Guangdong sees sense among the feathers...

Guangdong province in southern China is suspending its poultry markets. All of them. From 15-Feb to 28-Feb.[1] While the closures are only for 2-weeks, this will be very important for stopping human cases of avian influenza, particularity of the H7N9 subtype, during the bustling spring period in China. 

Live poultry market closures also remove a traditional dish of fresh cooked chicken. One can be certain that no-one will die because of the substitution of frozen or factory prepared chicken for a fresh chicken, even if chefs don't succumb to the tantrums of last year and refuse to prepare dishes made from anything but fresh market-selected poultry. One can be equally certain that if the markets remain operating during the peak season for influenza virus circulation as they have been, that human infections, and deaths, due to H7N9 infections, will also continue 

Guangdong province has been a major
source of human H7N9 cases in 2015.

Some restrictions were put in place back in December 2014 [2], but that did not stop human cases of infection or deaths.

Why does this closure in Guangdong matter? 

Guangdong province has been a major source of human H7N9 cases this year, as it was in 2014. If we look at the activity under the outbreak curves, we can see the brown line of Guangdong cases has been prominent in both years, only brought under control last year after the closure of the poultry markets...although their temporary closure may have been the reason for the long tail on Outbreak #2's epidemic curve compared to Outbreak #1. Will that tailing happen again in 2015 because Guangdong's markets are only being closed for a short period? Time will tell. 

Occurring at a similar time is the change in seasons. Seasonal change towards summer, makes the survival of influenza viruses in the environment more difficult. It's hard to tease out any one main cause of the precipitous case decline; the market closures or the seasons changing or both. Because most H7N9 human cases have exposure to poultry listed among their details when they are passed along and posted by the World Health Organization, live poultry markets clearly are one major factor for human acquisition of infection. There is literature that agrees.[3,4,5]

The activity under the epidemic curves for each of the three outbreaks. Guangdong province-acquired human cases are indicated by the brown line and features in 2014 and 2015.

Having these markets close is a great achievement for stopping these unnecessary and preventable infections and deaths die to H7N9. Its a big step, a sacrifice and its social change in action. But shutting them permanently would be better.

References...

1. http://news.xinhuanet.com/english/china/2014-02/15/c_126138118.htm
2. http://www.thepoultrysite.com/poultrynews/33938/guangdong-restricts-poultry-markets-over-bird-flu-fears
3. http://www.ncbi.nlm.nih.gov/pubmed/25340354
4. http://wwwnc.cdc.gov/eid/article/20/12/14-0765_article
5. http://jvi.asm.org/content/88/6/3423.long

Read More

Societal change and H7N9..

The importance of societal change for controlling infectious disease outbreaks really cannot be over-stated. 

For Ebola virus disease, it came down to stopping the tradition of direct contact with the body of those who have died and dircet contact in general. For MERS it

seems that occasional camel contact triggers insertion of the MERS-CoV virus into hospitals where lax infection prevention and control practices add to the case load. 

For influenza A(H7N9) virus cases, it is the habit of obtaining live poultry from retail markets where rare virus-laden chooks are culled and handed over because of a desire to see, choose and purchase the tastiest fresh chicken. 

There is a common thread among these stories about direct contact or inefficiently droplet-transmitting virus infections: we can stop their spread. 

But we also amplify and prolong their spread. 

However, when it comes to human-adapted, efficient droplet-spread or airborne-transmitted viruses - well, then we're in trouble. Of course we could all just lock ourselves in a room for a few weeks but that won't ever happen.

So its very important to head off these "emerging" viruses while we still have a modicum of control over them. Once they get away from that control, and theoretically that could happen in the blink of an eye-right now even-no amount of fancy infra red cameras, poorly donned surgical masks or fancy hospitals laden with machines that blink and go ping, will stop them from spreading globally.

Cheery.

In the meantime - here's hoping China speeds up the closure of those live poultry markets. Habits can be changed but death is forever.

Click on image to enlarge.

Read More

Avian influenza A(H7N9) virus found in more than half of wet markets in Guangdong...

It comes as no surprise to me, but is still a very welcome piece of data, that Guangzhou's ongoing live bird markets and concurrent continued cases of H7N9 in people, are also happening in a an environment of 60% of market stalls tested positive for the virus in April.

