Monday, 27 March 2017

Happy 4th birthday...

This blog!

I'm sure somene one said that a year in social media equates to 7 cat years. Maybe it 9.


Anyhoo, I'll be hunting down a cake for us all today - or maybe a muffin at the canteen.

My heartfelt thanks to those who have made writing for this blog so much fun. 

I hope we all keep learning about viruses together. Anything is worthwhile if you learn something from it. ...and have a reference to prove it was based on data...and cite that reference...and it gets cited by others...and peer reviewed....

Happy 4th!!


Sunday, 26 March 2017

The week that called out to me....

Me.

It’s been an interesting week in which some stuff was said about what I believe, how I unjustly unfollow people, how I see myself and how terrible I am to students. If you didn’t see any of what this refers to but are interested – see the Storify here.

This started when I suggested anyone could come together for the March for Science. I disagreed with some who said before we can march alongside each other in a common cause to value fact over fake, science should be perfectly balanced and inclusive. 

It was surreal to read how that spun up such specifically disparaging commentary delivered by people who didn’t know me at all. They hadn’t never gone to school or university with me, worked in science with me or been a student of mine. They had never even met me face to face. But they felt they had me all sorted out. Digest that for a minute; existence defined entirely by your last series of 140-character word exchanges in a darkened room full of shouting people? What if you hadn’t even said the things you were accused of saying? What if others who knew you better were silent? Friends are those who stick around.

Some insightful conclusions included that I was an absolute troll, a bigot, atrociously behaved, uncaring, incapable of basic kindness, horribly offensive, executing ad hominem attacks, a dick, noisy, abusive, a member of the tone police, a whitesplainer, a lost cause, a denier of realities, someone who doesn’t listen, argumentative (totally agree with that one), fragile, defensive (am not), a liar, sarcastic (okay, I added the one), someone who paints people in a bad light with no chance of response, a hole digger, biased, an ultimate betrayer, a victimizer, someone who punches down, a disappointment, tone-deaf, a clueless white man, march for science sentinel on troll patrol, well-meaning but unable to see past my privilege, someone who flees, gross, a seeker of validation, snide, generally deaf, a mis-stepper, a poor judge, not a good guy, intransigent, having my head up my own ass, wrong, reprehensible, a white male (yep), dismissive (I agree, I don’t stop to acknowledge other’s points often enough) and someone who doubles down.  

Not one mention of curmudgeon? 

Isn’t it impressive how people can be so accurate and specific in summing up someone, just through a few tweets? 

I’m writing this post for me (lots of “I” and repetition) and perhaps just to note that I have listened to what many have been saying for years now. I expect this text will be sampled and held up as an example for fragile white male privilege, support for …everything bad… and that I’m the only person still talking about this. If gas-lighting is about getting someone to question their own sanity, many people, including a couple I really had thought better of, did a wondrously expert job at making me doubt my own mind over the past few days and this is my final part of working through all that.

I’m aware of my ignorance on diversity, but don’t let facts stand in your way.

If someone wants to read between the lines of the next few points – perhaps their conclusions will say more about them than me. 

I have zero illusions about my absence of expertise on and around the topics of diversity, URM, POC, WOC, LGBTQI, MfS, PWD, intersectionality or #marginsci (look them up - I had to). Not once have I portrayed myself as an expert in these fields. If someone has wasted keystrokes telling me I don’t know what I’m talking about, it might have been because I don’t. I leave that to experts like Dr. Zuleyka Zevallos (@OtherSociology).

We don’t need facts to make authoritative sounding claims and statements. Today the United States presents itself to the world through a fog of “alternative facts” and “fake news”. Other countries, including Australia are also guilty of this. Science should be better than that. I believe it is better than that. But there are exemplars within science, as there are within any human group, of racism, sexism, colonialism, marginalisation and misogyny. There are bullies wandering around looking to call people out (see this piece on call-out culture) because bullies want to create a fight they can win and then parade the evildoer’s head around their clan as if that is an achievement. If people join in celebrating such unscientific and bestial victories, they are not living up the scientific method they purport to hold dear. 

