Tuesday, 31 March 2015

The weakening pulse of the Ebola monster...

As of this post, some of the most comprehensive publicly available data on an emerging virus is coming out of the Kingdom of Saudi Arabia in relation to the Middle East respiratory syndrome coronavirus (MERS-CoV). Yeah-that's what I said. Even with all the issues I complain about, its more detailed than for other current outbreaks. 

In 2015, China became a major disappointment in its poor publication of data for the avian influenza A(H7N9) virus's 3rd outbreak - choosing to release bulk updates and little to no detail on who, where or when. 

The continuing avian influenza A(H5N1) virus outbreak in Egypt is also a mystery to all but a very few. Something that is a concern I think, for a much larger number.

Data from the Ebola virus hotzone countries in western Africa has also had many ups and downs. This is not at all surprising given the conditions, the extent of mobile communications, the history of the region, the political and social issues, the poor health infrastructure and the speed with which Ebola virus disease (EVD) spread through Guinea, Liberia and Sierra Leone in 2014. Many different patterns have emerged over the past year among these numbers. 

One pattern is the "heartbeat" of EVD cases - the difference in number between update and summary tallies - seen when plotting the data reported by the World Health Organization.

Click on image to enlarge.
The peaks (Wednesdays and Mondays) and troughs in this chart both hide and reveal all sorts of tales. Principal among these is that the pulse is slowing. The life of the EVD epidemic monster is steadily draining away as the courageous aid workers in western Africa, those from within and from outside each afflicted nation, track the monster to its every hideout and starve it of its avenues for escape and further spread. 

It is perhaps the slowest and most painstaking of the phases of this epidemic, but the process still moves forward towards the goal of zero cases and the complete eradication of these particular variants of Zaire ebolavirus, from the planet.

Sunday, 29 March 2015

Where did the MERS-CoV comorbidity and animal contact fields go...? [UPDATED]

Is this the work of the US CDC and other visitors helping the Kingdom of Saudi Arabia (KSA) Ministry of Health (MOH) resolve their Middle East respiratory syndrome coronavirus (MERS-CoV) problem? Is it an arbitrary reporting change by the Command and Control Center (CCC)? Is it someone forgetting to unhide the relevant columns in their spreadsheet?
Changes to the KSA MOH MERS-CoV public 
reporting detail after 17-March-2015.
1. The MERS-CoV graph changed scale and caught up.
2. Three fields disappeared: pre-existing disease, 
animal exposure and contact with a known cases 
within a hospital setting
3. The promise of weekly updates was dangled-
without reference to a host site.
Click on image to enlarge.

I don't know why, but since 17th March, the KSA MOH MERS-CoV reports have stopped posting information about whether each newly announced MERS case had a comorbidity and whether they had animal contact. Granted, the last field was almost always "No" or "Under Investigation" - and thus of little use (we rely almost exclusively on the World Health Organization reports to provide useful animal data) - but I wonder why the MOH has chosen to stop posting even the heading this month? 

The much more epidemiologically significant description of whether the case was an "expat" or a "Saudi" citizen remains - whew! 

And the MOH has continued to do away with all of that pesky detail that might allow an observer to link a death to a previously announced case. Thank goodness we don't have that clutter to deal with - or the details from the found113 which I presume are now completely lost in the sands of time. 

I guess the removal of these latest 2 data fields is just all part of providing the world with more of that full transparency and up-to-date information about this emerging pathogen - like the MOH "News" page - all the latest info you could want from August and earlier is to be found there. 

Oh well, at least you can get the latest from the weekly updates...if Google Translate's efforts can be understood.

It really isn't as hard as it is being made to look to get the reporting aspects right.

Friday, 27 March 2015

Editor's Note #22: Two years old today..

On March 27 2013, around the time of Easter and the school holidays, I gave in to the urgings of my wife, to try this blogging thing. 

And today it's two years later and now very clear to me that writing for fun, but based around what I know in science, will be something I do for many years to come. 

At times it's been tough - or maybe other pressures made it feel tougher than it was - and I've considered stopping and have at times paused. As hard as it was though, I found myself wanting to chime in on stuff and could not stay away. I still find that weird, but it must have been a part of me all along - I just hadn't noticed it until after I turned 40'ish. I'm a bit slow sometimes. 

Turns out that I enjoy writing and I needed a hobby that I enjoy and that helped inform and generated such unexpected positive feedback. Everyone needs that I think. Bit of a shame that the typos don't get fewer but such is life. 

