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
  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)


  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.


  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....

  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.


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.


  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