Across two decades I’ve been privileged to mentor a couple of dozen students. This past week saw strangers online labelled me as a “silverback in training” who “punches down” to students (more later). This was clearly based on these people having no knowledge of me in real life. They jumped to conclusions. They didn’t act like scientists but like bullies and they were flat wrong. When so-called scientists or supporters of science chose feelz instead of facts, they lost credibility. People who didn’t read the source material yet passed judgement on intent and character, should ask themselves if they support science at all, or just like to misrepresent, threaten, yell and pre-judge. I have been privileged to have a good education, home and family and I try and use that to give back in various small ways. I don’t use my privilege to bully. Do you?

It was interesting watching the binary thinking on Twitter over the past week. Subject matter became all of that thing, or none of that thing, black or white – that thinking usually doesn’t help discourse. When I didn’t specifically spell out my position on everyone’s particular interpretation of a subject, I was deemed by some to have taken an opposing position to their beliefs and concerns. This was a teaching moment for me. I’ve often defended Twitter for being a venue where, with some care, you can convey your meaning and intent clearly.  But I was completely wrong and clearly na├»ve; I couldn’t even convey intent to those who I thought understood me a little. You can only communicate that level of subtlety with family and friends and with others who are willing to go back and forth; who are willing to answer questions at face value, ask questions, withhold assumption and conduct an actual discussion, with pauses to think and some space to clarify missteps. Discussion cannot happen against a gang or those pre-loaded for a fight in which they have already mentally engaged with an enemy. 

Some diversity exists in science labs, but I do not mean to imply that science is diverse enough…

Labs I’ve visited or worked in, those that I’ve worked with or have had people I’ve known work in – virology labs, molecular biology labs, veterinary labs and diagnostic labs in the countries listed above, do have diversity in them. How does that fit with the assertions of some that science labs are “not diverse”.

Science is not well balanced. I say that as someone who left research because of a range of imbalances. None of them were in that earlier alphabet soup list and none I could do anything about at the time. I do work to address the imbalances related to women in science and pop culture, because I have some experience with that. Those who have presumed that I believe there is equity, happiness and bounding unicorns throughout the science I have experience with are mistaken. That isn’t said to belittle others’ experience and it isn’t meant to justify that diversity is less common than it should be. I’m just stating this at face value. Please don’t call it dismissive – I am not disagreeing with anyone about anything other than with those who say that “science labs are not diverse”. I’ve seen diversity in labs in Australia, New Zealand, The United States and in a lab in the United Arab Emirates. There was likely more diversity that I couldn’t see. I’m also not arguing that what I’ve seen may simply represent tokenism. Much of what I’ve observed doesn’t reflect the makeup of the communities around us and even if science does one day reach perfect balance, problems with inclusivity may remain. 

So, to belabour my only point in response to those who yell loudly that there is zero diversity in science - diversity in science does exist. Only point. Just that one. Sometimes people assume everything that is not said is because it hasn’t been considered, or people presume it means support for the worst of what had been brought down on them and theirs. Those presumptions derail any chance to bring others with them. They short-circuit discussion. Maybe intersectionality is not about teaching others or raising willing newbies up to help. Maybe this is just a personal crusade for some. 

I’ve known labs where white men were in the minority. I’m not arguing with those whose experience tells me that this is not the norm but I have worked in labs with obvious diversity. Those were good labs. But they are only a miniscule sampling. I’ve sat on sex-balanced committees - was everyone able to contribute and be heard equally? I didn’t think about inclusivity at the time. I’ve spent most of my working life directed or managed by people in some kind of minority (in my country); never directly by a woman though. But women have occupied leadership roles, above my male managers, in different organisations that I’ve worked in. I’ve been lucky to see that because the data shows that it’s not the norm, yet some progress is being made. 

If labs exist filled only with privileged white male scientists, I’ve personally yet to see one. But labs run by these men remain very commonplace. Including human diversity in science is essential. The culture of managing humans in science roles has always felt to me like it was the last thing on anyone’s administrative tick list. Science feels like one of the holdout “old school” institutions. But today’s science is about teams and they perform best when they get along, treat each other equally, when they collaborate and when energised by the injection of fresh, new ideas and perspectives.

