Tuesday 29 December 2015

Congratulations to Guinea for defeating its Ebola virus disease epidemic!

After a very long and painful battle with many, many losses, Guinea has stopped the Ebola virus epidemic that began there in December 2013; two years ago.[1]

From Guinea, the Makona variant of a Zaire ebolavirus spread to and throughout Liberia and Sierra Leone. For Liberia, the wait for its third declaration of freedom from any new acute human cases, must continue until 14 January.[2] Two weeks and a bit. 

Sierra Leone has remained free any human cases since early November.[3]

My family and I were out having lunch when the clock ticked over and my 10-year old boy (10M) said "Dad, no-one at any of these other tables will know how good it is to hear this news". My family has talked a lot about Ebola virus and Ebola virus disease in the past year and a half. And we've all learned a lot by talking and sharing and generally communicating. We've also been frequently reminded of all that we have. But 10M was likely very right. 

From http://virologydownunder.blogspot.com.au/2014/07/ebola-virus-disease-evd-2014-west.html
For those of us that have been watching this tragedy unfold from the sidelines since the numbers started rolling out 23 March 2014, much more so for those citizens of Guinea and Liberia and Sierra Leone who have lived and died through this, for those who went to their aid, for those who facilitated that aid and for those in countries all around the world who received and treated cases - we are happy today in a way we have not been for nearly two years. Longer for some who were involved in caring for and trying to understand and diagnose the disease in the suspected index case, a small child from Meliandou village, Guéckédou in Guinea who became ill 26 December 2013. 

While cases and clusters may yet flare up in Guinea and elsewhere in West Africa there remain many thousands of survivors who are still suffering the consequences of infection and of viral persistence.

Good luck Guinea on your 90-day period of vigilance - and beyond. You have earned some dancing!


Monday 28 December 2015

Still chatting with the demons...

It's been nine months since I took the leap out of my 23 year research career and sideways into my fantastic current role; a role which I am very lucky to have. To a researcher, luck is a very close collaborator - although one who often doesn't answer their eMail. 

Nonetheless, the demons from that former life remain to be worked through. Chocolate sultanas help at this time of year. A fantastic family is much more helpful for the other 350 or so days.

This is the first Christmas in over a decade where grant writing has not directly consumed my "holidays" (I won my first grant funding in 2004, the year after I was awarded my PhD). During the other years, the shadow of the guilt from not preparing a grant has always been in the corner of my eye. The buzz of being awarded a grant began to last for shorter and shorter periods before thoughts of the next grant barged in. These are my issues of course, and they differ for, and are coped with differently by, others

Today I notice certain research career-related media stories more often, or perhaps there are more of them, but one that I read today grabbed my attention for hitting a slew of nails on the head.[1] 

I read this while enjoying my kids playing nearby, during a humid but bird-filled afternoon - things not always noticed by me during previous Christmas seasons. The need to write, review, compile and budget filled my world view with a greater urgency than some far more important aspects of real life. I see now what a bloody fool and a complete slave to the process I had become.

Anyway, the article from today posed the question, "How do you know when it’s time to give up and move on to another career?" 

Two of a few bells that tolled for me in answer to this question quite a while ago were :
  1. Not getting national grant funding - I succeeded when NH&MRC funded about 30% of Project grant applications, but certainly not at today's 15% or less. 
  2. My publication output (Figure 1) was on a decline (ignore 2016 obviously). It was always cyclical but naturally it was strongly linked to the successes and failures of #1. I needed more, or at least better, impact factors (or whatever measure you choose to use to define "bigger" journals).
    Also, the number of citations was dropping (Figure 2) as my ageing body of work was becoming less relevant to contemporary discoveries and bigger datasets- you cannot take your foot off the gas in research 

Figure 1. Number of my publications by year. Data from Scopus.
Figure 2. Number of citations of my publications by year. Data from Scopus.
There were other reasons, but these were significant indicators to me that research was better left to those who could keep up the necessary pace of grant-getting and publishing. There are so few dollars to be had for research that they should be spent on those with the ideas to test and with the intent to achieve some long term, real benefit(s). 

The reasons for leaving research differ for everyone I imagine, but check the walls for writing. It's always on them - you may simply not be able to read the words because of the particular Kool-Aid you're being served or because of the rose-coloured glasses you've chosen to wear.


  1. https://www.timeshighereducation.com/opinion/postdoc-blues-how-do-you-know-when-it-is-time-to-give-up

Friday 25 December 2015

Avian influenza A(H7N9) virus case data in humans: more chicken scratchings

This is an example of a 2015 case announcement from the World Health Organization (WHO). I think it aims to provide information on some avian influenza A(H7N9) cases that occurred in China.

From WHO Disease Outbreak News (DON) at
I suppose it does do that in the most basic sense. Yes, if you were a casual electronic browser to the WHO disease outbreak news site (...get out more!) then you would learn of 15 additional human cases of disease presumably due to H7N9 infection. Twenty percent of these cases died and this happened within a month. 