A report in the South China Morning Post noted 

"Upon conclusion of the trial on September 30, the city government proposes gradually extending the ban, covering chickens, ducks, geese and pigeons, to other parts of the metropolis. The ban is expected to be implemented citywide by 2024."

"Currently, it affects 298 live poultry stalls at 82 wet markets in Yuexiu district, and in parts of Tianhe, Liwan and Panyu districts, where vendors will sell centrally slaughtered chickens that will be provided by three designated suppliers."

This is welcome news and a positive step towards stopping not just H7N9, but a raft of other influenza viruses that jump to us from, and mix to create new virus within, birds.

Source...

1. http://www.scmp.com/news/china/article/1505389/guangzhou-begins-trial-ban-live-poultry

Read More

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.

Read More

H7N9 and human infections: not just a paltry matter

Jones and an all-star cast of colleagues from Hong Kong, Shenzen, Beijing and Tennessee have looked at songbirds and their susceptibility to a human isolate (infectious virus recovered from a human case of H7N9 influenza) H7N9 infection (1).

But before I note the good bits of their study, this paper is one of importance for adding a lot to our understanding of how H7N9 is jumping to people from poultry/live bird/wet markets. It's also a great reference if you want to better understand influenza and birds overall. 

We've read much about human cases of this avian virus having had contact with "poultry" and bird markets and  from that we assume that poultry are the pool in which H7N9 is swimming (reservoir); but where did the poultry get it from (source/natural host)? Its also interesting to note that: 

1. Very few poultry test positive for the virus; may simply be because of a test-based problem including using a test that is insensitive or sampling from the wrong end of the bird (testing the cloaca instead of throat as was discussed ). 
2. Looking at the sequences of the H7N9 gene segments suggested that wild birds (bramblings) played a part in the evolution of the virus currently infecting humans in south east China (4)
3. Pigeons have tested H7N9-positive (2,3)

So it might be that at least some of the human exposures are not from poultry but from other birds.

The authors of this latest article note the songbirds are common pets and so are in close contact with their owners. In the wild, such birds are likely to interact with farm birds.

Some key findings of this new study are:

• A/Anhui/1/2013 was the strain used for H7N9 studies; it was an isolate from a human but early on and similar to bird (6) strains. H5N1 (A/Vietnam/1203/05) and H3N8 (A/songbird/Hong Kong/SV102/2001) were also used for comparisons
• Zebra finches (Taeniopygia guttata), society finches (Lonchura striata domestica), parakeets (Melopsittacus undulates) and wild-caught house sparrows (Passer domesticus) were kept isolated for 3-weeks prior to experiments to let any naturally acquired infections burn out; none of the birds had antibodies suggestive of previous infection by an H3, H5, H7 influenza A virus (is that low prevalence normal?)
• Birds were inoculated with 10⁵ 50% egg infectious doses of virus via nose, eye and mouth (that should do it) and then put in the same cages, sharing water and food, with uninfected birds
• Virus testing was by growth using eggs (3/sample collected)
• All inoculated birds shed virus (only) from the oropharynx; finches shed most virus at 2-days post inoculation (dpi); parakeet viral shedding could be detected by culture for 2-days and from finches for 6-days
• Communal water troughs yielded culturable virus; zebra finches shed most virus but water consumption and drinking frequency were not measured and may have differed among bird species
• No virus could be detected at 8dpi
• 1 sparrow showed signs of disease and died; 1 zebra finch died without signs of disease (some loss of appetite)
• Birds in contact with infected birds did not often acquire infection but when they did, they also shed via the oropharynx
• In finches that were killed for organ testing, virus was mostly found in the trachea; some was isolated from brain and eye tissues of 1 society finch and in the small and large intestine and a high titre form the lung of the other. H7N9 was grown from the brain, lung and intestines of zebra finch. H7N9 was not found in surviving sparrow organ tissues; in the dead sparrow, some H7N9 was found only in the lungs
• Nearly all inoculated birds mounted a specific antibody response to H7N9 after inoculation. Among the contact birds, 3/3 zebra finches, 1/3 society finches (had highest amount of antibody), 2/3 sparrows and 0/2 parakeets mounted a response to virus indicating that they were infected but did not show signs of illness nor did they shed virus, at least at culture-detectable levels

So songbirds, can be infected by a human H7N9 isolate, they can shed the virus into the environment, they can die (presumably) due to H7N9 infection, 33-66% of songbirds in contact with an experimentally infected songbird acquire aninfection (even if it was rare to grow infectious virus from that contact which may be a sensitivity issue of the testing) and they mount an immune response to the infection. Given that H7N9 acquisition seems to be a numbers among humans, this degree of transmission among birds fits well.