It also turns out that blogging made me resign from my job of 23 years - which just so happens to co-occur with this very date. No, of course my resignation was not for such a simplistic reason, but blogging was one of a few major factors that set the process in motion. In particular, blogging about outbreaks of Middle East respiratory syndrome coronavirus (MERS-CoV), avian influenza A(H7N9) virus and the Ebola virus disease epidemic in West Africa. It was that last one that really had the greatest impact on me though. 

From blogging has come more interactions with the media (something I am now a firm believer in more scientists needing to do-communicate what we do to our stakeholders), new collaborations, papers, strange discussions with affiliate Institutes about why they'd rather me not link them in print or press to this press or these papers since I had no research funding for these viruses, friendly discussions with very high ranking Health officials, advice to documentary makers and then an invited role helping out my State's public health team. That one was the kicker. The feeling that the virology information and patterns I'd spent years accruing and piecing together in my head, and now blogging about and drawing graphs and graphics to describe, could be used for the greater good completely ruined me. But in a good way. It triggered many realisations about my current role, some were familiar to me as I had been living with them daily for years, others I had felt in the corners of my mind but they were too intangible and just wouldn't coalesce into anything that would describe itself to me and yet others that were patterns I simply didn't see. Told you I was a bit slow sometimes.

You could of course dismiss all of this as the rantings of a failed scientist who - despite an h-index of 32, 80 papers (15 with >100 citations), >400 citations per year for the past 9 years, 14 book chapters, roles as an Associate Editor at the Journal of Clinical Virology, a Section Editor at Biomolecular Detection and Quantification and an Editorial board for Viruses as well as having continuous competitive research grant funding since he was awarded his PhD in 2003 until 2014 - had missed out on achieving most of his recent grant applications. Go right ahead.

I wanted to use what I'd learned for the greater good. Yeah - as a comic nerd that makes even me cringe a little. But that's where I've been heading, knowingly or not, for some years now. Well, soon I'll be a part of a team that cam help me to do that. 

So I wish you a Happy 2nd birthday little VDU. You've helped me to grow and to learn at the rate of a human two year old. And in doing so, I've met and made friends with a lot of great people around the world. For such tiny things, viruses can have such an impact on us. Quite the hobby.

Monday, 23 March 2015

Useful Ebola virus disease graphics...

Good graphics can be really helpful to convey information quickly - and no-one has time to read words anymore right?

The one above came from CNN [1] and presents the number of cases that have been treated in the United States prior to the 11 or so contacts/associates of the last unidentified case being evacuated.

The second one, above, came form the European Centre for Disease Control and Prevention (ECDC).[2] These guys make excellent plane travel/infectious disease maps. This one shows that the UK has kept pace with the US in medical evacuations or repatriations of EVD cases, or suspected cases, from the hotzone in west Africa.


  1. http://edition.cnn.com/2015/03/16/us/new-day-five-things/index.html
  2. http://ecdc.europa.eu/en/healthtopics/ebola_marburg_fevers/Pages/medical-evacuations.aspx

Saturday, 21 March 2015

Liberia enters the next phase of Ebola virus disease (EVD) eradication with a new case...

version 2

What a heartbreaking disappointment this is for the people of Liberia, with a reported new case of EVD in a 44-year old woman who showed signs of disease 15th March and tested positive for Ebola virus on Friday 20th in Monrovia, Liberia.[2,7,8] after more then 3-weeks (28 days or more[6]) with zero new cases and no ongoing, known, transmission of Ebola virus in any county in the country.[5] The previous final case in Liberia tested negative around the 3rd of March (about 17-days ago), when the 42-day clock was started.[5] 

Now it has been stopped. 

Starting it again will await this new case returning a negative test as well as all their contacts (who will be monitored for 21-days) being declared infection- (actually disease-, but I say infection intentionally) free.

And thus we enter the next phase – that of a different type of frustration and heartbreak as countries within the tri-nation hotzone come tantalisingly close to being declared free of known cases of Ebola virus disease (EVD; see how those seemingly pedantic words [1] have added meaning now?) or virus transmission, or in fact succeed only to have a random case pop up from somewhere unexpected or travel across a border causing disappointment for the people of the country, the aid workers and the family and friends of the new case. 

A random case will also trigger all new contact tracing efforts to try and find the source and lock down further spread as quickly as possible. 

