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H7N9 snapdate: accumulating cases by region of acquisition

Click on image to enlarge.
This is what happens when you do nothing to stem the possible source of an influenza outbreak in your back yard. 

Nothing. Nothing changes.

The infection keeps spreading. 

Very clearly the H7N9 hotzone in China has now shifted from Zhejiang province to Guangdong province (the brown line that represent the second highest number of human cases of disease..75 cases representing 21.3% of all H7N9 cases.

As we read today, this province has just shut some of its poultry markets. By the look of this rate of new cases, the people of Guangdong province could be in for a tough 2-3 weeks and will be hearing a lot more about "bird flu" much to the poultry industry's disgust.

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 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

H7N9 keeps changing and mingling and mixing...

A new report in Eurosurveillance out today has once again raised the spectre of a pandemic H7N9 spread. 

Not just for what the Meng and colleagues from China and the United States have shown in their detailed analysis of the PB1 gene segment of (mostly) avian influenza A(H7N9) viruses from humans birds and the environment in 2013, but also for what they have indirectly highlighted: a massive absence of 2014 H7N9 sequence data on GISAID or GenBank sequence databases. 

Being asked for comment, which I provided in 2 stories linked below (2 and 3), I dug into the sequence databases and was stunned (yes, really!) to find that there are hardly any sequences available from H7N9 gene segments or genomes this year.
Given that this year's human case tally of H7N9 infections has surpassed that of 2013's 1st wave, I find that really surprising, and confusing. Also given a few subtle pattern changes that I've been writing about of late including the shifting age balances, sex ratios, fewer farmers, more family clusters, apparently limited impact on human case numbers from market closures >2-weeks ago...I would have said keeping our eye on the genetic ball was more important right now than ever.

What's going on?

Meng and colleagues use the PB1 gene to highlight changes to H7N9 resulting in 4 genetically distinct clusters with links through time and geography. 

There seems to be continued and active change in H7N9 based on analysis of this 1 segment. Not surprising for a virus whose genes exist as a deck of 8 cards, each capable of its own drift changes, just waiting to be shuffled but the next already-occupied host it enters.

I really wonder how much of the virus we knew of as H7N9 in 2013 has changed and what the virus we know in 2014 is like by comparison. 

The only way to answer that will be to see and analyse the sequences from 2014. And hopefully, do that soon. 

These bits of viral genetic material don't just make pretty trees (or hard to see ones like in he Eurosurveillance article), they identify significant changes to the virus that signal potential for, or real, change in transmission, disease type and severity, site of preferred replication and our likelihood of successfully detecting the virus using sequence-dependent, PCR-based diagnostics.

Sources...

  1. Eurosurveillance article.
    http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20699
  2. CIDRAP story
    http://www.cidrap.umn.edu/news-perspective/2014/02/h7n9-cases-pause-new-report-details-reassortants
  3. Bloomberg News story
    http://www.bloomberg.com/news/2014-02-13/pandemic-potential-seen-in-gene-changes-of-bird-flu.html

Thoughts from Bangalore, India: The East Teaching the West in Mental Health

When discussing global mental health, the conversation often focuses on whether psychiatrists can practice outside of their cultural context. What we sometimes forget is that psychiatric illness is organic illness of the brain, affecting equally large percentages of the world population from nation to nation. Illnesses such as bipolar disorder, autism, depression, OCD, schizophrenia and other mental diseases occur beyond cultural boundaries and they deserve a global conversation.  We know that Western thought and philosophy in this area is only about 150 years old; this begs the question of how ancient civilizations effectively treated mental illness.

Through my Partners Center of Expertise grant, I�ve been involved in some psychiatric cultural studies at the National Institute of Mental Health and Neuroscience (NIMHANS), a central government research institute pushing forward the fields of psychiatry, psychology and neuroscience in India. Here, they have an Advanced Center of Yoga where they are building modules of yoga postures to treat various mental illnesses. In modern society, yoga has been considered a type of exercise, but traditional yoga born and propagated throughout India, is a multifaceted way of life used to help practitioners increase their self awareness, flexibility in thought, and feelings of security. It focuses on a holistic sense of health, a beneficial perspective in mental illness. The Advanced Center for Yoga at NIMHANS is running multiple studies in yoga and has recently published a supplement in the Indian Journal of Psychiatry. This describes multiple controlled studies that show yoga improves quality of life and sleep in elderly, has antidepressant affects on the general public, and improves symptoms of ADHC, psychosis, dementia, and memory. The center has made yoga a standard therapeutic intervention and I have been lucky to be invited to experience the clinical treatment of patients here.

