The third outbreak of influenza A(H7N9) virus seems to be over...

Cumulative curves of reported H7N9 cases and deaths in humans.
Click on graph to enlarge.

By the looks of the curve on the right, the rush of cases that defined the third known outbreak of the low pathogenicity avian influenza A virus subtype, H7N9, is over...for another season anyway. 

If we get into the nitty gritty, as I have below, there are a couple of interesting things to see. First though - let us remember that these are just reported data:

• there may have been some cases that were not reported for whatever political, medical, social or personal reasons - these data are an idea of what happened - look at the rends and don't get hung up on the specific values
• the overwhelming majority of the cases have reported to a healthcare facility with respiratory disease due (presumably) to either infection - we have no idea how many other people have been infected, what proportion were mild or asymptomatic (as I've discussed e.g. here and here, so we know it is possible). It could be half as many again, or 100 or 1,000 times as many.
• these are only cases that have been examined with a laboratory test (as far as we know) - there may have been many other cases of "influenza-like illness" that did not get sampled and tested but were managed under (or not) the assumption that they were influenza of some type, subtype or strain.

Please note-the graphs used here can all be found on my fixed interactive H7N9 page at:http://newsmedicalnet.blogspot.com.au/2014/11/influenza-ah7n9-virus-detection-numbers.html

The interesting stuff includes:

• For the 2 outbreaks we have continuous data for - 2013-14 and 2014-15, the start of the outbreak seems to be around October/November, with the peak around January/February. 
• Outbreak 3 did not seem to reach the heights of the preceding year however, from what we could glean from pretty poor data, the link to poultry exposure was as strong as ever. Perhaps market closures in response to deaths were a little more effective/efficient/wide-ranging in Outbreak #3? Pure speculation

Click on graphs to enlarge.

• Most of the cases in 2015 (bottom maps) were on the east coast of China

Click on map to enlarge

• Most of the activity in the 3rd outbreak was focussed in Guangdong, Fujian and Zhejiang provinces (the red ones above) 
• Xinjiang Uyghur Autonomous region (in the far west) and Guizhou and Hubei provinces joined the list of host regions in Outbreak #3
• Xinjiang joined Guangxi and Jilin provinces (which reporting cases in Outbreak #2) as regions of China that share a border with another country - heralding the movement of this H7N9 variant beyond China's borders possibly into Vietnam, North Korea, or a -stan

Click on graphs to enlarge.

Keep an eye out for H7N9 Outbreak #4 - coming to a colder China around November 2015. 

But for now, it might be time to hit the FluTrackers line lists (okay, I've had 4 tabs open for ages) and graph the course of another source of concern - H5N1 cases in humans.

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Hubei province listed its first H7N9 case in April...some rare detail

A new province was recently added to the list of those reporting cases of avian influenza A(H7N9) virus infection in humans. 

Of course reporting does not mean capturing. Reporting has been weak this season. The cases that have shown seem to be just those who were ill enough to visit a Doctor/hospital and get a laboratory test. This is the same story for most infectious agents. We see just the tip of the iceberg, the beginning, the head of the arrow, we only scratch the surface, the glycoprotein on the envelope of the virus as it leaves the...okay, you get the picture.

This year has seen a very disappointing effort by China to provide useful public data that could permit tracking of what has become the annual outbreak of human cases of avian influenza A(H7N9) virus infection.

The human H7N9 case hotzone, at least since we heard about the virus infecting a human in February of 2013, have been on the east coast of China. We currently stand at 659 reported human cases, and over 200 deaths. Very. Roughly.

Click on image to enlarge.

I remember fondly a time when there were scads of data on H7N9-related human cases and deaths. Okay, China did over-share on a number of occasions....

Click on image to enlarge.
Story to be found here.

Click on image to enlarge. 
Story to be found here.

Click on image to enlarge. 
Story to be found here.

..but things have changed. 

For a comparison take the Kingdom of Saudi Arabia's Ministry of Health and their efforts to provide public data on Middle East respiratory syndrome (MERS) and its coronavirus (MERS-CoV). While there are a few gaping holes in the data set (c'mon guys-fill these in!), there can be as many typos as on this blog (but I'm not a public health Ministry - in case you were wondering) and the data can be intermittent, it represents the best public source of detailed, yet deidentified, human data on an ongoing zoonotic viral emergence. And that's saying something. But congratulations nonetheless!

