VDU has moved house....

If you're looking for new posts about viruses and virus-related stuff (which could be anything really!), from now on please go over to the new site with its easy-to-remember address...

virologydownunder.com

Hope to see you there!

Cheers,
-Ian

Editor's Note #27: Anakin Fencewalker joins the Force...

After 19 years, our furry family member had to leave us this Wednesday. His quality of life was decreasing and he had stopped eating - he made the call and he let us know.

He is missed enormously and remembered daily by his human family, for many things.

He saw two PhDs completed; he sat through the writing of 70+ papers, a book, 14 chapters, 11 reviews (all had late night writing components that required pats and scratches), he watched over the growth of two babies and has been with them all their lives; he lived in the two houses my family have known; he was a constant companion to my wife and he kept me (and my keyboard) company while I wrote many pieces for this blog.

Anakin Fencewalker.
12SEPT1998-28JUL2017

Thankyou Anakin.

May the Fence be with you.

Editor's Note #26: Virology Down under gets an award!!

Well this is some pretty cool news to wake up to on a Friday morning!!

Virology Down Under (this blog and its extended presence on LinkedIn and Facebook) has just been awarded one of InfectionControl.tips "Top Innovations of the Year of 2016" awards for global engagement. 

I'm one proud little blogger!

With the moniker of Join. Contribute. Make A Difference, InfectionControl.tips has been a welcome addition to the field of open, public-speak communication of health information and provides an avenue for health professionals to explain things to an eager and wide audience. 

My partner in crime (and life) @kat_arden and I have written a few pieces for this site now, including our latest effort - The Language of Zika Virus Testing. No doubt we'll contribute more as time allows and needs dictate. 

If you haven't already, it's also a great idea to have a try at writing in a different non-academic style of language too. IC.tips' editors can help you out with that if needed. 

We also love that IC.tips is open-access, free and shares our enthusiasm for wanting to make a difference in some way.

You can see other award winners at: http://infectioncontrol.tips/award-top-innovations-year/

Thanks team - #VirolDU is honoured to be a part of your goals.

Editor's Note #25: 3rd birthday...

3 years ago I posted my first blog thingy. 

It was on MERS-CoV.

863 posts, >735,000 recorded views and a continuous run of viral outbreaks and epidemics later - here we are.

Happy 3rd birthday Virology Down Under!

Thanks to all of you for reading and chatting and asking and thinking.

Roses are red

Violets are blue

When I talk on viruses

I use VDU

I also use Twitter and LinkedIn and Facebook a bit too.

Editor's Note #24 : Tweepidemiology Update #3...

I was involved with @UQ_News and others today in a discussion about use of social media for researchers today. I made the point that...

Oh-last thing @UQ_News - don't get bogged down in how many followers you have. Build it & they will come. Then go. Then others turn up. Etc

— Ian M Mackay, PhD (@MackayIM) January 19, 2016

Which reminded me.

I haven't looked at #VirolDU's Tweepidemiology for over 6 months! 

So here's how the followers have been accruing since my lsat Tweepidemiology update.

These are data generated in response to a blogger who tweets and writes about a sliver of the viral infectious disease outbreaks that affect the world...

Followers of my @MackayIM Twitter account (and this blog which gets
promoted through it) since I started tweeting.
This shows the cumulative rises, pauses and dips of followers and the relationship between the rate of that rise and some active periods of infectious disease outbreaks..
Click on the graph to enlarge

Because everything generates data and every load of data looks better when graphical'd.

Seasons Greetings from VDU...

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

Editor's Note #23: Tweepidemiology#2..

Thought it was time to update the "Tweepidemiology" graph I first posted back in September of 2014.

The Ebola virus disease epidemic of 2014 certainly drive the biggest of my Tweepidemics.

Followers of my @MackayIM Twitter account (and this blog which gets
promoted through it) since I started tweeting.
This shows the cumulative rise, and pause, of followers and the relationship between the rate of that rise and some active periods of infectious disease outbreaks..
Click on the graph to enlarge

This will be something I check back in on from time to time. Interesting stuff. 

As above but zoomed in to show the dip in followers of the @MackayIM Twitter account.
Click on the graph to enlarge.

Something else this little analysis showed me was still interesting, but very disappointing. That thing was one of the biggest losses of followers and slowest periods of follower gains that my Twitter account has had in its 2 years. 