It was also very interesting that water troughs often contained lots of shed H7N9 virus. This is not new in the world of influenza virus but its nice to cross the 't' for H7N9. The authors note that studies of transmission from songbirds to poultry via communal water sources are yet to be conducted. Seems like this would be a very important piece of the influenza puzzle and with broad application to future outbreaks and seasonality in birds via migration. 

Add to all of this that songbirds are present in many markets (thanks to @Crof, @Laurie_Garrett and @debmackenzie1 for supporting info via Twitter this morning; also see refs from Jones et al (1) and a related story from New Scientist (8)) and that older males are a key demographic for keeping songbirds as luck-enticing (and cute) pets. They are also over-represented among H7N9 cases (see adjacent chart). A good fit.

Another recent study (7) shows chickens and quail (a possible amplification host helping bridge the gap between wild birds and poultry) shed a lot of H7N9 after experimental inoculation via an intranasal route. Also, quail (but not pigeons) shed enough H7N9, for long enough, to pass it along to their contacts; less so ducks.

None of this may be very new to some of you, but it's nice to see data that confirm it all for H7N9. After all, as someone reminded me recently on Twitter, data is just how we roll.

It's not hard to see the circle of life for influenza viruses is there for the interpreting and that non-poultry birds may be important intermediate hosts of H7N9 and act as a source of other influenza A viruses. 

Just how many human cases of H7N9 are acquired by songbirds vs chickens/ducks/quail/geese remains unquantified....perhaps unquantifiable.

References...

1. Possible Role of Songbirds and Parakeets in Transmission of Influenza A(H7N9) Virus to humans.
   http://wwwnc.cdc.gov/eid/article/20/3/pdfs/13-1271.pdf
2. A summary of Influenza A(H7N9) virus findings in birds and humans
   http://newsmedicalnet.blogspot.com.au/2013/10/a-summary-of-influenza-ah7n9-virus.html
3. Emergence of avian influenza A(H7N9) virus causing severe human illness - China, February-April 2013.
   http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6218a6.htm
4. Sunny summer or birds on the wing?
   http://newsmedicalnet.blogspot.com.au/2013/05/sunny-summer-or-birds-on-wing.html
5. Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses
   http://press.thelancet.com/H7N9genetics.pdf
6. Genetic analysis of novel avian A(H7N9) influenza viruses isolated from patients in China, February to April 2013http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20453
7. Role of poultry in spread of novel H7N9 influenza virus in Chinahttp://jvi.asm.org/content/early/2014/02/20/JVI.03689-13.long
8. Budgies may be behind latest spread of H7N9 bird flu
   http://www.newscientist.com/article/mg22129542.000-budgies-may-be-behind-latest-spread-of-h7n9-bird-flu.html#.Ux5CnvmSx8F

Read More

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://newsmedicalnet.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

Read More

Live bird market closures continue...

Changsha, capital of Hunan province has had its live poultry markets closed since 21-Feb (1).

H7N9 case map.

So that can be added to Shanghai, major markets in Hangzhou, Ningbo and Jinhua cities in Zhejiang (15), markets in Guangzhou, Guangdong ((3); plus a previous 2-week pause for disinfection in Shenzen (15) ), Hong Kong recently extended its ban (4) on live poultry imports from mainland China and Fujian provinces markets were closed fro disinfection back in 21-Jan. 

No word, that I can find anyway, on market closures in the Jiangsu province (11.8% of all H7N9 cases), other sites in Fujian province (5.5%) or Anhui province (2.5% but over-represented in cases recently).

And yet with no cases announced yesterday - the latest in a recent precipitous decline in total human cases per day - it's tempting to wonder whether market shutdowns in regions that have had the highest case activity (Zhejiang and Guangdong provinces) and which produce or trade a lot of the nation's chickens, have had enough of a flow-on effect to stem the tide in other regions supplied by these. 