I’ve certainly been privileged to work for or with some great organisations in my time in science – these have and continue to do better and to make things better by being more inclusive. They ask for help and they seek input. Overcoming institutionalised diversity and inclusivity problems won’t happen quickly – certainly not before the science march occurs. I’m also certain it won’t happen because of aggressive, overbearing, condescending groups behaving akin to privileged white men, bombarding, dismissing, overwhelming and belittling those who engage with them or disagree with their beliefs. Science certainly grows stronger from vibrant and robust discussion, but neither science nor the community will put up with bullying. Bullies have no more of a place representing diversity in science than they have excluding diversity from science.   

“Real science labs” are diverse teams… 

I think of a real lab as those that have a mix of the best scientists to get the job done. An idealised lab would have constructed that mix by actively biasing against the lack of diversity visible in other labs and reflecting the community it serves. A real lab works as a team with purpose, supporting and raising up its junior members using the experience and contacts of its senior ones. A real lab gives opportunities to the next generation of scientists. A real lab spends time bringing the community along with it as it explains its achievements and consciously makes itself available outside its own communication silos. 

I never got to run a lab so I’ve never been able to control any of that. And until recently, I openly admit, I wouldn’t have given this enough attention nor would I have unpacked what that “balanced mix” meant. I’d have been navigated by what was being done around me – by the guidelines written down and by the white males running things nearby – I’m not at all proud of that. I have a wife and Twitter to thank for slowly opening me up to my lack of understanding over very recent years. In my lab roles I’ve mostly been driven by the urgency to produce papers and get grant funding and supervise new students and keep a job so I could help with having a family. This other stuff did not then have a subheading in the CV. 

The use of Storify for its intended purpose…

Storify is an online tool that lets us collect social media content and order it chronologically then post the list. It’s not an intuitive tool, it lacks flexibility and for tweets it means a lot of manual re-organisation if you want to try and accurately represent a lot of different, concurrent threads of conversation. I listed some of the tweets after the call-out was slowing down and kept curating it for a little while thereafter. Sure, it looks like a pedantic effort – of course it is. I also think this exchange is one others may learn from.

To get an outside call on whether I was using the tool in contravention of any terms of service, I used the Report Abuse link to report my own Storify. Turns out that I wasn’t in breach of anything. 

Tweets are in the public domain and all these were tweeted by adults who didn’t care how they looked or what they yelled into the world. Kinda like when you screams and gesticulates at the car in front of you because it cut you off. And then they stop and block you in and get out of the car with an angry scowl as you scramble to wind the window up. As your blood chills, you realise this is real-life and not a computer screen, and there are real consequences for your angry actions. Twitter can be an equally real yet vile cesspool of angry affectation.

I wonder how your employer finds your behaviour online? How about your mother – or your kids when they stumble across your screen-captured swearing, probably out of context, decades from now?

Social media 101: If it goes into the public domain, it stays in the public domain. Stand by what you said, apologise for it, or don’t say it in the first place. But don’t whine about it later; look to yourself. 

The affront at unfollowing a person on twitter: that direct message…

Much was made of my choice to ignore some sage advice given by another person from the twitterverse, the morning after. They suggested I apologise for all my recent wrongs and read an excellent article by Prof. Emma Johnston on how men and women can help reduce gender bias in science. It was a piece I’d tweeted and added to my Scoop.It board nine months earlier. Highly recommend it by the way - Prof. Johnston has some excellent points and an enviable writing style. 

Some people finally read the piece and accused me of outright dismissal (Denying: one of Prof Johnston’s four Ds) of the existence of inequity. I’ve tried to explain why that is not the case here. If someone believes otherwise, please back it up with examples.

By the time I saw the unsolicited but well intended DM I had already deleted Twitter from my phone and tablet. The @MackayIM “brand“ and everything else looked unsalvageable to me at that point. 

When I saw the DM tweets I decided to unfollow the person to avoid more of the ‘sit down and shut up’ sage advice I’d received from people the day before. Clicking this virtual button was clearly an egregious and divisive action because it sparked a screen capture of the DM tweets by the sender which was then distributed for the next day or so. I was also blocked by this person so I initially missed all the aggrieved tweeting. 