I'm not including Ebola virus disease data-gathering here - the fact that we have had so much data - despite the initial lack of infrastructure and people trained to collect, collate and report that detail - is a fantastic testament to the efforts of those on the ground in Guinea, Sierra Leone and Liberia.

But this season H7N9 data that have been reported by public health sources have been released in blocks and lack any consistent or useful detail, except the province. Some detail is available when harvested from media reports by the ever assembled FluTrackers team. I rely heavily on their line list (to be found here). 

One example of the poor data quality this season, take a look at this text from a recent Disease Outbreak News provided by BigBlue (that's the World Health Organization, or WHO, for those not accustomed to my street groove)... 

No-one will be reading that and feel overly informed.

One is left to assume that this is how these data are coming out of China - infrequently and without detail. We regularly see that when better data are provided - and again, I hold up MERS-CoV case descriptions here - they get publicly listed by BigBlue. 

And before you head to your keyboard to ask "Why should we have access to these data?"...I will first ask you - why shouldn't we? They are collected and collated internally. They are of interest to epidemiologists, model builders, public health planners and data tinkerers the world over. And it's not as though the details are subsequently released in peer-reviewed publications. They are not. 

It's just disappointing.

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Avian influenza H7N9 human infection emerged 2 years ago...

Seems like only 365 days ago I wrote about H7N9 being 1 year old.

Now - it's another year later.

While we have studied, written, read and learned much, much more about this emerging respiratory virus than we have about the Middle East respiratory syndrome coronavirus - even after its 3 years among us - we are still watching a new outbreak of human H7N9 cases spread across China. 

Each year more provinces are added to the list to report human infections - more infections likely go unnoticed, unrecorded and/or unreported. Gaps in the reporting is not unexpected and not unusual. 

Each outbreak with its accompanying economic damage, financial losses, human illness and death is because of the desire to maintain a tradition, namely the consumption of freshly extinguished poultry.

We're really good at getting ourselves into pickles. And we seem to be doomed to repeat the patterns, playing catchup and never getting in front of our new and emerging infectious diseases problems. And each time we seem amazed at what we learn, but really, we learn the same thing over, and over and over again. Eventually we'll run out of infectious threats I guess. 

Or they'll run out of hosts in which to incubate in and spread from.

Happy Lunar New Year.

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H7N9 outbreak #3 underway?

What better way to start 2015 than a snapdate!! For those who are new to them here on VDU, they were initiated here and defined here as snap updates - posts that don't have lots of detail and chat...although they almost always end up having lots of chat!

Figure 1. H7N9 cases by week of onset (or hospitalisation
or reporting dates of the preferred onset date was
not made public).
Click on image to enlarge.

This one is an update of the situation of one of the many avian influenza viruses ("bird flus" if you must) around again - avian influenza A(H7N9) virus, or just 'H7N9'.

In Figure 1, I've taken the huge liberty of adding in the start and end dates of the 3 outbreaks of H7N9 to date; and in doing so, I've said that China is in the early stages of one right now. I may well be wrong of course - this is a blog and these are my opinions - but it looks that way to me. 

Figure 2. China's northern laboratory network influenza
surveillance data up to Week 51 of 2014. [1].
Click on image to enlarge.

The case numbers for H7N9 in Figure 1 have been above zero for a little while and in particular November looked like a busy month (see weekly and monthly tallies here). Keep in mind that there is also a reporting lag - the time between date of onset (obtained from more detailed World Health Organization data) and the date the case was publicly reported (I rely on FluTrackers line list for these details). That delay can be a month or more on occasion; up to 38-days in late December. I suspect this is because China reports cases to the WHO in batches, something instigated toward the end of the 1st and 2nd outbreaks. So I suspect we will see more cases assigned to December, during reports that come out in January.

But it look like 'tis the season for influenza in humans in China (see figure 2 and the Chinese National Influenza Centre [2]) - and as some of us have discussed on Twitter, this is most probably due to the changes in weather (environmental conditions) which result in sustained viral survival on cough and sneeze-contaminated surfaces and in wet and dry propelled droplets and droplet nuclei; in both man and bird (see Hong Kong avian influenza detection report dates [3]). 

That sustained survival may well be all it takes for more of us to pick up an infectious viral dose.