Aside #1: Poultry eggs are mainly produced by >1-billion birds in Henan, Shandong, Hebei, Liaoning, Jiangsu, Sichuan, Hubei, Anhui, Heilongjiang and Jilin (7,8) whereas >4-billion broiler chickens (bred for meat) are more concetrated in Shandong, Jiangsu, Guangxi, Liaoning, Guangdong, Anhui, Sichuan and Henan provinces  (2,6,8,9,10,11,12,13).
Aside #2: An interesting to read (5,9) that the volume of chicken consumed per capita has risen by 9-fold or more in recent years - it has not always been the staple but is part of the tradition.

Sources...

1. http://english.cri.cn/11354/2014/02/22/2702s814226.htm?utm_source=dlvr.it&utm_medium=twitter
2. http://www.globaltimes.cn/content/843788.shtml#.Uwl4ovna6-1
3. http://newsmedicalnet.blogspot.com.au/2014/01/zhejiang-live-bird-market-closures-and.html
4. http://www.interaksyon.com/article/81029/hong-kong-extends-ban-on-live-poultry-imports-from-mainland-china
5. http://www.iatp.org/documents/fair-or-fowl-industrialization-of-poultry-production-in-china
6. http://www.forbes.com/sites/russellflannery/2013/04/13/by-the-numbers-chinas-poultry-industry/
7. http://www.prweb.com/releases/chinas-egg-and-poultry/industry-research-2013/prweb11170628.htm
8. http://www.ccagr.com/content/view/117/184/
9. http://www.newschinamag.com/magazine/poisoned-plucked-processed
10. http://www.tysonfoods.com/Around-the-World/International-Operations/Tyson-China/About-Tyson-China.aspx
11. http://www.wantchinatimes.com/news-subclass-cnt.aspx?cid=1103&MainCatID=11&id=20140219000043
12. http://articles.chicagotribune.com/2012-04-19/business/sns-rt-us-usa-china-food-factboxbre83j05v-20120419_1_hog-farm-province-hubei
13. http://english.agri.gov.cn/hottopics/ah/201310/t20131028_20492.htm
14. http://news.xinhuanet.com/english/photo/2014-01/22/c_133063832_2.htm
15. http://news.xinhuanet.com/english/china/2014-01/31/c_133087279.htm

Read More

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

Read More

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.

Read More

H7N9 case announcements dropping: is Wave 2 under control? [UPDATED]

Its a very tough question to answer. There has been public pressure by China's poultry-farming groups on China to take measures to stem the industry's financial losses. These have been driven by the public concern that H7N9 can seriously afflict people and in about a fifth of recorded instances, kill them. 

And rightly so. The concern for those of us outside China is that reporting may be artificially halted, reduced or stemmed to calm the public - while doing nothing to stop the march of H7N9. This concern extends into thoughts about why we have so very few 2014 H7N9 sequences to date. Background for this paranoia about non-biological reporting limitations takes the form of :

• MOA noting no evidence of H7N9 in poultry farms (1). Perhaps time to propose an alternative source then?
• Poultry industry writing to demand that descriptors like "H7N9 bird flu" or "people infected with H7N9 avian flu" be changed to "H7N9 influenza" (2)(4). No argument from me there - bird flu is not part of the WHO nomenclature anyway. It's a media thing. Seriously though, will the name change the infections? Of course not. Same virus, same bird/poultry association with human disease. Call it Frank if you like but the process of infection, morbidity and mortality in 1:5 cases will go on.
• Poultry industry groups asking Guangxi and Guangdong provincial governments to stop reporting each H7N9 case (3). Not acceptable and not addressing the problem at the source.

Click on image to enlarge.
Cases per day for all of Wave 2 (arbitrarily selected as
Oct-7-2014) and specifically for 2014. 
Orange and blue dots mark the rolling average
(each dot [data point] is the average of all data points
before it). The grey dots are the cases with illness
 onset on that day. The green bar reflects he current
laboratory turnaround time; the time between date
of illness onset and the date of reporting which we
hear about 2-3 days after the case is reported by
the jurisdictional Ministry. The pink bar indicates
that 2-3 day WHO delay period. Please allow for the 
fact that I am doing this from Australia which is 
ahead in time from the Northern hemisphere so my 
data are from "yesterday" and the x-axis extends into
a day you haven't had yet. The date the Hangzhou bird
markets in Zhejiang closed, my sentinel Province for a
market impact, is indicated. 