Just to be clear, I didn’t initially block them, just unfollowed them. Unfollowing someone on Twitter means not having to see their content in my timeline and stopping them from sending DMs to me. They could still email me of course. Or contact me on Facebook where this person had access to my profile. Or contact me though LinkedIn.

In my opinion, DM’ing is for private one-on-one or “Direct” chats. And sure, there was no content of mine in the tweets but the intent was obvious – to malign me for the simple act of unfollowing them. Nevertheless, I get to choose who can contact me through private channels. I’m very glad I didn’t share anything personal, because it would likely have been used as further fuel for the alternative narrative fire. It’s worth remembering that Social media 101 comment above. This teaching moment reminded me that we know nothing about the integrity of the person on the other side of the screen. Just what they choose to reveal to us.

Punching down to a junior is an unconscionable act but also a serious accusation when it’s unfounded…

Another point on the pillory list of those who have never met me was the way I treat students. I’m told my university and employer were contacted to warn of my recent “attack” on a student I had been acquainted with on Twitter. Just to be clear, we have no student-supervisor relationship. We are on opposite sides of the planet. We had exchanged tweets since late 2014 or so, as people who have never met do. Check them out for yourself if you have real concerns. 

The suggestion that I am acting in the role of a supervisor or mentor to any student through Twitter or that this Twitter disagreement equated to me affecting the professional life of the student or that there was any discourse between me speaking as an Advisor and anyone speaking in the role of a student is strange, perhaps ludicrous at best, and defamatory at worst. It may have affected my professional life though when a rallying call was tweeted to contact my employer (none of my online opinions are linked to any other organisation but those of the neurons in my head) because someone was offended by being unfollowed and egged others on. Unprofessional behaviour much?

I still hear from a bunch of my past students (mostly female FWIW). My first PhD student was male. My second was a female from the Middle East. Both wrote up great PhDs. We’re still in touch. I have mentored them to the best of my abilities; I tried to teach, support and guide them well. Only they can say whether I succeeded. I am no longer a principal advisor for any student. I miss their enthusiasm and the expectation of being taught new things by them while training them in science and its lab-based politics.

It hurts enormously to be accused of betraying the trust of a student in any way. Pain was the intent obviously, nevertheless this was a misrepresentation of an exchange between acquaintances that had nothing to do with our current career roles and was unrelated to our ages. The exchange with this person is documented in the Storify. I’m glad that I created this record despite not foreseeing this particular accusation, and despite the Storify’s creation being described as an unprofessional, biased, an inappropriate act. I’m not sure if that’s more related to how the tweeters see their own public record when they re-visit it with a cooler head, or just their frame of reference. 

The teaching moment for me was that someone I thought knew my character a little had eagerly and publicly misrepresented that character to the world for reasons I still don’t understand. This in no way changes the fact that this person is the smartest 20-year old I’ve ever met and they would make an excellent and expert addition to any laboratory lucky enough to have them. 

A few final thoughts.

If I could live last week over again I‘d take back the “all” from “all labs have some diversity”. Over the past few years on Twitter I’ve been trying to remove absolutes from my vocab. Failed on that one. I also wish people had been able to pause before they tweeted their assumptions – or anger or abuse – and thought about maybe talking to me to see what I thought or believed instead of calling in and energising a thoughtless mob.   

I’m still mulling this whole ‘call out’ fiasco over most minutes of the day, so some of these views may change, as they already have since 18th of March when this started. 

Returning in full to Twitter doesn’t excite me right now. However, there are still 9,300 followers who haven’t yet dropped me like toxic waste. I know some of those who were quick to pick up a pitchfork are still following - they may just not have unfollowed yet. But please do - my privileged white male snowflakiness can take it and I’m unlikely to ever trust your judgement or anything you have to say. 