There is noise on twitter (see Tweet below) and in the media quoting authorities [6] noting that the case may have been from a sexual contact with a previously infected male. Infectious virus has been found in semen in the past in which it can linger for more than a month [3,4], but this has not been a factor in the timing of release of convalescent males in the recent epidemic. If this is the route of acquisition, then the ensuing costs, scope of the response, risk to a country that had nearly cleared the virus and to the stamina of an Ebola-ravaged country may serve to justify additional testing the future.
The route of acquisition in this latest case remains totally unconfirmed at writing.[7] I'll update this post as I find more details.

My thoughts are with you Liberians – stay strong – it’s a setback to be sure, but you were very close this time and will get there. 

  1. http://unfoundationblog.org/mali-42-days-free-of-ebola-transmission/ 
  2. http://www.bbc.com/news/world-africa-31991748?ocid=socialflow_twitter
  3. http://www.ncbi.nlm.nih.gov/pubmed/25467652
  4. http://virologydownunder.blogspot.com.au/2014/08/ebola-virus-in-semen-is-real-deal.html
  5. http://apps.who.int/ebola/current-situation/ebola-situation-report-18-march-2015
  6. http://www.aljazeera.com/news/2015/03/ebola-case-ends-liberia-countdown-virus-free-150321003004879.html
  7. http://time.com/3753233/ebola-liberia-new-patient/
  8. http://www.nytimes.com/2015/03/21/world/africa/liberia-reports-first-ebola-case-in-weeks.html

Wednesday, 18 March 2015

Catching Ebola: mistakes, messages and madness [amended]

Written by Dr. Ian M. Mackay and Dr. Katherine E. Arden

Despite obvious community and media fear, speculation and exclamation that Ebola virus would enter and spread widely within countries outside the hotzone, such an event did not come to pass in 2014. The early public health messaging on Ebola virus and disease were, for the most part, spot on. 

In 2014 and 2015, thousands of cases of Ebola virus disease (EVD) ravaged Guinea, Sierra Leone and Liberia in 2014 (the "hotzone"). A smaller outbreak was defeated in Nigeria [8] and another distinct Ebola virus variant drove an outbreak of EVD in the Democratic Republic of the Congo[7] - they too controlled spread of the virus. Ebola virus travelled from the hotzone to other countries including Senegal, Nigeria, the United States of America (USA), Mali and most recently, the United Kingdom. It did this by hitching a ride in a usually unknowingly infected human host. 

Over 40 people have been intentionally evacuated or repatriated for observation or more aggressive supportive care - and perhaps the use of experimental therapies - to France, the USA, Spain, Sweden, Norway, Denmark, Germany, Netherlands, Italy, Switzerland and the United Kingdom.[1,18] 

Recently, the last country outside of Africa to have unintentionally acquired a case of EVD, the United Kingdom, passed a milestone; 42 days since the last ill patient tested negative for Ebola virus. They were declared free of known virus transmission.[17]

Containing the spread of each imported case has relied upon stringent infection prevention and control measures and the identification and monitoring of each and every contact of an Ebola virus infected person. And these have been used with great success. No country, apart from the three in which transmission has been widespread and intense, has seen the appearance of multiple and continuing rounds of new EVD cases. A rough calculation of the numbers of contacts falling ill from each EVD index case who travelled outside the hotzone is shown in the table. It only includes those with data available publicly.

On average, fewer than 1 in 100 contacts (0.8%) came down with EVD. Not the easiest virus to catch? If you compare that to measles, 9 in 10 non-immune people close to an infectious measles case will acquire disease (90%).[19]

Table 1. Index cases and the proportion of contacts they infected
a-man travelled overland from Guinea while infected; b-man with EVD repatriated from Liberia; c-man who flew while symptomatic to Lagos, Nigeria with a stopover in Lome, Togo; d-man flew from Liberia while infected; e-male healthcare worker returned from Guinea; f-a 2 year old girl travelling overland while infected; g-male travelled by car to a clinic in Bamako, Mali from Guinea (assumed Ebola case); h-female healthcare worker returning from deployment in Sierra Leone; i-this figure may indicate all contacts for  both Mali cases
The extent of the fear inspired by the first imported EVD case was especially clear from the massive spike in social media content from the United States which followed the arrival from Liberia of an individual with EVD; far more social media activity than had been seen in the United States to that point, or since.[14,10] This month, even though 11 contacts/associates are being flown back to the United States for observation; on the heels of the index case, social media activity has barely responded – in fact Twitter is possibly more positive/neutral about Ebola in the US in March 2015 than in August 2014, rather than excessively fearful, mean or just plain hysterical.[10] 

Some of the heat may have been taken out of the emotional response to Ebola outside Africa because it is now clear that a catastrophic pandemic is not going to happen. Kinda like we were told. I know; it;s so uncool to be reminded that you were told something by a grown up - and it was right! 