This dip happened immediately after I changed the background on my avatar to reflect my support for the US Supreme Court's legalisation of same sex marriage. I kept that background for a week. I haven't been able to find anything else to attribute to the dip - I haven't been any more annoying or rude than I usually am! I don't blog to gain followers per se but followers are very helpful because they help spread sometimes useful information further than it might otherwise reach. Also, because you're mostly a likable bunch of course! In the scheme of things it was a blip - and there is always a turnover of newcomers and "newleavers" and the latter generally increases in proportion to a decrease in my level of engagement. It just strikes me as sad that people feel so much dislike or annoyance that they need to respond by leaving the table in disgust or annoyance like a child who doesn't get what they want.

Data. So many things to learn from them.

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.

Editor's Note #21 Far better resting place I go to than I have ever known...

I've spent all day analysing why the death of a person I never knew makes me sad. And as the day draws to a close, I've settled on the fact that it is what he represented to me, so many years ago, and for so many years since, that makes me sad that he has left the world. So I've devoted my day to remembering Star Trek and Spock - Leonard Nimoy's most iconic of characters, and to being grateful Mr Nimoy put so much of himself into that role so many years ago.

In the passing of Spock I'm revisiting so many things he inadvertently taught me as a younger version of myself; things that have some part in making me who I am today.

Top of the list is science. Spock got to look for stuff, understand stuff, deal calmly and logically (I fail greatly here) with things, and was a valued and integral member of his crew. Of course I'd have loved to be on an Enterprise, seeking, learning and finding stuff in space, too! I can't quantify how much Spock and Star Trek have shaped my drive to search and find some more earthly things - seek new viruses, learn new knowledge and find out how infectious diseases are caused.

From here.

Spock was Mr Nimoy. But more than that-all Vulcans must now have elements of Mr Nimoy's portrayal of this one character or for many, they are not Vulcan at all. That's quite an acting legacy. You can't just write "be logical" down on a script-you have to have seen a Vulcan. A part of Nimoy was given to Spock. Other actors achieve this too of course - to my mind all Klingons are represented by Michael Dorn, Rangers by Viggo Mortensen, Wolverine is Hugh Jackman, Tony Stark is Robert Downey Jr, Batman is Christian Bale...and so on.

As Bones said in Star Trek II: The Wrath of Khan (from which the image above is borrowed): "He's really not dead, as long as we remember him". 

Of course we will remember him. How could we forget the person, the character, the message of hope, tolerance and that use of logic? And the accidental humour. Spock was a perfect foil used so well to look both at, and into, ourselves.

Today I still very much respect and admire the ideals that represent the many iterations of earlier Star Trek voyages - care, knowledge, teamwork and a sense of shared goals chosen for the betterment of us all. 

In a world  that can so often be filled with hate, pettiness, self-interest, fractured communities, an absence of care, a disrespect of knowledge and lack of desire to work together, Trek still contains hope that others who share the mission and vision will eventually rise high enough in their roles, often enough, to make the world a better place. Many already do. Star Trek's creators and those who brought its many stories to us, are owed much.

We should always strive to continue the ongoing mission to explore, seek and boldly go where no-one has gone before, in whatever it is that we choose to do. 

Spock understood the need to work for everyone's benefit. He voiced it so well when he reminded Kirk that he has no ego to bruise and that "The needs of the many outweigh the needs of the few". We should try and stow our own egos more often, and work towards the bigger needs. We should do that as part of the same cree more often too - that of the spaceship Earth.

The ship is not yet out of danger Spock, but you gave us a lot to help make it work better. 

LLAP

Gung hei fat choi! & Gong Xi Fa Cai!

..to the Cantonese and Mandarin speaking readers who may stumble across this blog, as well as everyone else who visits!

May all who read this have a happy, healthy and prosperous Lunar New Year, an enjoyable Spring Festival and much luck in the Chinese Year of the goat (mounrain sheep)!

Editor's Note #20: Tweepidemiology...

Updated 05JUL2015

Followers of my @MackayIM Twitter account (and this blog which gets promoted through it) since I started tweeting. It shows the cumulative rise and rise of followers and the relationship of the rate of those rises to very active periods of infectious disease outbreaks and epidemics over the past 18-months or so.
Click on the graph to enlarge

While it's hard to separate whether I pick up followers because of the delivery of specific content or because as you pick up followers, they help spread the word and you pick up more followers, to simple old me this cumulative graph looks like MERS-CoV and the West African Ebola virus disease outbreaks drove people to seek information. Sometimes those people have done me the honour of following me on Twitter, accompanying me on my own journey to understand what's going on. I'm constantly amazed at that, let me assure you.