When finding yourself in an avalanche like this, I recommend not defending yourself. Just stop. Right. Away. Shut up. Stop typing. Not because some loudmouth tells you to but because these are subtle conversations and the subtleties cannot be addressed in anger and never in a mob. That’s was a problem for me because I’ve spent three years aiming to respond in some way to every direct tweet I receive. The teaching moment here was that sometimes one needs to drop the social from social media. Proper discussions can be had by eMail or DM – I’ve had a few nice chats this week (thank you by the way, they each helped me a lot) – and they can be had face to face. For some without filters or empathy, it is too easy to be emboldened by the alluring anonymity of the glowing screen.  Some cannot help but say things in a way (I hope dearly) that they wouldn’t if speaking with a real person over a coffee. 

This group was not like other groups though. They (I do not intend to be ‘othering’ anyone here, please don’t take it that way) are not like anti-vaxxers for example. I only use that example because of my recent experiences with them. The attempts by anti-vaxxers at piling on are relatively feeble, although they do share some similarities with my recent experience. Both groups tend to make ridiculous leaps in logic, to generate unsubstantiated claims and treat others with the same contempt that they rage against receiving. 

In any social media morass such as this was, there are also sheep; desperate to be recognised but not actually contributing anything useful to the world except noise. Some members of this week’s group had much pain, much anger and some have reason and justification for it. I can imagine this comment receiving an “oh, thank you sooo much for your permission”. 

These people are not aimless, they are not just being deconstructive and they are not selling a book or a carton of dinosaur memory water. They have real grudges for real reasons and they have a host of real issues that people like me have been integral in creating, yet only understand a bare minimum of. I was perceived to be stepping uninvited and uninitiated onto their lands.  As much as possible, I do get that. My intent was only to discuss why we as diverse human beings couldn’t support science in facing the immediate stupidity, hatred and danger at the door, and facing it together. 

Maybe another day.

Further reading...

If you want to learn more about equity and diversity, you could try the writings of Dr Zuleyka Zevallos.
  1. https://othersociologist.com/otherness-resources/
  2. https://zuleykazevallos.com/about/
  3. http://www.latinorebels.com/2017/03/14/the-march-for-science-cant-figure-out-how-to-handle-diversity/
Also...

Tuesday, 14 March 2017

SNAPDATE: H7N9 by map...

With the latest numbers out from Hong Kong's Centre for Health Protection, Week 10 marks the second week of around a dozen human spillover cases - likley to be poultry to human infections.

Click on image to enlarge.
While the number of cases at each geographic location within China is small given the millions living in each region, this week's cases are spread across 10 provinces or municipalities. A huge area. 

Guangxi province is adjacent to Vietnam. It's always worth remembering that an outbreak anywhere can turn into a threat everywhere

From these numbers, there is no obvious escalation of human cases to suggest anything has changed in the way H7N9 infections are acquired; they remain relatively rare and from animal-to-human close contact.

While the cases are still coming, the totals (see weekly and daily bars below) shows a levelling off - at last suggesting a slowing of this season's epidemic. But stay tuned.

Numbers of human H7N9 cases.
Image taken from the VDU static H7N9 graphs and numbers page.
Click on image to enlarge.




Sunday, 5 March 2017

Avian influenza A(H7N9) virus in humans: lay of the land...

I'm getting a little more of a grip on the H7N9 numbers thanks to the data from the Hong Kong Centre for Health Protection (CHP) [1] - which have been a solid source in 2017.

Keep in mind that these numbers :


  1.  are imperfect because they are reported inconsistently by those who have the data and because they only contain partial detail - death details are impossible to come by.  Please keep in mind that there is no global, running-tally of H7N9 cases presented to the public, by any public health entity. There is a great line list from the citizen-run FluTrackers list, ([2]my usual go-to) but in 2017 they got swamped by these unsatisfactory data.
  2. will only represent those cases that have been lab tested. Any people who have met the criteria for being a "Case" [pick from 3-6] - which in most instance means being sick. In some instances a cases is identified because diligent doctors have followed up those people who had contact with a known case - which is called contact tracing. Sometimes these contacts may virus positive by only mildly ill or have no illness at all.
I've graphed these wrangled data using one of my older formats - to show which province, municipality or autonomous region is contributing to the peaks as the site of origin for an H7N9 case.

Sometimes where a case has been detected may not be where they were infected. I prefer to talk about where a case "acquired" their infection. 