Nations with better (some!) healthcare infrastructure, preparedness, healthcare to patient ratios and those who got advice and help quickly, curtailed the spread of EVD. Kicked it out. Stomped on it. Terminated it. This was true even when contacts had been classified as at high risk of getting sick.[15] 

Public health messaging made some big calls early on. Some examples include tweets by Head of Public Relations for the WHO, Gregory Härtl, and later by the Centers for Disease Control and Prevention’s Director, Dr Tom Freiden.[11] They made it clear that Ebola virus was not easy to catch and that measures to stop an outbreak were known.[16] At the time, this didn't jibe with other voices and the unprecedented number of EVD cases and deaths, especially from August onwards, that were tallying up at an exponential rate in west Africa. But those messages, while technically correct, probably didn't convey enough of some of the biggest factors in a disease outbreak - fear, ignorance (meant only in the sense of no specific knowledge of Ebola virus and EVD), tradition and history - the human factors rather than the viral ones. Some comments about transmission suggested essentially no chance of even a single new case happening on the home soil of richer countries - they were overly enthusiastic. They were unjustifiable and when some hospital workers in non-African countries became infected, they were ultimately seen for the mistake in message crafting that they were.

Much of the science of the Ebola epidemic is yet to be written, but what we know today is that it is unlikely that Ebola transmission is any different from what was observed decades ago. Direct, physical contact with a very ill person’s fluids is the overwhelmingly biggest risk factor to target in reducing disease spread. And even then there's no guarantee that disease will result from all instances of contact. We still have much to learn.

What has changed since the bad old days? We’ve learned how to better manage and support EVD cases. EVD is a disease that caught us a little unawares in its combination of "skills" - it spreads by care and through direct contact, accrues a lot of virus in the blood but also vast quantities in explosively propelled fluids produced from "both ends"; virus that remains infectious for even longer in urine and semen than in blood. Quite the mix of issues to deal with.

EVD is no longer a death sentence, and this needs to become part of the new messaging paradigm. It's a message that may still be highly relevant to those in Guinea and Sierra Leone who seemingly would still rather risk death than seek care at a treatment unit. Post-mortem detection of EVD cases is ongoing, although may be on the decrease but also nearly a third of cases in Guinea and Sierra Leone are arising from unknown human sources.[21] Contextual communication is needed from within each country and region. That aspect cannot be allowed to wane. 

With early care, and active care, rather than the palliative model that seemed to occur when the ratio of EVD cases to healthcare workers was too high, patients mostly surviveThe EVD treatment center at the Hastings Police Training School near Freetown, Sierra Leone stands as a model for successful life saving and is the best described example of this from the west Africa epidemic to date.[20]

Ebola virus infection is not easy to catch, it can be survived much more often than was generally accepted and its spread can indeed be stopped. Stopping an Ebola outbreak quickly seems to be helped mostly by prior education, ongoing communication, forewarning and preparation but also needs ongoing surveillance, functional healthcare infrastructure, a range of experienced workers and all of that must all be under-written by money.

But even with all that help in place, mistakes will be made and lessons will be learned, by everyone, all the time. Embrace that. We're all human.


  1. http://www.nytimes.com/interactive/2014/07/31/world/africa/ebola-virus-outbreak-qa.html
  2. http://apps.who.int/iris/bitstream/10665/137510/1/roadmapsitrep_5Nov14_eng.pdf 
  3. http://www.who.int/mediacentre/news/ebola/20-november-2014-mali/en/ 
  4. http://www.who.int/mediacentre/news/ebola/17-october-2014/en/ 
  5. http://www.nyc.gov/html/doh/html/pr/press-statements.shtml 
  6. http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/united-states-imported-case.html 
  7. http://www.nejm.org/doi/full/10.1056/NEJMoa1411099 
  8. http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20920 
  9. http://apps.who.int/ebola/en/status-outbreak/situation-reports/ebola-situation-report-14-january-2015 
  10. http://www.symplur.com/blog/the-life-cycle-of-ebola-on-twitter/ 
  11. http://www.foxnews.com/opinion/2014/08/09/truth-about-ebola-us-risks-and-how-to-stop-it/ 
  12. http://www.nytimes.com/interactive/2014/10/20/us/cascade-of-contacts-from-ebola-case.html 
  13. https://www.gov.uk/government/news/ebola-contact-tracing-underway
  14. http://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(14)62016-X.pdf
  15. http://www.who.int/mediacentre/news/ebola/3-september-2014/en/ 
  16. http://www.bloomberg.com/news/videos/b/4a798222-3666-446d-81ff-f21412a3f068?cmpid=yhoo
  17. http://www.euro.who.int/en/health-topics/emergencies/pages/news/news/2015/03/united-kingdom-is-declared-free-of-ebola-virus-disease/_recache
  18. http://ecdc.europa.eu/en/healthtopics/ebola_marburg_fevers/Pages/medical-evacuations.aspx
  19. http://www.cdc.gov/measles/about/transmission.html
  20. http://www.nejm.org/doi/full/10.1056/NEJMc1413685
  21. http://apps.who.int/iris/bitstream/10665/156273/1/roadmapsitrep_18Mar2015_eng.pdf?ua=1&ua=1