Once the seasonal influenza viruses get a foothold in us, they spread well, causing disease in those who are susceptible and probably a bunch of unnoticed infections in those with previous exposure to that strain plus a healthy immune memory of that intrusion. By "seasonal influenza virus, I mean those that replicate in and circulate efficiently among humans, as opposed to the relatively inefficient avian subtypes.

So stay tuned to H7N9; it's not yet very good at spreading between humans but its established in birds and has been spilling over into humans since at least the beginning of 2013. We know how influenza can deal us a rough hand if the stars and its genetic segments align favourably (for it). Oh, and the continued reliance on fresh chicken obtained from and killed at live poultry markets. The majority of cases have very clearly had contact with poultry as defined by the WHO. 

References...

1. http://www.cnic.org.cn/eng/show.php?contentid=738
2. http://www.cnic.org.cn/eng/surveillance.php
3. http://www.chp.gov.hk/files/pdf/global_statistics_avian_influenza_e.pdf

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Influenza A(H7N9) virus: detection numbers and graphs...

This is a static page that will house my graphs of influenza A(H7N9) virus ("H7N9) numbers produced by the various Ministries of Health for the provinces and municipalities of China, the World Health Organization and FluTrackers.

They may take me a little while to get back up-to-date in this new format so stay with me. I will Tweet each update as I do for MERS-CoV and Ebola virus updates.

There is also an accompanying map page which for now is located here.

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Reminders: 

• The graphs above, as with all on VDU, are made for general interest only. They are also freely available for anyone's use, just cite the page and me please. The data can be downloaded by clicking on the "Download" link at the bottom-right of each dashboard. It may be that I have misinterpreted the language in the reports (sometimes a little tricky to wade through) or miscalculated some totals based on the way data have been presented.
• In any outbreak, epidemic or pandemic caused by a know or emerging pathogen, the numbers presented publicly, and used in these graphs, are expected to represent only a fraction of all the cases that have and are occurring. This is just the nature of the imperfect biological'ness of these events.
• I am only able to plot what is publicly available-you could do this too. No secret associations or back-room deals provide me with these data.

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Now for something (not so) completely different: H7N9 maps...

Now it's time to mess around with influenza A(H7N9) virus mapping using Tableau.

I've (only just) realised the my esteemed peer, Shane Granger has been using Tableau to do this for ages (see here), and that this will be duplicating his excellent work. So I'll try my best to consciously differentiate my maps from his - but there's only so far you can go with that and there will be overlap. 

The page below is a very early first play with H7N9. It's just detections broken across 2013 and 2014, by province most likely to have been the source of the infections (as far as I can tell) in mainland China. 

If I can master this I'll try and add more details in the future. For now, these numbers a a little out of date but he trends are similar. This charts 449/452 detections.

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H7N9 Snapdate: some quick charts...

Click on image to enlarge.

I don't have a lot of time tonight so this is just a quick post of some updated charts with a few summaries of some key features of the influenza A(H7N9) virus situation in south-eastern China. At writing it was at 432 detections with media reporting 128 deaths

Click on image to enlarge.

Guangdong is where H7N9 is still most active and it is this province that is the source of the continued cases trickling off Wave 2's peak.

Most H7N9 cases overall have been in Zhejiang and Guangdong provinces but lately, post-peak of Wave 2, there has been continued activity in Jiangsu province including a recent healthcare worker with no mention of "contact with poultry"; the absence of which stands out in World Health Organisation (WHO) reports because most cases are followed by affirmation of that phrase.

Click on image to enlarge.

In  the  survival chart above we see that most of the fatal cases, shown in red, are defined by an older age. Unfortunately, a lot more of the fatalities have been reported through the media without identifying details (48 of 128), than have come through official Chinese channels and out via the WHO. This lack of detail makes it impossible to clearly link a lot of the deaths to the case announcements. Only the custodians of these data know what this chart should really look like. NB: Since making the chart this morning I've found a handful more case details at FluTrackers, but public detail on fatal cases remains the weakest of any of the H7N9 data.

Click on image to enlarge.

We can see in the weekly chart on the right that the two H7N9 waves differed in timing, the width of their bases (more cases in Wave 2) as well as how "tight" their peaks were. Wave 2 has tailed off, but continues to spit out cases, while Wave 1 comprised both a steep climb and a steep decline in human cases.

Click on image to enlarge.