Click on image to enlarge.
Data for this graph can be downloaded from my static H7N9 graphs page, here.[9]
We can see - perhaps - that the major contributors to the peaks in January and February's 5th Wave are Jiangsu province (green circles) followed by Zhejiang province (orange circles) then Guangdong (brown circles), Anhui (purple circles), Hubei (red squares) and a range of smaller contributor regions.

Guangdong and Zhejiang are familiar to H7N9 watchers as being hotspots for human spillover and while Jiangsu has always had a presence in the outbreaks, it has had a very big season this time around.

It remains to be seen whether a range of market live poultry market (LPM) closures has cut the flow of virus into these markets and to their many, many visitors. These closures have been in response to cases rather than to prevent the outbreaks but no obvious nationwide coordination is apparent. It seems likely that spread of infected fowl will continue until more markets close, the source is contained or the seasons for influenza spread (winter and colder shoulders) is over.

Stay tuned to the CHP update this week - last week's tally was lower than previous weeks; a blip or a trend? 

A few things about this graph.
  • It mirrors the FluTracker's line list numbering scheme up until FT816. From entry No. 817 it uses data from the CHP reports. These are PDFs but as they helpfully told me by email this week - you can extract the data yourself using Adobe Acrobat Pro. If you don't have that - I've already done that extraction and am happy to share an Excel version of it with you. Shoot me an email, leave a message or Tweet me @MackayIM.
  • The Outbreak numbering - or waves - is based on when cases appeared or stopped. Its imperfect too. There are published schemes but they also differ from each other [e.g. 7,8]. This isn't life or death - you get the idea from the obvious peaks and troughs. FYI - this year I've updated my numbering for previous outbreaks.
  • Market closures include long term or short term shutdowns or rotating closures for one or more days for disinfection followed by restocking. Each province is a populous place. Often markets are closed here or there but not everywhere in a province and certainly not all provinces at once. 
  • Data are plotted by week of illness onset (hard data to come by) or when the case was reported. The grey peaks indicate totals from all provinces for that week
References...
  1. http://www.chp.gov.hk/en/guideline1_year/29/134/332.html
  2. https://flutrackers.com/forum/forum/china-h7n9-outbreak-tracking/143874-flutrackers-2013-17-human-case-list-of-provincial-ministry-of-health-government-confirmed-influenza-a-h7n9-cases-with-links?t=202713
  3. https://www.cdc.gov/flu/avianflu/h7n9/case-definitions.htm
  4. http://www.phac-aspc.gc.ca/eri-ire/h7n9/case-definition-cas-eng.php
  5. http://ecdc.europa.eu/en/publications/publications/h7n9-interim-case-definition-april-2013.pdf
  6. http://www.who.int/influenza/human_animal_interface/influenza_h7n9/InterimSurveillanceRecH7N9_10May13.pdf?ua=1
  7. http://ecdc.europa.eu/en/publications/Publications/rra-influenza-a-h7n9-update-five.pdf
  8. https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-016-2049-2
  9. http://virologydownunder.blogspot.com.au/2014/11/influenza-ah7n9-virus-detection-numbers.html

Friday, 24 February 2017

H7N9 numbers....no-one agrees...

Tuesday, 21 February 2017

H7N9 virus in humans in China: just how big is this?

...I don't really know, but a lot bigger than I thought when I was tinkering with the numbers for the last post (which has since been updated by the way). 

As far as I can make out - the tally could be at 1,378 cases - that dwarfs any of the previous 4 waves of H7N9. You can see that below in the crudely estimated monthly tallies.

Dwarfs by quite a lot. 

Coming into this season there were about 808 human cases, so there could have been as many as 570 cases this season.



 As you may know, I follow FluTracker's line list for my H7N9 data.[1] Sadly, they recently lost the ability to list individual cases when those details mounted up too quickly and without enough clarity. 

The above is a very crude graph mainly because it is unclear whether any of the numbers up until December were reported by the Hong Kong Centre for Health Protection (CHP) in any of their recent posts. 

It is quite possible I'm up to 150 cases over in my count - but even so, 1,222 recently reported by the WHO [1] is still a big season.

Hopefully we'll find out when the next authority issues a total. 

I've updated my other graphs on the static page (click on the Avian Influenza|H7N9 tab above or here)

References...