So, when we see a chart like this one, we may have those doubts at the forefront of our minds; more so than other reasons for what appears to be a constant decline in case reporting in recent days.

One such reason would be that the market closure (22-days ago for Zhejiang) and the laboratory reporting delay (currently 8.7-days for Wave 2) have finally caught up to the present day - and we are seeing a real impact of reduced exposure of humans to birds (poultry or market-based wild/song birds). 

As @influenza_bio (please follow him if you have an interest in flu - a real repository on influenza) noted on Twitter, it may also reflect a change in bird migration patterns. To me that that seems to be 2 coincidences in a row given a similar relationship between cases dropping and markets closing last year. The different could be that weather changes helped speed up the case decline in 2013. Maybe.

None of you reading this (since I believe the blog cannot be accessed in China) know the actual reason for this decline. 

In the absence of any other data or a change in climate, I'm proposing that the case decline to a direct effect from the market closure. If that hypothesis is correct, we will see continued decline in cases in Zhejiang and wherever else markets were closed. 

That decline in total H7N9 human case announcement began 3-days after Hangzhou markets closed. Given that most cases were accruing from Zhejiang province, I still think that's a good place to watch.

Sources.

1. Xinhua story.
   http://news.xinhuanet.com/english/china/2014-01/27/c_133078220.htm
2. Xinhua story (needs translation)
   http://news.xinhuanet.com/2014-02/04/c_119212598.htm
3. South China Morning POst
   http://www.scmp.com/print/news/china-insider/article/1421319/chinas-poultry-industry-wants-hush-bird-flu-news-damage-control
4. China Animal Husbandry Association
   http://www.caaa.cn/show/newsarticle.php?ID=329866

Read More

If not poultry then what? [UPDATED]

Maybe China needs to look at other
animals, both within market 
environments and at the source farms 
(using sensitive molecular tools as they 
have been), to find the "smoking chicken" 
(shamelessly stolen from Mike Coston)...
which may not be a chicken at all.

Mike Coston has written a nice post about the Chinese MOA denying that there is any proof of direct transmission of H7N9 from poultry to humans. 

Technically, they are of course correct. 

We have yet to see a human put in a cage downwind, but separated from, a flock of infected chickens or duck or geese to see if the human acquires H7N9 infection and disease. Nor have we seen any card-playing lockdown transmission scenarios to investigate aerosol, droplet and direct transmission routes. 

Nonetheless - if you take a look at a snippet of my list of H7N9 cases compiled from various public sources, "poultry" contact is mentioned...a lot; 72% of those rows (if you exclude the 19 awaiting WHO notification data; see below for update). 

Of course it may be a "poultry" euphemism or a translation error (I'm asking @WHO) for contact with any feathery creatures, so song birds and wild birds may be the source in the markets....or another animal altogether of course but I think something non-feathery would have shown up as a pattern by now.

[UPDATE] Gregory H�rtl notes..

.@MackayIM @WHO "Domestic" birds are also being looked at,but so far wild birds r not being looked at as a source of human infection. #H7N9
� Gregory H�rtl (@HaertlG) January 31, 2014

Only one way to tell what's happening now; get more samples and RT-PCR them. Serology is historically solid and well relied upon, particularly in the world of influenza surveillance. See expert comments on this in a recent CIDRAP article here. I'm just not convinced its providing enough sensitivity at a suitable speed to feed the needs of rapid response and control measures for an emerging virus like an influenza. A virus which is spilling into humans from somewhere not yet convincingly defined to everyone's satisfaction. 

But I'm new to flu and am coming at this from an endemic human virus detection and characterization angle. I may be waaay off point.

Read More

Freeze those chickens....

As 8 new H7N9 cases are announced today we see a very welcome comment from Hangzhou City's mayor, Zhang Hongming...

