H7N9: the dotted lines that make sense of things...[CORRECTED]

Click on image to enlarge.

The latest H7N9 case-per-day chart shows that the trickle of human cases of confirmed avian influenza A(H7N9) virus infection is becoming a drip. The tap? My money is still mostly with the market closures. What precisely in the markets is the source of human H7N9 acquisition? Dunno, but the consensus seems to be poultry; songbirds also look pretty good though. It doesn't have to be, and is unlikely to be, just 1 thing of course. We know that this virus, as with other avian influenza viruses, can be shared around among bird species. It can even go into a human and that isolate be used to infect a bird again. See my recent post on some of this.

Click on image to enlarge.

What's also particularly intriguing, among the many interesting aspects of H7N9's acquisition and spread among humans, is that we're seeing much more "shouldering" in the Wave 2 epidemic curve than we did in Wave 1's.

Instead of the precipitous decline we saw back in 2013, we're seeing a drop down to ~10 cases per day, but then a slower decline the rest of the way. Is this because we started human cases from more sites this time around?; because markets took longer to close after the cases numbers began to climb?; is it related to markets being closed at different times, in different ways, in different locales? Who knows?

Cases by region acquired, per week, with different
 regions highlighted by coloured lines and the 
total case number in the background (grey).
Wave 1 and Wave 2.Click on image to enlarge.

Dr Katherine Arden suggested I have a look at what's happening in each Province or Municipality and see whether any particular place can shoulder the blame for the shouldering. And that does seem to be the case if you look at the adjacent chart. Guangdong province seems to be the major culprit contributing to the shoulder effect. 

Cases by region acquired, per week, with different
 regions highlighted by coloured lines and the
total case number in the background (grey).
Wave 2 only.
Click on image to enlarge.

In the zoomed-in version that focusses on Wave 2 alone, we can see that the Wave 2 "peak" has in fact 2 peaks; the 1st peak dominated by Zhejiang province cases and the 2nd driven by a surge in Guangdong provincial cases. Guangdong cases took longer to drop away, and are in fact still being reported, possibly because the major poultry markets there were closed later than in Shanghai and Zhejiang province and only temporarily for a clean. Or perhaps the bird outbreak @influenza_bio and I discussed has a source in Guangdong province?

It's all speculation beyond the data we can actually plot.

Guangzhou reopens live poultry markets: Good idea or too soon?

Curve of H7N9 human cases in the two most hard-hit
Provinces in China Zhejiang and Guangdong.
Hangzhou shut its poultry markets 24-Jan.  Guangzhou shut
its markets 15-Feb. Similar rate of cases in Wave 2 of H7N9.
The difference? Zhejiang's markets remain closed.

Well, that seemed like a very quick 2-weeks. But it is 2-weeks (see my earlier post when the markets shut) and a lot of financial hardship for the local poultry industry. They will breath a sigh of relief as the chickens start moving through the crowded markets once more.

With new H7N9 human case announcements reduced to zero for the past 2 nights (my time), we'll now get a look at what happens when a market gets restocked after the region it serviced has had a transmission interruption, and the weather moves towards Spring and its subtropical rainy season. Will the market be restocked from virus-positive farms? Is the weather still conducive to maximising H7N9's chances of being picked up by humans? Will surveillance methods have changed at the markets in Guangzhou? 

"..poultry traders are required to clean their stalls every day, carry out a thorough sterilization once a week and close business one day a month."                                                                                   Shanghai Daily.

It is like watching an experiment played out in real-time. Without the Aims. Or hypotheses. Or controls. Or stuff.

h/t to @Potrblog as my source for this article.

Related links...

1. Zhejiang province leads the way in H7N9 cases and their decline 3-weeks after market closures...
   http://virologydownunder.blogspot.com.au/2014/02/zhejiang-province-leads-way-in-case.html
2. Guangzhou reopens live poultry markets
http://www.shanghaidaily.com/national/Guangzhou-reopens-live-poultry-markets/shdaily.shtml
3. China.today Guangdong Province weather
http://www.chinatoday.com/city/guangdong.htm
4. Shenzen shopper weather
http://shenzhenshopper.com/weather

Shanghai and Hangzhou to permanently stop live poultry markets.

According to the report on CNTV.com ENLGLISH linked below, the poultry industry in Shanghai and Hangzhou (the capital of Zhejiang province) is about to change significantly (h/t Crawford Kilian's H5N1 blog post and Tweet on this).