I thought it worth having a look at the Tweepidemiology of my Twitter account. That is, the epidemiology of my Twitter followers - a bit of a long bow - but you follow me because I talk about infectious disease outbreaks and stuff and because I like my new word...I'm keeping with it!

I paid Twitter Counter to get my Twitter data, plotted it in Excel, tidied it using Illustrator and here it is. 

I started Tweeting a little after I started blogging - this Twitter thing is for the young people and their constant need to take selfies and update the world on their lives...live and learn. 

Despite VDU blog posts on the emergence of influenza A(H7N9) virus in China dating back further in time, I came to Twitter well after H7N9's Wave 1 was engaged. So the slow burn could have been due to that or just because no-one knew me or that I could generally be trusted and generally don't spout drivel. 

Generally.

So there ya go - Tweepidemiology - a way of looking at when and perhaps why one gains followers through social media when it's used to engage the public and try and help people understand what's happening with new or emerging viruses and diseases . Perhaps I should check what happens when I post photos of my cat too.

Updates...

1. Corrected some typos and grammatical errors

Editor's Note #19 VDU takes a pause...[UPDATE]

With so many other great, and sometimes overlapping, graphical sources of MERS-CoV information around right now, this seems like a good time to take a break from blogging for a while. 

In the short-term, I'm going to devote my hobby-time to some other virus-related reading & quite a few career-related tasks as well. Sadly, while I immensely enjoy this new-found science communication and writing gig, it does not contribute anything to my "day job". Not a jot...well 2 papers and a review in the pipeline and a million media interviews (those are not viewed with much value by the job, but I feel they are of use for the much wider community). I'm not talking about financial benefits here, I'm referring to blogging not ticking any boxes that contribute to my role description. Social media is still very much though of as a place for selfies and not sciences in many (?most) circles. We're still quite some way off the day when researchers will be expected to be able to engage their stakeholders or share around their knowledge. Sure, there are words on paper here and there, but reality and recognition? Not on my horizon anyway. Sad but true. Also, the level of additional research that goes into this hobby is pretty hard to sustain.

So, while I'm off having a change and a think about things, please do enjoy the back-catalogue if you need a VDU fix.

Note #1: Its not my intention to stop blogging for those concerned about that!

Note #2:  Thanks to Prof Racaniello's inspirational comment (stop whinging, do more - see here), I'll try and make some more time to keep up with the blogging.

Editor's Note #19: Just a pause...

Hi all,

Nothing fills me with more self-loathing than seeing VDU's charts being used when they are out of date...and I only have myself to blame! 

Generally speaking of course, I love seeing the charts used - that's what I make 'em for. But for some events, like the MERS-CoV localised epidemic, VDU's posts are out-of-date as quickly as the front page of yesterdays newspaper. So there is a need for a lot of night work.

I've been a little occupied with (drowning in) other paperwork of late - I do have a day-job after all - including a review of the fairly diverse MERS-CoV literature for a manuscript I'm writing.

As a result, I've fallen behind in updating my MERS-CoV (detections consistently roll in overnight but in smaller numbers than during April) and H7N9 (not many to add) charts.

I'll remedy this as soon as I can.

Cheers,
Ian

Editor's Note #19: An indication of the level of interest in MERS?

I know this is just a little blog and one tat is pretty nichey, but if it's visitor numbers are any guide, interest in the Middle East respiratory syndrome coronavirus (MERS-CoV) is at a fever pitch. This past week (13th-19th of April-2014) was the biggest week, in terms of site visits and views, for Virology Down Under, since the VDU blog came into being.

Countries from which visits to VDU have originated
between 30-Mar and 19-Apr 2014. USA 1st. 2nd most
visiting country; the Kingdom of Saudi Arabia.
Thanks to @AB_Algaissi for asking.

13 of the 18 posts in the past week were MERS-CoV themed and each drew between 80 and 652 views. Yesterday most of those users were new visitors. So why don't you come back??? Oh well, I'll keep a light on ;)

The light is slowly dawning among researchers, that the many messages of science can be so much better conveyed through social media platforms than through scientific papers. And the public seem to be enjoying this slow moving change.