While the focus for my global health project is on cultural contexts in diagnostic practices of academic psychiatrists, I wanted to highlight the yoga center in the blog. It is a perfect example of why the study of psychiatric disorders should be global and why communication and teaching in global health should be a two-way street. It also highlights the need to put some thought into broadening our scope in psychiatry rather than limiting it due to cultural differences. See pictures of the Yoga Center below:
 Here is the entrance area to the Yoga Center at the National Institute of Mental Health and Neuroscience

This is a class that uses the yoga model for anxiety related illness.

Jhilam Biswas, MD

Forgot to ask you...


My plan in Guwahati was to start launching our research project on quality of life of people suffering from cleft disease.  Even though the estimate is that 1:500-1000 children are born with cleft disease, it remains to be defined what the burden of this disease is, as in United States and other high-income nations, all these cases receive surgical repair, along with dental, speech, and psychological support right at the beginning of life.  But Guwahati, is a different place.  Here resources have been scarce and the majority of the population lives on what they make as farmers for big plantations of the world-famous Assam or Darjeling teas.  There is an estimated backlog of 30,000 cases of cleft disease and that also means, unfortunately, a lot of people with cleft that are reaching adulthood without having received any care.  I knew this, and this was precisely what attracted me to Guwahati.  In preparation for this trip, I tried to educate myself on how is cleft disease seen in the global health arena.  What I found was that cleft was lumped in a category known as �congenital deformities�, where club foot, polydactily, etc. were also a part of.  And it was thought of as a condition that had very low mortality and low morbidity, so therefore, it ranked low for disability-adjusted life years (DALY�s), a common currency metric developed to compare conditions against in each other and ultimately, have a priority setting that the United Nations, World Bank, World Health Organization, countries� ministries of health and funders all refer to when making their own agendas and resource allocations.  Surprisingly, cleft patients were not part of the process of obtaining an idea of what disability cleft disease carried, especially if it remained untreated.  That is exactly what I set myself to do and Guwahati seemed like the right place to do it. 



As I trained the research assistants, who were 3 pleasant Assamese women, all in their early twenties, all with masters in social work or child development, I started to wonder, how much of these questions on quality of life, written and validated in developed nations with likely way more education than the patients coming into the center had ever had, were really going to get through to them and the patients we were about to interview.  But, I kept on and asked the questions.  I would simplify the phrases when necessary and assess their body language to see if they understood me.  But still I wondered. That is when I interviewed Kiran (named has been changed), father of 7 year-old, Meena (name has been changed).  His girl was about to have surgery that day, and they had come 8 hours away by bus.  I asked her about his Meena and how she was feeling about getting surgery.  As the translator explained to me, his girl had been suffering in school as she was teased for her cleft lip and palate, because her mouth looked funny and kids could not understand what she said.  She wanted to play with the rest of the kids, she wanted to be liked by her peers.  He shared that as soon as she found out that there was surgery that could fix her cleft lip and palate, she asked her father daily, �when will you take me to get the surgery?�  I tried to hold my own sadness, thinking how her father must have looked into her child �s pleading eyes, and wonder how he could help her.  But now she was here and his father�s broad smile, revealed to me, this was not a moment to dread or to be nervous about, this was a moment of joy.  He said that his daughter will go back and go show everyone her new lip, that she is already talking about that moment.  And as I listened to him, despite the world of experiences that set our lifes in different directions, I understood and I could hear Meena through her father's story, loud and clear.

Just in!

After 27 hours of travel, Dr. EJ Caterson and I landed in Guwahati, India.  Even though neither of us had ever been here, the place has the familiarity of any town in the so-called �developing� nations.  It reminded me of the border towns in Lima, Peru, of the South countryside of Dominican Republic, of the Mayan towns away from touristy Yucat�n, of some of the forgotten towns around my own hometown in Puerto Rico.  The half-painted, half-roofed and half-built buildings, the dust that deposits in everything living or nonliving, the entropic flow in the narrow streets full of motorcycles, cars, cows and many street dogs, all avoiding collision and the road holes with miraculous success. 

But we were decidedly in India, with the women in saris coloring the streets, the incense in the air, the glimpses of gold against the beautiful dark skin, the cricket fields and the ever-present crowds.  We had gotten the first welcome to the Monsoon when we landed in Mumbay with a loud rain at 2 am.  Now the rain had passed and the tropical humid air damped our foreheads as we went from the airport with a quick stop to drop our luggage and into the hospital to start the real adventure. 