A new plan for the use of processed poultry in place of live or freshly butchered birds will be rolled out in late February.

Brilliant news!

As you can see in the short news video, some (n=1) of the public see the sense of a change as well as the benefits of not having to deal with slaughtering and plucking chickens while others (n=1) complain that there will be a taste difference. 

I've never known much truly fresh chicken (I'm more a fan of the flavours its cooked in) so in my ignorance I don't know whether I'm missing something special or not. 

I do know what it is to miss a bad bout of the flu though. That's something I'd go the long way around to avoid crossing paths with.

This change seems so much more in concert with a China made of glass and steel. Good work. I hope it catches on elsewhere.

Sources...

1. CNTV Report
   http://english.cntv.cn/program/newsupdate/20140215/103244.shtml
2. H5N1 blog
   http://crofsblogs.typepad.com/h5n1/2014/02/china-hangzhou-to-build-h7n9-prevention-system.html

Zhejiang province leads the way in H7N9 cases and their decline 3-weeks after market closures...

Click on image to enlarge.

It's the Province in China that has seen more H7N9 cases confirmed in human than any other Province (39% of all cases have originated here). 

It reached 50 cases faster in 2014 than 2013. 

It closed its markets back in 24-Jan. And for a little while it kept finding new cases. 

But the past 2-days have see no new cases announced from Zhejiang province. Eerily reminiscent of 2013 sudden disappearance of cases announcements.

If we look at the data by date of onset of illness (pretty much all of the second wave data are this thanks to WHO's reporting and data fill-in) in the chart above, we can see this decline clearly depicted. 

After three weeks of cases nearing 20/week, they've dropped to less than half and then a quarter of that rate. 

Cases are still coming out of Guangdong Province though, but I don't have market closure dates to hand for Guangdong. 

Actually - now I do. Guangzhou's markets have just been shut (Friday, 15-Feb but only until 28-Feb) according to a timely update at Crawford Kilian's H5N1 blog as I write this. Well, that's pretty late in the game and will certainly not be a long term solution. 

I'm surprised that the vocal poultry industry has not yet realised that this sort of money-haemorrhaging close-disinfect-open-restock cycle of events will continue to recur so long as this way of presenting chickens continues. 

Instead of crying fowl (oh yes I did) it would be worth investing that energy and money into educating the population about the freshness and safety of factory-prepared refrigerated/frozen poultry. To my mind anyway. 

Create and promote new oversight and checks and balances to assure the population that the chickens won't be prepared in some dodgy way; about the cold chain; about the benefits in the longer run. 

Of course those assurances would rightly need to include some proof that concerns were unwarranted that poultry were being presented that had:

• died from disease or poisoning due to pesticide, melamine or grain fumigants
• been treated with harsh chemicals such as bleach or other disinfectants (credit: anonymous). 

A long road a ahead if this path is ever chosen but it would life-saving benefits both at home and worldwide. Hopefully the industry will find a way to evolve and still make a profit when it is able (or is forced) to see past its grief and current anger at everyone else. 

But back on topic, if Zhejiang is anything to go by - expect to see the Guangzhou (who knows about the rest of Guangdong province?) cases decline steeply within 3-weeks.

Zhejiang remains as my sentinel Province for watching the potential impact of live bird market closures. Last year, daily case numbers dropped by 97-99% within about 3-days of market closure in different Provinces.

Will the drop we've seen recently in Zhejiang be maintained in 2014 as it was in 2013, or will cases take off again? If so and in the absence of data to support any other reason for human cases declining, I think Zhejiang should be used by China's Ministry of Health as an example with which to "educate" the poultry industry on what happens to an emerging lethal infectious disease when you take the live poultry markets out of the equation.

Stay tuned.

H7N9 snapdate: Zhejiang in the East, Guangdong in the South

Click on image to enlarge.

Zhejiang province is still climbing in eastern China despite market closures almost 2-weeks ago. 

Guangdong in the south surpasses 50 cases as well as Shanghai municipality and Jiangsu province, in terms of total counts.

Fujian province adds a few cases (at least some markets have been closed for disinfection) and now Hunan province is rising above the background "noise".

CIDRAP recently noted that United Nations Food and Agriculture Organization (FAO) was confident that Vietnam, on the border with Guangxi province (now at 3 cases), had not detected any "signs" (ill people, PCR positive birds..?) of H7N9 to date but intimated porous borders were a reality. And in China, market closures do not necessarily mean a halt to the purchase and household preparation of live/freshly killed poultry; they just necessitate a longer trip into the countryside to maintain spring festival meal traditions.