Monday, 9 March 2015

Last country outside the hotzone to pass 42-day period-awaits official announcement...

The United Kingdom (UK) reached the 42-day mark, during which no new known cases resulted from the index case, on the 6th March 2015. 

The UK's accidentally imported Ebola virus disease (EVD) case, a female healthcare worker returning from deployment in Sierra Leone [1], last tested negative for Ebola virus on 23rd of January. She was discharged from hospital on 24th of January.[2]

Timeline of the UK EVD case. 
Green=onset; pink=hospitalization; blue=date of final NEG test on which the 42-day clock started; grey box=country considered, if not yet declared, free of known ongoing Ebola virus transmission.
Click on image to enlarge

All that remains now is for an official announcement...from someone (else) official, singing this achievement from the rooftops. 

A Public Health England report (below), posted on the UK government website has already acknowledged the 42 day mark. 

A bit understated even for the mother country!

From here
Click on image to enlarge.

  1. World Health Organization Disease Outbreak News (DON)
  2. Ebola Situation Report - 4 March 2015

MERS in the UAE...

Over my weekend, the Robert Koch Institute (RKI) in Germany reported that they had a Middle East respiratory syndrome case (65 year old returning German) under their care, imported from the United Arab Emirates (UAE).[1,2]

There have been two other MERS cases hospitalized in Germany - 1 from Qatar and the other originating from the UAE, where infections are presumed to have been acquired.

This latest case is nothing astonishing but it does act as a warning that there most likely are other MERS cases circulating in the UAE. Alternatively, this person may have visited the Kingdom of Saudi Arabia (KSA) before travelling to Germany, acquiring an infection there. 

When cases emerge in other countries they can be very telling. They speak of what might be happening in the host country. The UAE has only reported (this is the important word for any outbreak observation) a single case since July last year. Was RKI just "lucky" to pick up the only other MERS-CoV case in the UAE over the past 8 months? Highly doubtful. In the absence of other information (WHO detailed data will surely follow soon), it is much more likely that MERS-CoV is circulating in the UAE, as it is in the KSA and possibly neighbouring countries, but that cases are going either undetected or unreported.

When animals were described alongside human cases.
Click on graph to enlarge.
Taken from MERS number page.
Current MERS-CoV circulation would be in keeping with the popular theory that MERS is a seasonal zoonosis (animal infection that spills over to humans causing disease on occasion), and that more primary human cases, although still relatively rare, emerge during periods when more infections are occurring in camels - which seems to occur around this time of year. That seasonality in camels has not really been established yet and still it is one popular theory among those who do not completely deny any involvement of camels in MERS whatsoever. Also worth repeating is that MERS-CoV appears to be inefficient at transmitting between people - at least so far as the testing done to date has revealed.

From the rare spillover cases acquired by humans from camels, humans proceed to do the lion's share of the work in continuing to spread MERS-CoV among humans. Yay us. 

In recent WHO disease outbreak news reports [3,4], the detailed information reveals multiple instances of cases having shared wards with laboratory-confirmed MERS-CoV cases - and despite assurances that the same healthcare workers did not attend both people, some form of contact has apparently occurred somewhere, somehow. The precise details of what that contact was, still seem to be beyond the capacity of the Saudi disease detectives to capture. But in that detail lies some important hospital (or community) transmission clues - even if those clues are as simple as revealing that the wring question are being asked, too few contacts are being tested, healthcare workers movements are not being tracked sufficiently, or finding that people (patients, contacts and healthcare workers) do not answer the question fully. 

A little thing called infection prevention and control is apparently still not being adequately adhered to in some parts of the region. 

In other words, MERS is a rare but preventable disease.


  1. Flutrackers post
  2. Robert Koch Institute [German]