  1. https://flutrackers.com/forum/forum/china-h7n9-outbreak-tracking/143874-flutrackers-2013-17-human-case-list-of-provincial-ministry-of-health-government-confirmed-influenza-a-h7n9-cases-with-links?t=202713
  2. http://www.who.int/csr/don/20-february-2017-ah7n9-china/en/

Sunday, 19 February 2017

H7N9 in humans - biggest ever season in humans - most poorly reported as well

UPDATE: No.1 20FEB2017
Below is the best I can do to plot avian influenza H7N9) virus cases in humans against month.

And just to be clear - it's a very big underestimation. WHO is reporting 1,222 cases in humans [3] - but patchy public data exist for about 1,000.

Click on image to enlarge.
NOTE: This is a big underestimate as it only includes cases
with public detail available to identify them. There are 
approximately 200 cases missing. 
Ideally the charts above woudl be based on the month that illness onset occurred - when each person became ill. But those details just are not publicly forthcoming from China's massive human and animal influenza surveillance and testing system. 

I'm sure the data are to hand internally, and they may be on hand at the World Health Organization (WHO) - but you wouldn't know it by looking for them publicly. 

The WHO used to be helpful with providing H7N9 data but it seems their latest efforts to provide more detail on MERS cases has exhausted them.

Hong Kong's Centre for Health Protection (CHP) has been valiantly chipping away, but they also fail to provide sufficient detail to link cases with media or other reports. What they do provide are summary totals.

As for fatal outcomes from H7N9 infection - forget understanding who dies when and why. Those numbers have been frankly a pathetic mess for four years.

This week marked the fourth anniversary of our knowledge of H7N9 in humans - the first case became ill February 18th 2013 in as part of a Shanghai family cluster. Since then we've seen less and less detail on cases. And by "detail" I don't mean their names and addresses - just case age, sex, date of illness onset/hospitalization/death, linkage between case and death, poultry or human contact and place infection was likely acquired. Basic and standard stuff.

Meanwhile the mainstream media report every bolus of data that are dumped as if these were new cases and deaths that have just occurred. In reality, the huge January spike below may include many cases and deaths from a month or more earlier. It may mis many cases that have not been detected.

We're definitely having a huge H7N9 season in 2016/17 (n=176 human cases using public case data, but over 400 based on announced totals[3]). We had bigger detailed tallies in 2014 (n=326) and 2015 (n=220), but never a season as big as these totals make it out to be now. 

This is the largest H7N9 season ever recorded.

In media interviews over the past weeks, I've put the current season down to lethargy in closing live bird markets as cases and deaths have mounted. The response has been faster in previous years.[1,2] Poultry is a big deal in China.[2] Perhaps the poultry lobby has won out over human life this season. 

  1. Amended to indicate the scale of the case numbers, based on totals, not individual detailed cases, in the 2016/17 seasons. The largest season of H7N9 in humans...on record.

Friday, 10 February 2017

Science needs to talk more but I know many scientists who don't...


A comment I just replied to on LinkedIn which I thought was worth expanding on here - a rare moment of clarity pre-coffee.


Scientists don't engage the community - wearing their scientist hat - for a range of reasons. These can include...
  • because their Organisation doesn't support them
    ..or actively discourages them
  • because they fear making a mistake
    ..but errors are correctable and making them is a normal human(ising) trait
  • because there are no rewards
    ..selfless is for others huh? With less snark, there are only so many hours in the day and if engagement isn't able to be measured and put in a CV with outcomes, some academics simply won't partake. This needs to change - with or without someone having worked out a way to quantify these efforts - the world needs science voices. I'm pretty sure we can come up with innovative ways to make engagement part of the job/day/grant/life.
  • because they don't realise the need for such communication is dire
    ..and it really is
Apart from talking about what we do know and applying it to other situations in the news, science can bring logic to the other aspects of our lives - yes, that includes political aspects of life of which we as humans are always involved.

There is also a need for scientists to communicate clearly to the public about what we and do not know.