But consider these questions for a moment:

  1. Why would you visit the WHO to learn of this, if you were not seeking some actual detail and evaluation of risk?
  2. If you were a casual browser, I expect you would come away from this with some out-of-context concerns about a bolus of cases in such a short period, spanning a wide age range and occurring across considerable geographic distance. Should you be worried? Is this the precursor to some larger outbreak? Each difficult to answer from this very small cross-section of information.
  3. These public data are relied upon by some when they write papers or release infectious disease reports - so why not include key - yet deidentified - demographic detail in a line list format - remember MERS-CoV in South Korea anyone? That WHO list [4] was messy [5] but it was a step forward for those outside the WHO network who wanted free, publicly available basic data, quickly
In my opinion, the premier emerging disease tracking and publishing - at least in terms of accessible, basic, rapid, searchable, freely accessible and up-to-date emerging infectious disease information - is the team at FluTrackers. Keep your predictive modelling - I'd trade it all in for a clone army of these guys any day! The FluTrackers line list on H7N9 includes some of these cases[6]...and as you can see in the snippet below, even their scouring of the media from China does not help to fill in the data gaps on these cases...
From FluTrackers' H7N9 line list at
https://flutrackers.com/forum/forum/china-h7n9-outbreak-tracking/143874-flutrackers-2013-15-human-case-list-of-provincial-ministry-of-health-government-confirmed-influenza-a-h7n9-cases-with-links?t=202713 [6]
So why does the WHO bother with this information at all? I can't speak for them. But one reason may be because it is relied upon by those who study and prepare for the emergence of new or re-emergence of old infectious agents.[1] These people consume this sort of information to track what's happening outside their own back yard and to weigh the risks that a new bug may come knocking at the gate thanks to a speedy international plane flight. But when the host country is slow or perhaps even reticent to identify key case details, a knowledge gap emerges and may widen. This particular gap has been growing since 2014's H7N9 3rd wave. Perhaps since the 2nd wave.

When sufficient - or any - detail is lacking, then it comes down to the public to look for any answers they seek...by themselves. In this case, that has been FluTrackers & Co; this source has proven itself very worthy for this and for other viral threat monitoring, but cannot be expected to fill this need indefinitely.[2,3]

H7N9 is a good example of an absence of obvious change to the flow of information that the world's public, citizen scientists and its more professional scientists receive about new infectious threats. And this is all a bit strange because I was sure we'd heard a lot about the need to do much, much better on this sort of tracking and chatting in 2014/5 during one of the biggest modern moments of being "caught with our pants down" - the Ebola virus disease epidemic.

Time and viruses wait for no person. Be faster.

Ho. Ho. Ho.


  1. http://ecdc.europa.eu/en/publications/Publications/RRA-Influenza-A-H7N9-update-four.pdf
  2. http://www.ncbi.nlm.nih.gov/pubmed/24885692
  3. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140362/pdf/jphr-2012-2-e29.pdf
  4. http://www.who.int/emergencies/mers-cov/MERS-CoV-cases-rok.pdf?ua=1
  5. http://virologydownunder.blogspot.com.au/2015/06/matching-mers-case-identification.html
  6. https://flutrackers.com/forum/forum/china-h7n9-outbreak-tracking/143874-flutrackers-2013-15-human-case-list-of-provincial-ministry-of-health-government-confirmed-influenza-a-h7n9-cases-with-links?t=202713

Thursday 24 December 2015

Seasons Greetings from VDU...

Wishing you all a very Happy Christmas and a safe, happy and healthy New Year.

Tuesday 15 December 2015

One man has a lot of MERS on his mind....

Professor Christian Drosten heads a sizable, very friendly and diverse team of scientists seeking to understand all aspects of the Middle East respiratory syndrome coronavirus (MERS-CoV). 

And not just understand, but also to detect, educate, vaccinate and generally interrupt MERS-CoV transmission in camels and to and between humans. 

That's a heckuva lot to think about.

From the First WHO-EMRO Training Workshop on MERS-CoV Laboratory Diagnostics in cooperation with the Central Veterinary Research Laboratory (CVRL). 

Sunday 13 December 2015

Where I am this week...

With my personal thanks to the University Hospital Bonn's organizational team, the World Health Organization - Eastern Mediterranean Regional Office, the Central Veterinary Research Laboratory (CVRL) and the United Arab Emirates Ministry of Health.

Saturday 5 December 2015

The season of the MERS...is mainly whenever the infection control fails

I still only see a "seasonality" to MERS and human MERS-CoV detections that is made up of the times when hospital outbreaks spread cases due to missed opportunity to control and prevent infection wihtin their walls. In other words - no real season at all. 

MERS-CoV is an opportunistic virus - which includes making the most of the frequent opportunities we humans provide for it to spread.

Data from public sources up until December 3rd 2015.
Click on image to enlarge.

Any true seasonality is in that small percentage of cases that are the result of a primary, sporadic infection from an infected and infectious camel. Those cases may be related to times of camel calf weaning when young camels acquire their first infection, or it might just be whenever a particular herd has MERS-CoV raging though it.

MERS-CoV: Saudi Arabia still tops the chart..by a long way

A quick reminder that MERS and the MERS-CoV remain a thing of the Kingdom of Saudi Arabia from where 80% of detections have been reported.

South Korea's hospital outbreak comprises 11% of all reported detections.

Tuesday 1 December 2015

Want me to review your manuscript for free? Then be polite...

"It has been 3 days since an E-mail inviting you to review XXX-YYYYY-ZZZZ, entitled "Rbah blah blah". Could you please inform us of your decision by clicking on the link at the bottom of the page with your decision as soon as possible?"

"Actually mate, I have already replied to this email address, which I assume is yours. 

I did that in the 28th of November, a Saturday, and approximately 10 minutes after I received your review request - that was 10:47pm at night, my time. 

But given your tone, I should probably have just ignored it for the spam it must have been. 

A professional journal would make a second approach for my review with some degree of professionalism. I am acutely aware of how hard it is to get peers to reply, let alone agree, to manuscript review requests as I am a Section Editor, an Associate Editor and on 2 editorial boards myself. However, I have never chased up a potential reviewer using such a short tone. 

Please remove me from your list of potential reviewers. I would no more review for you or this journal again, than poke myself in the eye with a sharp stick."