Sunday, 19 February 2017

H7N9 in humans - a very busy, but poorly reported winter in China

Below is the best I can do to plot avian influenza H7N9) virus cases in humans against month.

Click on image to enlarge.
Ideally  this would be month that illness onset occurred - when they 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. 

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 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. 

We're definitely having a big H7N9 season (n=176 human cases) - but as far as I can tell - we had bigger tallies in 2014 (n=326) and 2015 (n=220). 

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. 

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/

Thursday, 26 January 2017

WHO sets the table....and lays it with MERS-CoV details

This just made my day. A Tweet from scientist and program manager at the World Health Organization (WHO), Dr Embarek. In the tweet he noted that Middle East Respiratory syndrome coronavirus (MERS-CoV) data will now be presented by WHO in an easy-to-access Mirosoft Excel table...


An example is in this latest update.[1]

Excerpt of new MERS-CoV data from [1]
This will make data collection for scientists, public health teams and researchers looking to follow what's happening with this camel-borne virus as it spills over to humans so much easier. I've been painstakingly entering data from several sources since 2013 - and this will really streamline the process.

Thanks to those at the WHO for making this happen.

Now, could you please also do this for all the other pathogens you keep track of....different influenza viruses (H7N9, H5N6, H5N1), zika virus, dengue virus, yellow fever virus....and make it retrospective....

References...
  1. http://www.who.int/csr/don/26-january-2017-mers-saudi-arabia/en/


Monday, 26 December 2016

Snapdate: influenza H7N9 cases in humans, by the numbers...

An updated chart.
[SNAPDATE'S are snap updates that don't have lots of detail and chat...although they almost always end up having lots of chat!]

A summary of the monthly, weekly and daily data graphing human avian influenza A(H7N9) virus infections in humans reported from the hotzone, China.

Daily weekly and monthly H7N9 numbers, taken from the
FluTrackers curated line list [1] and the World Health
Organization disease outbreak news reports
.
Click on image to enlarge.

References...

Friday, 23 December 2016

H7N9:2016 has been the most quiet year to date...

Influenza A(H7N9) virus, or 'H7N9', has had a quiet year when compared to past outbreaks.

All human cases to date have been linked to China. The majority of human cases have had some link with poultry - chickens or ducks - although we do hear of human-to-human transmission, this seems to be limited. H7N9 has been found in poultry from backyard farms and in live poultry markets (LPMs) in China - sometimes in the company of other influenza viruses, like H9N2.[1]

Cases and deaths each month over the 4 years we have known
about human cases of H7N9 infection.
Click on image to enlarge.

Despite the slow year,the 2016 graph above shows the usual December uptick in human cases. It will be what happens next that matters. Will be see a big January surge as in 2014, or a later Feb-April surge as in 2013 and 2015? Will live LPMs be quickly closed, disinfected, the animals destroyed and any outbreaks in 2017 squashed or will they remain open allowing more human cases as the virus spreads among market animals?

Time, and testing data - which China generates lots of but does not seem to enjoy publicly reporting - will tell.

In 2016 - 2 new regions were added for the first time - Tianjin municipality and Liaoning province - both in the north-eastern coastal region of China. 

In 2013, no sustained human-to-human transmission had been reported [2] - this remains true up until today.

References...

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911810/pdf/nihms749408.pdf
  2. http://www.nature.com/news/mapping-the-h7n9-avian-flu-outbreaks-1.12863

Sunday, 18 December 2016

Happy Festive Season to all who read this....

..whatever your shape, colour, gender, sex, size, beliefs, weight or disposition. 

May 2017 be a better year for those of us who wish to see humankind progress in many peaceful, intelligent, creative and joyful ways.

I wish for you a festive period that is safe, healthy and good to you and your loved ones, your friends and your pets.

Take care.
Ian M. Mackay, Ph.D.



Sunday, 4 December 2016

Zika virus-positive microcephaly in Colombia...

The latest epidemiological report (epidemiological week 47) from Colombia, which includes data on Zika virus (ZIKV) disease (ZVD; 20NOV2016-26NOV2016), has been produced by the Colombian National Institute for Health team.[1]
NOTE: While these data were reported the past epidemiological week (EW), they may not be from that week. See earlier post about possible reporting lag.

As of this report, 60 (+0 from last EW) live births have been diagnosed with congenital ZIKV syndrome (CZVS; microcephaly/central nervous system disorder), confirmed as being ZIKV positive. That represents 1.0% of all confirmed ZIKV positive mothers-a slowly but steadily rising proportion.

The change in confirmed ZIKV infection numbers when detected in
association with a microcephaly diagnosis, Colombia, compared to the
preceding week's total (yellow bars, right-hand axis). Those diagnoses still in question and under investigation are shown as yellow dots (left-hand axis).
Data are from [1]. 
Click on graph to enlarge.
It has now been 415 days, or 1 year, 1 month and 18 days, since ZIKV was first confirmed in Colombia on 16th October 2015.[5] Keep in mind that when talking about microcephaly - we have to think back in time to what insult or infection might have occurred during pregnancy. The counts of ZIKV occurring this week will have zero impact on what happened back then. Also keep in mind that Colombia may be reporting things differently from Brazil.[3]

The cumulative curve of confirmed ZVD cases
(green circles, left-hand axis) and the change in confirmed ZVD case
numbers when compared to the preceding week's total
(green bars, right-hand axis). Data from [1].
Click on graph to enlarge.

No new laboratory confirmed ZIKV detections have been reported in Colombia for eh 20th week (green graph, above).


Brazil first reported positive (but unconfirmed) laboratory tests for ZIKV disease on 29th April 2015. Brazil then started to report a rise in foetal anomalies (an initial 141), in the form of microcephaly on 30th October 2015. This was 184 days - or about 6 months later.[4] However, the genetic analyses suggest ZIKV was in Brazil from around 2013. It had a lot longer to get established. Perhaps this is the difference between Brazil and Colombia, given reports a growing 2,180 ZIKV congenital syndrome diagnoses [2] compared to Colombia's 60.

References...

  1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/2016%20Bolet%C3%ADn%20epidemiol%C3%B3gico%20semana%2047.pdf
  2. http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&Itemid=270&gid=37143&lang=en
  3. http://virologydownunder.blogspot.com.au/2016/06/the-elephant-squeaked.html
  4. http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&gid=35139&Itemid=270&lang=en
  5. http://www.nejm.org/doi/full/10.1056/NEJMoa1604037#t=article

Friday, 18 November 2016

The reality of the post-truth world's impact on science communication...

So:
 We tweet 2each other. 
We write 4each other. 
We're considered elite. 
We don't understand our community. 
We can't reach them. 

Cool. [sarcasm]

P.S.
Post-truth is now defined by the Oxford dictionary...

ADJECTIVE

Relating to or denoting circumstances in which objective facts are less influential in shaping public opinion than appeals to emotion and personal belief:

‘in this era of post-truth politics, it's easy to cherry-pick data and come to whatever conclusion you desire’


‘some commentators have observed that we are living in a post-truth age’