Apart from being stodgily written or sometimes incoherent, even to other scientists, such papers can be placed behind a paywall which cannot be accessed unless you have links to a University. Scientific papers are also frequently slow to emerge (reviewing and copy-editing and layout and such can take weeks, depending on the journal) and are aimed towards only a very select few; at least unless you have results that make it into a luxury journal like Science or Nature. The sloth like turnaround time is in start contrast to the emergence of an infectious disease outbreak and so the public, and many professional too,  must look elsewhere if they want to know the facts behind the latest "Killer virus mutates" media banner. Many big organisations have resources and professionals devoted to providing those answers; sometimes they are hard to wade through too, sometimes not.

If our research findings are good enough to be if interest to the scientific media, we may get a much wider pickup for our message. The trick then is being able to convey that message in understandable chunks. Ever been to a accountant/lawyer/banker/statistician? Then you know that half of what they say slips into their own tech-terminology. Yeah, we  scientists do that a lot too. Its a hard habit to break out of. We just get used to using that language in our day-to-day dealings even though it may confound (see?) others. But don't put up with convoluted tech-speak; ask for clarification. 

Realistically though, most submissions to luxury journals get rejected. Unfortunately, media attention can often be drawn to work appearing in those luxury journals rather than some journal with a lower impact factor. Yes, impact factors still get used in the real world at many levels from grant review panels to fellowship panels to contract renewals to attracting media attention. Why? Because your work has been deemed by some to be interesting and important enough to get there in the first place. 

And so the circle of scientific life goes on.

Thanks to all who read and visit. I hope its been worth your average 1min 29sec visit. ;)

Editor's Note #18: VDU on MERS in the media..

Many thanks to Andre Berro, MPH, CPH, SCPM, Public Health Advisor at the Centers for Disease Control and Prevention for pointing out, on LinkedIn, that VDU got some media mentions of late. 

These follow on from a Twitter interview on the weekend with the Wall Street Journal's Ellen Knickmeyer. She and Ahmed Al Omran published an article: Deadly Virus's Spread Raises Alarms in Mideast Saudis Defend Approach to MERS Outbreak, Even as Cases Increase.[1] Part of the article was also quoted in a WebProNews article, MERS Virus Surge Seen in the Middle East [2] and in a story augmented with a VDU chart (Woo-Hoo!) in a Doha News article, Amid regional surge of MERS, official says no new incidences in Qatar.[3]

While missing from 2 of the articles, I will note here that I'm actually a virologist - despite all these charts I keep posting, and that those 3 articles should all be considered to list my affiliation with the Australian Infectious Diseases Research Centre (AIDRC) at The University of Queensland. The AIDRC have been very kind in allowing me to affiliate my professional academic and educational comments to the media, conducted on my personal time, to their Centre of which I am a grateful member. But to be very clear though, this blog, also managed on my personal time, is separate from those comments. This is a thing of my own construction, curation and opinion (using real data available to all) and is not affiliated with The University of Queensland or any other Inquisition or Organisation. 

Thanks to all involved.

Sources...

1. Deadly Virus's Spread Raises Alarms in Mideast: Saudis Defend Approach to MERS Outbreak, Even as Cases Increase
   http://online.wsj.com/news/articles/SB10001424052702303887804579499831393801054
   Full article ...
   http://online.wsj.com/article/BT-CO-20140413-701881.html?mod=googlenews_wsj
2. MERS Virus Surge Seen in the Middle East
   http://www.webpronews.com/mers-virus-surge-seen-in-the-middle-east-2014-04
3. Amid regional surge of MERS, official says no new incidences in Qatar
   http://dohanews.co/amid-regional-surge-mers-official-says-new-incidences-qatar/

Editor's Note #17: 500th post

Just noticed that there are 500 posts listed on this blog (501 now). I still have a few to port across from the old site but its kinda weird to think I've posted on stuff that many times. I only have ~60 actual scientific papers...although a lot more citations for VDU's blog than for those papers. Hmm. What does that say about my impact or chosen profession?

Anyhoo - Cool bananas!

I wasn't planning on blogging again for a while but Ebola has drawn me back for a little bit. 

Editor's Note #16: VDU takes a break...

Hard to believe it's been 1 year since I blogged my first blog. 500 posts ago.

To celebrate, I'm taking some time off!

Feel free to read through earlier material. There  are plenty of posts that remain relevant, unanswered questions to ponder and knowledge to absorb.

Editor's note #15: Twitter followers

Thanks to all 508 of you who now follow me on Twitter (@MackayIM). Very cool!

I hope I can keep it interesting and worthwhile.