Zhejiang province surpasses 100 avian influenza A(H7N9) cases...

As of tonight's 2 additions, my tally shows Zhejiang province on 101 H7N9 cases, 41.2% of all 245 human infections confirmed to date. The BBC recently noted 55 deaths which would result in a PFC of 22%. This continues the lower trend we've seen in the PFC for a while now; the result of a sharp increase in new cases but few deaths among those.

In reality both the Zhejiang and the total case numbers are very likely a massive underestimate of the actual number of human infections, but until we have any actual lab testing results, we won't know that for sure and can only speculate on what's "out there" based on our experience, extrapolation from other outbreaks, epidemics and pandemics, 60+ years of respiratory virology research and a touch of logic.

Overall, in the most active of the case acquisition periods of 2013, we saw case numbers rise an fall abruptly...

• Week 5: 7 cases
• Week 6: 17 cases
• Week 7: 29 cases
• Week 8: 40 cases
• Week 9: 22 cases
• Week 10: 6 cases

In 2014 we seem to be right in amongst that now as we (in Australia) see out Week 49..

• Week 45: 6 cases
• Week 46: 26 cases
• Week 47: 33 cases
• Week 48: 12 cases
• Week 49: 17 cases

We are still seeing a few cases with illness onset in Week 47 (6-Jan to 12-Jan) so tat could yet reach Week 8's levels, or more unless the market closure start to show an impact soon.

Zhejiang live bird market closures and enhanced monitoring of farms, wild bird habitats and parks...

Crawford Kilian is always on top of the market closure announcements, and Xinhua in general. His recent blog post is particularly welcome; halting of live bird trading in Hangzhou's markets (on Friday 24th). Markets in 6 districts will be closed and disinfected and some/more monitoring of birds (hopefully not just for H7N9) will be launched on supplying farms and in wetlands and parks. I hope that's all RT-PCR-based.

Hangzhou is the largest (2.5-million people), and capital city of Zhejiang province, a region that has served as H7N9's playground over the past few weeks. 

This action comes on top of 2 other districts (1 in Hangzhou and one in Jinhua) already having closed their markets.

Shanghai closes up 31-Jan to 30-Apr, for the Spring Festival. 

The Xinhua story quotes Li Lanjuan of the Chinese Academy of Engineering and director of State Key Laboratory for Diagnosis and Treatment of Infectious Diseases as predicting that...

"China will see more human H7N9 cases in the future as the virus tends to become more active during winter and spring"

...or at least, human cases appear more often then.

References...

1. Crof's H5N1 blohg
   http://crofsblogs.typepad.com/h5n1/2014/01/h7n9-hangzhou-halts-live-poultry-trading-shanghai-reports-2-deaths.html
2. Xinhua article
   http://news.xinhuanet.com/english/china/2014-01/24/c_133069407.htm

Zhejiang province: then and now in H7N9 town

Click on image to enlarge.
The data are plotted as number of cases (y-axis)
vs. week of illness onset (or date reported if
onset data was not reported). The time span is
the same for both graphs (2-months) and the
number of cases is fixed at a 50-cases on
the y-axis of both so that the slopes can be
compared.

A quick look at what life was like in Zhejiang province, the current H7N9 hotzone, over a 2-month period (top) when cases really took off in 2013 compared to the past 2-month period this year.

The current slopes is less steep and the case tally is a little lower, but it is not hard to see that both will increase if the current rate of cases continues; of the last 18 H7N9 cases, 12 (67% or two-thirds) were from this province.

New influenza A(H7N9) virus case in

Chinanews reports a new infection by H7N9 today.

A 57-year old male was confirmed as positive 27-Nov and is in hospital in Hangzhou, the largest city in Zhejiang province. Zhejiang province was the hot spot for H7N9 earlier in the year.

This is the 141st case of H7N9 which emerged in 2013 in south east China. Most of the recent cases have been in Zhejiang.

Two deaths and 5 new confirmations tip the numbers above 100

..avian influenza A(H7N9) cases. Nothing has changed since yesterday, apart from Zhejiang province now surpassing Shanghai municipality in the total number of cases reported and accelerating (see chart below) in case numbers at a very rapid rate.

Still, but a 3-digit number tends to sound more scary to some - so expect the media to carry big banner headlines akin to "100 cases of killer virus in three weeks!"

Shanghai still has the highest case load..

...but Zhejiang has surpassed Jiangsu to take second most active spot for H7N9.