"Hangzhou is planning to close live poultry trading markets permanently and promote the supply chains of frozen poultry products instead"

If Zhejiang Province can carry this off, it would be perhaps the single biggest intervention and risk mitigation step possible. 

Centralising poultry slaughter and providing chickens in a partially prepared and refrigerated/frozen condition could buy the time needed for research to catch up with public health needs. This could include further enhancing farm, market and human screening and finding the feathered or furry fiend(s) acting as the source(s) for these putative zoonotic transmissions (also for H5N1, H7N7, H9N2, H10N8, etc). 

Such change would also radically reduce the chance of selecting more efficiently transmitting human-adapted flu viruses by simply reducing contact between the large numbers of birds (and other animals) and humans occurring on a daily basis in the market environments and through the transport and slaughter of live birds throughout their heavily populated surrounds.

The changes in social behaviour and habits required the Chinese are huge, but such change should be considered as being as great an investment in the future health of the local and global populace as vaccines have proven to be.

Source...

1. Xinhua
   http://news.xinhuanet.com/english/china/2014-01/27/c_126071190.htm

Read More

Zhejiang: more live bird market closures...

FluTrackers have posted a report originating from the Ningbo evening news in China stating that more markets in Zhejiang province, in the regions below, have been closed for cleaning and disinfection in an attempt to bring the Province's H7N9 outbreak under control...

These regions have already suspended trading...

• Hangzhou city (which I noted here)
• Xiaoshan District
• Yuhang District
• Jinhua
• Shaoxing City

This new report notes closure of the following markets in the "main city of Ningbo" from 26-Jan..

• Haishu District
• Jiangdong District
• Jiangbei District
• Yinzhou District

Exotic bird imports and pigeon flying has been banned.

Read More

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

Read More

Market sampling: H7N9, sensitive testing, market closures and small numbers

A World Health Organization Western Pacific Region update on influenza A (H7N9) virus has a few interesting bits of information that pulls together a recent flurry of reports. This is the situation as of 22-Jan...

• 18/200 (9.0%) "pathological samples" from markets (listed below) in Zhejiang province, presumably using PCR-based methods, were H7N9 positive  
• Sanliting Agriculture Products Market (6 oral/cloacal swabs, 2 environmental faecal swabs)
• Central Agriculture Products Market (2 oral/cloacal swabs, 1 environmental faecal swab) 
• Fenghuangshan Agriculture Products Market (1 oral/cloacal swab)
• Guoqing Poultry Wholesale Market (3 oral/cloacal swabs, 3 environmental faecal swabs).
• 2/2,521 (0.08%) pathological samples were H7N9 positive in Guangdong province
• Pathology specimens from the provinces of Jiangxi, Liaoning, Jilin, Heilongjiang, Jiangsu, Fujian, Shandong, Hubei, Hunan, Guangxi, Yunnan, Qinghai, Xinjiang Provinces and Chongqing and Shanghai Cities were H7N9-negative
• 7-Jan, H7N9 RNA was also reported  in 3/17 samples collected from the kitchen of a restaurant in Haizhu District, Guangzhou City, from the chopping board and sewage water. 
•  Meanwhile H7N9 RNA was identified in 8 out of 34 environmental monitoring samples collected from the Guangdong's Longbei Market, Jinping District, Shantou City.
• Ningbo city (Zhejiang Province) has stopped commercial live birds entering the city
• Shanghai city will suspend live bird trade all over the city from 31-Jan to 30-Apr. Live poultry from other provinces will not be allowed into the city except for transport to a centralized slaughterhouse.

It's great to see some data from other provinces and municipalities that have not reported any human H7N9 cases to date.  I do wonder about the relatively small numbers of market samples though. Some of these samples pale in comparison to what was tested in 2013; which reacted earlier than this, the second time around. While 2,00 samples is not an easy day in the lab, we saw >800,000 bird samples tested by "virological" (?culture) and serological methods in 2013 (see other thoughts on the use of PCR in birds here).

So what have we learned here? 

1. Further confirmation that live bird markets house H7N9-positive birds. With most human cases this year having come into contact with poultry, the transmission chain is in place. Market closures seem the most effective way to stop transmission abruptly and they have a precedent for this in 2013. This is happening. Will it be enough? What  about the market-supplying farms?
2. RT-PCR testing is more likely to uncover influenza in birds than culture methods and is better than antibody testing (although how much better is hard to judge from the information provided). Added bonus: RT-PCR is more likely to tell you what's circulating now rather than a little while ago...although no-one really responds to the lab results that quickly anyway.