The community is more educated than it was and the questions it asks are more sophisticated than they ever were. Brushing them off - and I'm thinking about vaccines in particular here - with "but there's been no sign of harm" in the short term, is not good enough. If we as scientists, even if from outside a particular field of research, cannot find and point to work that answers a question about harm - how do we expect a member of the public too? Assumption: they've actually looked. If this happens then we need to roll out that tired old grant-writing adage, "more research is needed". Truth over sophistry is required today.

Not all scientists can communicate or can communicate in ways that non-scientists can understand. Not all scientists can engage with annoying people without losing their temper-or becoming annoying themselves. Not all scientists have knowledge on all topics (du-uh). I know what I'm talking about here because I'm talking about myself. So what I'm saying is that we scientists are just like any other human being. But, because of our training and skills, we scientists can also add clarity to biased discussions or rebut crazy conspiracies calmly and with reason. If we can, we should.

In my opinion, many individual scientists that could be good at any of those things are yet to wade in and stay for the long haul. One does not have to do this while representing an Institution or Organisation. Scientists are citizens and can simply apply our accrued education and experience to a range of problems. Of course, having a supportive and vigilant Institution may make a positive  difference to the scientist's initial brand and trustworthiness.

Let's use our science powers for good, not just for papers and funding.

Friday, 27 January 2017

H7N9 is having a big season...Happy New Year!

My how things can change in 5 weeks. 

If you look back a few posts you'll see that in late December, the data suggested avian influenza A(H7N9) virus was having a wimpy season - its slowest to date. 

Well, thanks to 100+ cases in China which have been bulk reported by the ever vigilant Hong Kong Centre for Heath Protection (CHP) - and captured and listed by FluTrackers - the situation has changed dramatically. 

Never take your eye off influenza virus - especially during its favourite season. And this season is a particularly active one for avian influenza all over the world.[4]

H7N9 is an avian influenza virus (hence the  "bird flu" moniker) that to date has been localised to China - especially but not exclusively to its eastern coast provinces - and it's a flu virus that doesn't make the birds it infects noticeably sick. 

These "low pathogenic" influenza viruses can sneak silently through poultry flocks because infections are mild - they don't cause infected birds to get sick or die. 

Data on human infections with avian influenza A(H7N9) virus. Data from [1]
Click on image to enlarge.
The H5 avian influenza viruses on the other hand - H5N1, H5N8, H5N5 or H5N6 for example - are called "high pathogenicity" avian influenza viruses because they kill off infected birds. Thankfully, H5N1 is the only H5 avian influenza that has caused a sizable number of human infections. H5N6 is gaining some ground though. The other H5s do not reportedly cause much impact in humans. Whether this is because they are not found or not sought in humans who have had contact with infected animals is unclear.

Disease in an H5-infected flock can serve as a sentinel for an outbreak of the virus. 

With H7N9 though, it's humans falling ill that set of the alarm that H7N9 (or another influenza virus) is in the house...or the market. And there are a sizable number of deaths among those - often male - who already have some sort of underlying illness and then acquire an H7N9 infection.

Most human cases of H7N9 result from contact with a "wet" market, also called a live bird market (LBM) in which chickens and ducks can be chosen, killed and dressed to provide a super-fresh meal. These tasty treats are especially in demand around this time of year as Chinese New Year is upon us. 


Chinese New Year is also a time when we observe the largest seasonal migration of humanity in the world. [2] Loved ones travel across a massive country to visit each other, share stories, traditions, meals - and the occasional respiratory virus like influenza. 

From [3].
In the coming weeks, as the gatherings disperse, it will be very interesting to see whether the current spike in human H7N9 infections is reflected by a steep rise in human cases acquired during the New Year celebrations - some of which include contact (direct or indirect) with infected poultry in backyard farms or LBMs.

Stay tuned. And don't forget to wash your hands often and cough/sneeze into the crook of your elbow.

References...

  1. http://virologydownunder.blogspot.com.au/2014/11/influenza-ah7n9-virus-detection-numbers.html
  2. https://www.nytimes.com/2017/01/26/world/asia/chinese-new-year-home-lunar.html?_r=0
  3. https://www.cdc.gov/flu/protect/covercough.htm
  4. http://news.trust.org/item/20170126150919-05z2c/