If we zoom in on Wave 2 we can see by looking at cases per day in the chart on the left, that between 0-4 illness onsets per day are being reported, as they have been since late Feb-2014. 

Is this the legacy of those regions whose live bird markets remained open or were only shut temporarily for disinfecting and restocking? Those regions with markets that were shut for much longer, or for good, do not seem to have contributed much to the continuing leak of H7N9 infections despite being key contributors during the peak periods before markets were closed.

Click on image to enlarge.

In zooming in on Wave 2's cases by week, but this time based on the region of likely acquisition of infection, we see that Guangdong province (brown line) has been the most consistent contributor of human H7N9 infections both late during the 2nd of the Wave 2 peaks, but also after the peak's decline almost everywhere else in south-east China. There was considerable publicised unwillingness from poultry producers to permanently close markets in this Province, a location with a major role in the nations poultry production. And so this little experiment incubates further and I have little doubt we will see the impact of that unwilingness late in 2014. 

Click on image to enlarge.

As noted above, public H7N9 death data do not allow good linkage with official case announcement data for about 48 fatalities, so my second-last chart tonight uses both public and media-release numbers to try and illustrate how the proportion of fatal cases (PFC) has changed across both Waves. The PFC seems to be holding fairly steady now between 17% and 30% (depending on source of numbers).

Click on image to enlarge.

And finally we see that the age and sex distribution across all cases (both Waves) is skewed to wards older males. Same as usual. If we look at this distribution (ran out of time to put in here) for the fatal cases, it is much more tightly grouped around the >60-year olds, but that females appear to dominate males in deaths during Wave 2, whereas it was the other way around for Wave 1.

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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.

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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

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H7N9 snapdate: age with time

Click on image to enlarge.
Age groups selected to convey clearest trends
without too many lines.

A quick look at some age bands followed each week during the course of both waves of the avian influenza A( H7N9) virus outbreak.

The interesting line to watch is that of the youngest age group (0-19-years) which has lifted to comprise 50% of cases in the week beginning 27-Jan. Also, the proportion of cases in the oldest age group (70->90-years) has dropped down in the past 2 weeks. 

There have been a rash of children in recent announcements; 8 of the last 45 cases have been <10-years of age. For a virus with a median case age sitting at 58-years, this is quite a departure. 

Is this due to an increase in familial clusters? Does it herald a shift in the way the virus is spreading? Intrafamilial transmission may provide a hint at increasing transmission efficiency. It might also be a sign of increased testing augmenting clinical observation of close contacts of ill family members. 

It bears watching closely whatever is happening because its different for some reason. Also worth watching is the downward creeping age. In 2013 the median age was 55.5-years and in 2014 it is 53.5-years. Among the past 45 cases it sits at 52.0-years. 

Tonight we have 310 H7N9 cases ( a third in Guangxi province bordering Vietnam has just popped up while I was writing this paragraph and I've altered the numbers above), with at least 50 deaths (that can be accounted for using public data).

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H7N9: Zhejiang in 50 cases...

Click on image to enlarge.

A quick look at the same number of cases (50) during the same period of time (2-months) in Zhejiang province, across 2-years. In 2014, between 23-Nov to 23-Jan, H7N9 case numbers surpassed 50 whereas in 2013 H7N9 cases did not reach 50 during the 1st wave.

Back on the 23-Jan it did not look like it would make it. Things move fast in influenza-town and prediction is a mug's game.

All a bit arbitrary, yet it is another indicator in addition to starting earlier and from more provinces than in March 2013, that H7N9 case numbers will be higher in 2014 than we saw last year and may well tear through the human case tally for that other "bird flu", H5N1.

As @influenza_bio noted on twitter this evening, there have been a lot of farmers listed in the FluTrackers case list of late.

A quick tabulation shows that 9.5% of FT cases between #1 & #137 have "farmer" in their description while none do between #139 & #177. However, 33.3% of the cases between #178 & #274 are described as farmers. What type of farmer, and how thoroughly this description was initially reported in the provincial media release is completely unknown so take this paragraph with a big grain of chicken salt.

There have been 6 new H7N9 cases added tonight, so far including 2 deaths, one among the new list and 1 of a previously reported case.

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H7N9 snapdate: new charts for sex and age distribution and region of acquisition...

Two new charts.

Click on image to enlarge.

