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.



This is a very crude graph though because its unclear whether any of he number up until December were reported by the Hong Kong Centre for Health Policy in any of their recent posts. 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. 

It's 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 of 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.