar presenting signs and symptoms occur in the West African region so this is not at all unexpected. We see the same thing for other viral outbreaks, like influenzavirus, all the time.
2. The WHO does not posted "grand totals". The DONs present totals for each region (currently Guinea, Sierra Leone and Liberia), which I've tallied up above.
3. Its worth remembering that this outbreak was happening back in early Feb, so there was a passage of time during which people were exposed and did not know precisely what was causing illness. This creates a lag between the time of the first announcement and when the situation can come under some semblance of control. Control requires that the various teams arrive, are coordinated and set up in the area to test, trace, educate and reduce virus spread. Each time a new region has a case, the same flurry of activity may well ensue, so case numbers will seem suddenly spike - but as we can see, they do not continue to rise exponentially, or even at all in some regions. This is thanks to the expert teams including those from the WHO, jurisdictional Ministries of Health, UNICEF, the Red Cross and Médecins Sans Frontières (apologies to all those I've missed - you are all doing a fantastic job under extreme conditions and you are extremely  appreciated)
4. Posts on this outbreak do not occur daily - I presume, as for avian influenza virus outbreaks etc, posting of numbers is based on when those data are collated, summarized and provided to the WHO.
5. There are reports of 4 haemorrhagic fever cases from Mali (some of whom had traveled to Guinea; a suspect case is also reported in Ghana coming from Mali although there are questions about where from precisely) that are not, at writing, laboratory confirmed.[5] Samples are being sent to the United States for confirmation. Why not to the Institute Pasteur in Dakar, or Guinea field labs I do not know; presumably because of pre-existing arrangements?
6. Liberia has 1 suspected EVD case in a hunter who seems to have acquired his infection locally (no contact with know EVD cases or with Guinea). This suggests to me that the vector is actively infected in the region. Perhaps this is a migratory season (seasonal change, following food sources, breeding) for this Ebola virus's animal hosts, previously found to be fruit bats, chimpanzees, gorillas, monkeys, forest antelope and porcupines in particular, eaten as "bushmeat". I admit to knowing nothing about animal movement in the region however.
7. While EVD is "highly contagious", close contact with an infected animal host or an infected human cases' bodily fluids (blood, organs, mucous, urine, vomit, faeces and semen for up to 7-weeks post-infection) is required to acquire an infection. Generally the virus doesn't spread across distance as well or quickly as for example, influenzavirus does. This is largely because the virus is not spread the same way:
• Sneezing and coughing is not considered a method of EVD transmission
• Once the patient is symptomatic, they do not move around as much; from that point, spread of the virus to new people requires those people to come to the ill person. This is why healthcare workers, especially early on in an uncharacterized outbreak, and close family members caring for an ill or deceased relative number highly in new cases of EVD. 
• Basic levels of infection prevention and control can interrupt transmission. These include good hand hygiene, use of personal protective equipment and prevention of needle stick injuries.
8. Airborne transmission is not considered a risk factor for acquiring EVD; this is not the movie Outbreak where the fictional "Motaba" virus mutates into an airborne ebolavirus-like pathogen. Also unlike the movies, bleeding from orifices and the skin can occur, but much more rarely than the movies lead us to believe
9. EVD signs and symptoms start suddenly 2-21-days (8-10 more common[3]) after virus acquisition and usually include fever, headache, joint and muscle aches, weakness, diarrhoea, vomiting, stomach pain, loss of appetite and may also include rash, sore throat, red eyes, hiccups, cough, chest pain, breathing and swallowing difficulties and sometimes internal and external bleeding. Not everyone dies from infection however the higher end of the mortality spectrum for the species Zaire ebolavirus can reach 90% in outbreaks with >1 case identified.[4]
10. A person with no signs or symptoms of disease is not considered contagious.
11. While a border closure (Senegal) and some flight restrictions have come into play, these may only serve to disadvantage the outbreak region rather than provide any true risk mitigation. Closing a border may hinder the flow of food, medical supplies and daily goods as well as interrupting the normal commerce of the country, impacting both economically and directly on the lives of the overwhelming majority of people who are not infected. I'm not aware of any evidence that shows closing a border has any reducing effect on an Ebola outbreak. Closures are a knee-jerk reaction caused by the fear of a scary disease.

And that last point is an important one. Ebola evokes some scary images outside of Africa. And so it's important for us not to run around like a decapitated Gallus gallus domesticus. We need to rein in the excessive over-reaction. As Maryn McKenna aptly noted recently over on Superbug, many things are killing more people, more regularly every day both in and outside of Africa. Having said that, I can totally understand the reactions of those living inside of West Africa just now. Among them, those who both have or have never looked this pathogen in its filovirusy-eye and stared down the barrel of its disease before. 

Viruses can be pretty scary things indeed.

References..

1. WHO Global Alert and Response (GAR) Disease Outbreak News (DONs) Articles
   http://www.who.int/csr/don/en/
2. WHO African Regional Office (WHO-AFRO)
   http://www.afro.who.int/en/media-centre/pressreleases.html
3. Signs and symptoms of EVD or Ebola haemorrhagic fever (HF) from US Centers for Disease Control and Prevention
   http://www.cdc.gov/vhf/ebola/symptoms/index.html
4. WHO EVD fact sheet
   http://www.who.int/mediacentre/factsheets/fs103/en/
5. WHO AFRO EVD West Africa SitRep for 4-April-2014
   http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4079-ebola-virus-disease-west-africa-5-april-2014.html
6. A Patient in Minnesota Has Lassa Haemorrhagic Fever. (Don’t Panic.)
   http://www.wired.com/2014/04/minnesota-lassa/