Read More

H7N9 hasn't left, it's just been building capacity... [UPDATED WITH NEW WHO DON]

Click on image to enlarge.

I updated this chart a week ago, when the avian influenza A(H7N9) virus tally was at 158.

This morning I check FluTrackers list and its sitting at 189 cases; 31 reported so far this week. Just to be clear though, not all of those cases acquired their infection in this week. Some cases go back to mid-December 2013. 

This week has so far seen 10 cases with disease onset listed as occurring in it (5, 17 and 6 in going back by week in time). For comparison, at the height of the 2013 H7N9 outbreak, in Weeks 6-9 (March and April) there were 17, 29, 40 and 19 cases in each of those weeks respectively. We don't seem that far off from those numbers right now - except that this outbreak/wave we're seeing cases starting from more regions than last time. Without some serious intervention, I think 2013's peak of 40 case acquisitions in a week will seem small in 2014.

We can also see from the chart that Fujian province is emerging from the background noise of a handful of cases and could be starting that steep'ish climb that suggests bird-to-human transmission events are on the rise. That adds to ye other "newcomer", Guangdong province. In 2013 Shanghai, Zhejiang and Jiangsu were the hotzones, and they have all reported cases in recent weeks. H7N9 hasn't left, it just built more capacity to transmit...because that is a virus's life.

Which brings me to a whinge. 

You could be forgiven for thinking that from all we've learned about H7N9 and all that we already knew about influenza viruses and markets and transmission and detection and diagnosis and treatment) from...

• The 318+ research papers
• The many words written in a vastly greater number of news articles, blogs and comments
• The many (I expect) millions of dollars invested in learning, battling and cleaning up after H7N9 over the past 48 weeks
• The strong link between a precipitous drop in new cases and the closure of live poultry markets in 2013 

..that a similar response to the liver bird markets would have been triggered this time around. In 2013 the first key market closures were underway by Week 8 (1st week of April'ish) after the first known H7N9 case became ill (Feb-18). This time around we're already at 15-weeks after H7N9 cases started to accrue again (taking the start as the week beginning 7-Oct).

I forgive you for thinking this way because I think that way too. This much newly and recently accrued knowledge should have informed the decision to close markets by now. Or change the markets. I get that fresh poultry is an ingrained and cultural issue. But I also get that public health is at serious risk just now, not just in south east China but globally. Is it worth your life or the life of a family member just to get a clucking chicken from a market rather than a farmed pre-prepared one? The solution to reduce that risk to people and the world lies in the live bird trade and associated habits. Closing down a market here and there for "sanitation" (or aerosolising everything by hosing it out as @Laurie_Garrett suggested in a fantastic Twitter exchange earlier today), doesn't appear, to the casual observer, to be slowing infections. Can a "market" really be suitably sanitized? Not just the one-off cleanup, but the more conceptual idea of a market as a large gathering of animals frequented by hundreds of thousands of people each day, meeting there, handling, haggling, buying, breathing, drinking, eating... 

Can you ever get ahead of that risk while markets exist in their current form?

Laurie Garrett also mentioned a practice involving the sniffing of a chicken's butt to see if it is healthy. Beyond the laughter that image triggers, flu is a gastro virus in birds. Better cleaning of a market's environs won't stop that practice, nor other risky practices, from being  a source for influenza virus acquisition.

Perhaps sanitizing markets is working. Perhaps we'd be seeing a lot more cases if such cleansing had not been happening. But aren't the markets just being restocked with HXNY-laden birds the next day or week?

The H7N9 cycle wasn't broken when the markets were shut in 2013; it was just temporarily halted. 

We know that these birds have multiple influenza viruses in them including H9N2, H5N1 and H7N9. 

The conditions for the emergence of viruses we already know, and those we have yet to meet, continue to be created and maintained. 

The spectre of "the next pandemic" will not get the banishment it deserves while the live bird market system continues as it has. It's just our luck that may run out as it did for those infected by H7N9.

Read More