What had started as a dreamlike conversation on evaluating delivery of surgical care in low-resource settings one afternoon a year ago in the HMS green lawn with my mentor, Dr. EJ Caterson, was finally having a home with discrete GPS coordinates in the real world.  The home for this project was located in the public hospital of Guwahati, in a ward donated by the Assam government to Operation Smile India, as part of a public-private collaboration between the two.  This collaboration expanded beyond the hospital, as the community health care workers, known as ASHAS, were trained by the personnel of the center on how to recognize the condition and refer it to Operation Smile, reaching statewide coverage and even neighboring states.

As you walked through the hospital, bare-bone conditions with windows overlooking trashed green areas transitioned to the newly painted murals and order of the Operation Smile Center.  Inside the glass doors that led to the center, blue painted walls sheltered a waiting room, the administrative offices, dental, speech pathology and nutrition offices and even a play area with toys and facemasks for the children to familiarize themselves with the strange objects they will be in contact with in the operating room. 

All shoes off and scrub shoes on, we get into the perioperative area.  The operating room consists of a large room with 5 operating tables with their ventilator machines, like Siamese twins, all lined-up, with that aseptic smell and look, universal to operating rooms.  In the operating rooms, I relax, as I watch or assist the attending surgeons, as this room is familiar and a respite from the over stimulating of colors, odors, and movement in the busy streets of Guwahati.  I secretly preferred being in here, where I felt useful versus the streets of Guwahati, where in Yesterday�s walk to the hospital I had encountered a 3 year-old child with sunken black marbles for eyes laying on a dirty blanket with a tin bowl by her side and a head bubbled by untreated hydrocephalus, among piles of tropical mangoes, guavas, bananas, and street trinkets for sale.


Inside the operating room, I marveled.  I marveled at this well-oiled machine of cleft surgeries biting away at the more than 30,000 untreated cleft cases in the state of Assam.  Biting 1/3 of the burden of the disease in only 2 years!  Firm and steady bites of well thought, protocoled, state of the art, high-standard surgery.  This is what I wanted to see, this is what resonated right in my heart, the idea of the best we have to offer for all, the truism of the universal declaration of human rights soft murmur, now in the loudest decibels screaming �it can be done� in the off-the-map and off-the-beaten-path and off-the-charts Guwahati. 

First Taiwan, then Hong Kong, now Malaysia becomes a holiday destination for an H7N9 case...[UPDATED x2]

Mike Coston has just made us aware via a Tweet that avian influenza A(H7N9) virus has escaped its usual roosting ground in southern eastern China by hitching a lift in a tourist to Malaysia

A more detailed post on his Avian Flu Diary wrangles the issue of language very nicely and tells us that the infected Chinese tourist has been hospitalized and is currently in a stable condition. 


Brief details..

  • 66-year old female
  • Fever, 01-Feb prior to leaving China
  • Travelled from Guangzhou City in Guangdong province to Peninsular Malaysia 04-Feb then to Sabah, Malaysian Borneo 06-Feb then to Kota Kinabalu
  • Hospitalised 07-Feb in Kota Kinabalu, Sabah, Malaysia 
  • Laboratory confirmed 11-Feb and remained positive 13-Feb and 22-Feb
  • No sign of R294K (N9 numbering) mutation associated with oseltamivir resistance despite virus "persistence" wihc may have been related to treatment with steroids
  • 191 contacts; 6 were symptomatic but tested negative for H7N9
It is worth highlighting here that this sort of export is not unexpected and not even surprising. We live in a hyper-connected world. It's nigh on impossible to stop respiratory viruses from spreading. This case highlights that even when we're ill, we still feel the pressure to continue on with our jobs, our daily routine or our holiday. After all, we've all been a bit crook before and it has mostly been nothing much to speak of. Why should this time be any different? 

To date, H7N9 does not jump easily between humans as far as we know. The 20 negative contacts stand in testimony to that. But if you see some articles or posts or Tweets in the coming hours and days which suggest that the sky is falling...I think you can rest assured that this is not it falling. 

Not yet anyway!  

Now, go follow Mike via @Fla_Medic if you are not already.

Sources...

H7N9 snapdate: H7N9 totals by month, 2013 vs 2014 to date

Click on image to enlarge.
January has so far tallied 1.6x more cases than the peak month of 2013 which was April. And those cases are still being reported.

But only 2 lab-confirmed cases were added to the list last night, perhaps things have started to slow at last? 

That is extrapolating a bit much from 1 night of reporting with low numbers, but let's wait and see what happens tonight (today for you guys up north!). Seems to be the mantra for this sort of stuff.

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