Firstly, the "age pyramid", a revised and combined version of the age and sex distribution charts for 265/267 H7N9 cases to date. This one comes with many thanks to Shane Granger for helping me learn a new trick. Please follow him @gmggranger or visit his chart-tacular blog, Random Analytics at http://gmggranger.wordpress.com/.

Secondly, we have the latest map of the H7N9 hotzone; adjusted to account for Zhejiang tipping over the 100 cases mark (new colours!), and for the addition of a new province into the world of H7N9 human infections; Guangxi. This marks the first new region and 13th to generate cases overall, since 9-Aug-2013. 

H7N9 has thus crept sideways towards the west and as FluTrackers noted, Guangxi shares a border with Vietnam. An entire other country. The first shared land border since we learned of H7N9 I think. I'm no expert in this topic, but trade in poultry and tourists between these two regions seems commonplace, as noted here, here and to the extent that research such as this study (and its references) indicate H5N1 sequences are shared between the regions.

Do we know if Vietnam actively employs laboratory methods to screen poultry for H7N9, H9N2, H10N8 screening of their birds? I suspect we'll learn soon if not.

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Influenza H7N9 in the news....

Some snippets of information about H7N9 from China in recent releases include:

1. The description of H7N9-induced disease has changed in 2014 from an "infectious disease" to a "communicable acute respiratory disease". For what that's worth.
   Still technically infectious, just more about what sort of disease.
2. 7 patients have died with H7N9 infection in 2014
3. The incubation period for signs and symptoms to develop after H7N9 infection is 3-4-days; if patients develop severe pneumonia, it will be 3-7-days after signs and symptoms begin
4. Chinese Vice Premier Liu Yandong said
   "China will strengthen monitoring on live poultry, continue vaccine research and development, tighten international communication and cooperation in epidemic prevention and control, and publicize disease information in a timely manner"
5. "DNA rapid tests" (PCR-based) suggest a batch of chickens being imported into Hong Kong from Foshan, Guangdong may be H7 positive. H7N9? Further testing is ongoing. [Update - looks like they were POS as Hong Kong has suspended imports and will cull 20,000 chickens already there]
6. 12 cases in Zhejiang province have died from H7N9 in 2014 alone! I have 2 listed. 7 in total 2014. Looks like we've lost traceability on the numbers again.

Sources...

1. South China Morning Post
   http://www.scmp.com/news/china/article/1414939/beijing-downgrades-h7n9-bird-flu-description-new-cases-spike
2. South China Morning Post
   http://www.scmp.com/news/china/article/1414939/beijing-downgrades-h7n9-bird-flu-description-new-cases-spike
3. Xinhua
   http://news.xinhuanet.com/english/china/2014-01/27/c_126066004.htm
4. Xinhua
   http://news.xinhuanet.com/english/china/2014-01/27/c_126065993.htm
5. South China Morning Post
   http://www.scmp.com/news/hong-kong/article/1415003/one-batch-live-chickens-may-be-infected-h7-virus-health-officials-say
6. Xinhua
   http://news.xinhuanet.com/english/health/2014-01/27/c_133078729.htm

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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.

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H7N9 Welcome to Week #50....

Chart of weekly cases from @influenza_bio

Let's play duelling charts!! My colleague on Twitter, @influenza_bio, (whom you should follow if you are not already - he's got a knack for (a) getting across some nice flu-facts in a easy-to-understand way and (b) he rants - who doesn't like a ranter!?! That sounded less weird in my head.

Today's chart update from me shows the avian influenza A(H7N9) virus weekly and accumulation case chart. In case I haven't mentioned this lately, the human cases of infection by this newly emerged (in humans) virus is all from south eastern China. 

Given that cases keep on coming, this chart has changed a lot in a few days. The last chart is now already 4-days old. Ancient. See it here.

Click on image to enlarge.

My latest chart lists 246 cases and is based on the FluTrackers curated list (to be found, and checked regularly, here) and includes all recent WHO update information which provides some extra details - including date of onset of illness and hospitalization since late October. WHO has a few cases to catch up on.

These are useful additions since cases can be noted in the media or by the relevant ministries or public health institutions many days after the illness manifested in the patient and even after they were admitted to a hospital, usually in pretty poor medical condition. 1 more was added form Jiangsu last night that missed those charts.

I've arbitrarily listed the 2 "Waves" of H7N9 cases - if there is an official designation for dates, I'd be happy to hear of it.

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