Happy Wednesday!
(hardly interesting or worthwhile was that for my 498th blog post)

Editor's Note #14: VDU in the scientific literature

Virology Down Under gets a 2nd citation (1)!

Dr Anne S De Groot and colleagues used a VDU graphic for a recent paper and cited VDU for it. Many thanks!

To read the paper entitled Cross-conservation of T-cell epitopes: Now even more relevant to (H7N9) influenza vaccine design hop over to..

• Human Vaccines & Immunotherapeutics 10:2, 1–7; February 2014; © 2014 Landes Bioscience
  https://www.landesbioscience.com/journals/vaccines/article/28135

1. 1st citation for VDU at http://virologydownunder.blogspot.com.au/2013/10/concise-overview-of-mers-from-mid-2013.html

Vale Dr. Albert Z Kapikian

Others will no doubt write more cogently and personally than I can about Dr Kapikian's >56-years of medical and virology expertise, skills, discoveries and personality but I wanted to make a just a few quick comments on his passing in relation to a group of viruses for which he is not as often associated; the rhinoviruses (RV).

Dr Kapikian was an expert with electron microscopy (EM), learning the use of it from June Almeida at the Royal Postgraduate Medical School, University of London in 1970. His use of immune EM led him to discover the viruses we now call noroviruses in 1972; a major cause of gastroenteritis. He also found instances of rotavirus (RoV) in the United States and went on to lead the development of an oral vaccine to prevent the serious diarrhoeal disease associated with infection by RoVs. 

He has over 200 publications listed on PubMED.

I exchanged a couple of eMails with him in 2009 (which Al graciously replied too in excellent detail) but never got to meet him, much to my disappointment. My first knowledge of him was from my work with rhinoviruses. While these were not his research focus, he Chaired the group that published the 1st (and 2nd in 1972 and co-authored the 3rd in 1987) formal description in 1967. This report gave the largest group of distinct respiratory viruses their 100 names. He helped to bring together RV researchers and their often identical isolates from around the globe and helped to create the 1 key to link them all in a single unifying scheme; HRV-1 to HRV-100. Having had a tiny role in doing that for the latest species, RV-C, I can more than imagine how much of a challenge that must have been at the time. Dr Kapikian also used his immune EM expertise to visualize the rhinoviruses in 1972.

That Dr Kapikian is so highly regarded, described as warm-hearted and the smartest and nicest guy in the room, speak volumes of him as a human. His track speaks to his role as a leader and medical virologist of huge impact.

Another trailblazer has moved on.

Dr Albert Z. Kapikian, Chief, Epidemiology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health in the United States, died 24-Feb at 86-years of age.

References...

1. National Institutes of Health statement on the death of Dr Albert Z Kapikian
   http://www.niaid.nih.gov/news/newsreleases/2014/Pages/AlbertKapikian.aspx
2. Seeing the new calicivirus: norovirus
   http://jvi.asm.org/content/10/5/1075.long
3. Context for the discovery of norovirus
   http://www.ncbi.nlm.nih.gov/pubmed/?term=kapikian+a+s295+norwalk
4. Sabin Gold Medal
   http://www.sabin.org/sites/sabin.org/files/GoldMedalSpeech2005.pdf
5. Dr Kapikian's publication list on PubMED
   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=%28kapikian%20az%5bauth%5d%29
6. NIH on the Sabin medal
   http://www.nih.gov/news/pr/may2005/niaida-12.htm
7. Children's Vaccine Initiative Pasteur award summary at NIH
   http://nih.gov/news/pr/nov98/niaid-10.htm
8. Alumni Award of Distinction from Weill Cornell Medical College where Dr Kapikian got his MD
   http://weill.cornell.edu/news/news/2001/06/kapikian-and-szeto-receive-alumni-awards.html
9. Awarded Fellowship of The American Academy of Microbiology
   http://nihrecord.od.nih.gov/newsletters/2012/06_25_2012/story6.htm
10. Visualising rhinoviruses by immune electron microscopy
    http://jvi.asm.org/content/10/1/142.long
11. First rhinovirus numbering system report
    http://www.nature.com/nature/journal/v213/n5078/pdf/213761a0.pdf
12. A collaborative report: rhinoviruses--extension of the numbering system from 89 to 100.
    http://www.ncbi.nlm.nih.gov/pubmed/3037780
13. A collaborative report: Rhinoviruses-extension of the numbering system
    http://www.sciencedirect.com/science/article/pii/0042682271903291