MERS-CoV cases climb...still a one hump camel

Click on image to enlarge.

..not that I'm implying anything about camels!

We're about 97-weeks or 1.87 years into the MERS-CoV outbreak. That' sis calculated by taking the week beginning Monday 19-Mar-2012 as Week 1 (if Excel hasn't failed me at least). It was in Week 1 that a 40-year old healthcare worker in Jordan showed signs of disease onset (See the literature on this here). 21-Mar-2012 to be precise.

Unlike avian influenza A(H7N9) virus, there has been no similar precipitous drop in MERS-CoV case accumulation. Why would there have been? The source of acquisition remains unknown. And the disease is still very much one reported by the Kingdom of Saudi Arabia (KSA). Although of late there have been no new confirmations. The last public case announcement was on Xmas day, 25-Dec. Has something been done to limit or control exposure to the virus or are cases just not occurring? Or are we just hearing about them any longer?

Whether the KSA is the main site of viral activity we don't know for certain, but it is certainly the main origin of case reporting. I seem to remember that Qatar had actively  sought other instances of MERS-CoV. I'm hoping to see some more research papers about that and other efforts to seek out MERS-CoV among humans...at some point. Negative results are results nonetheless!

Overall MERS-CoV numbers are still very small in the global scheme of things and while transmission to close contacts and healthcare workers does occur, it is not frequent. One round of transfer (from ill person to contact) seems to be the end of the transmission chain. I wonder if anyone has tested the contacts of the contacts?

Still no sign of any prospective in-country molecular (PCR-based) screening of well and mild general respiratory illnesses. This mean there is no real evidence to dismiss that the virus could be circulating in great numbers with only minor signs and symptoms. For all we know, MERS-CoV is contributing to the seasonal "common cold" and "influenza-like illness" burden in the region. This is not a difficult unknown to address by any means. PCR-based screening of upper respiratory tract samples; decent numbers will give you a trustworthy answer. Pretty basic stuff. Oh well.

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Middle East respiratory syndrome coronavirus (MERS-CoV) by sex...

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I haven't updated my MERS-database since before Xmas. 

Wow.

It's painful to look at. 

Not because of a swag of new cases, I mean its tough to actually look at what's happening because the data, even with WHO expanding their coverage to include a more fixed set of information (the inclusion of animal contact is particularly welcome), is just so patchy. 

Some cases have sex but no date of onset of illness, some the other way around, hardly any have the date of lab confirmation or hospitalization and often it's near impossible to determine in which region the case was initially acquired. 

There is also still a question mark over the Tunisian cases and whether they originated in Tunisia or elsewhere I believe. The Spanish cases remain as probables (@WHO noted that they could not be confirmed via Twitter), so they are not on my list.

Nonetheless, I'll update my other charts as best I can. Keep an eye on the little bits of text in each graphic, they define the data gaps...164 of 177 possible total cases for example. In this instance, we are missing the sex of 13 MERS-CoV cases and I can only find identifying details for 73 of 75 deaths but 2 of those have no sex data either. You get the picture.

What is clear? Males (50% of those with data are >55-years of age) still dominate in the total cases and in those who have died of MERS-CoV infection (49% of male deaths are >55-years of age). That death is possibly due to exacerbation of an underlying disease or co-morbidity since they feature prominently in the MERS-CoV hospital-based population.

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Tracking virus-related deaths using publicly available data...

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Here's the cumulative case chart overlaid with the cumulative deaths and PFC. see the story behind the term PFC here, created by VDU to avoid issues around case fatality rate/ratio (CFR) which relies on knowing when cases have recovered.

I have two PFC values charted here. In black dots, is my curated list based on fatal cases (n=40; red dots) that have been announced publicly. 

In yellow are the numbers gleaned from media releases and the WHO - the latest number being 52 fatal H7N9 outcomes. 

Somewhere towards the end of the initial H7N9 outbreak in May, we stopped seeing reports from China that could link fatal cases with those H7N9 cases they initially announced. If anyone knows of a complete public list of fatal H7N9 outcomes that contains all 52 cases with age/sex/date of illness onset/date of death/province, I would be most grateful to be made aware of it.

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

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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.

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A quick comparison of the rate of H7N9 case climb over different 2-month periods...

Click on image to enlarge.

While there has definitely been a lot of H7N9 human case activity centred around Guangdong province of late, but how does it compare with the 2013 H7N9 hotzones of Shanghai, Zhejiang province and Jiangsu province? 

This rough comparison of a 2-month period uses the same y-axis (50-case maximum) encompasses the most active periods of case announcements. It shows that the Guangdong province case tally has not risen to the same peak in the same period as the other 3 regions in 2013. With 2 new Guangdong cases announced this evening (my time) and a Shanghai case, all in males, it will be interesting to watch this ascent.

H7N9 cases now at 182, 52 (28.6%) fatal.

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H7N9 cases: trekking to the next peak

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I have switched this chart to depict the case number per 
week using a line rather than bars. While not technically accurate,
 it is just more clear than a bar format as the dataset grows. 
Please be aware that the dots on the line are the actual 
data points.  The connecting lines are just for show. The red bar
above the "mountain peak" is a 7-day lag time - see below
for description.

We can see from this chart that the next H7N9 wave is well underway. 

There has been a distinct upward trend in new confirmed case announcements since about October 2013. 

Despite what looks like a slow-down at the top of that peak (the pale blue mountain), remember that there is a lag between a patient getting sick and when that patient is announced to the public as a laboratory-confirmed H7N9 case. How long is that lag though?

Click on image to enlarge.

As I did in 2013, I've plotted this lag as the time taken between date of confirmation (or date the case was reported publicly) against the week that case became ill. The data gaps represent times when there were no H7N9 confirmed/reported cases. The lag is currently sitting at approximately a week (6-8-days). So think of the slowing at the top of the peak in the earlier chart as more of a "guide" to what to may be coming rather than a true indication of now. 

I'm bet that slope will continue as we plug in today's and tomorrows and the next day's new cases; right up until we get a precipitous decline when the live poultry markets finally get shutdown in the face of overwhelming concern about case numbers and deaths. 

It's all well and good to prefer seeing a healthy chicken before purchasing it, but what about ensuring a healthy family afterwards?

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H7N9: males and females among total and fatal lab-confirmed cases...

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Males are the predominant host for H7N9 cases that are severe enough to warrant a hospital visit (or the contacts thereof). 

As ever, we have no real idea of the extent to which H7N9 is circulating among those who are not ill enough to present to a hospital. Only the use of a sensitive virus detection method on less ill or healthy people could tell us that. Such testing seems to be anathema, perhaps due to cost (?), for H7N9, MERS-CoV or H5N1 for that matter. So much we don't know but settle for in the respiratory virus game. But some of us go collectively bananas when a case turns up somewhere "unexpected".

Finally, the H7N9 fatality data are severely hobbled by a lack of linkage between H7N9 case notification and which cases died. That linkage broke somewhere after April. Reporting has improved drastically of late with the WHO confirming cases and details but 12 fatal H7N9 cases are publicly lacking enough information to use in sex-related charts, age-related charts, dates-of-onset/reporting charts or dates-of-death charts. 

I'm grateful to the WHO today for responding to a request and noting that 52 deaths have been reported to them, bringing the proportion of fatal H7N9 cases to 29%.

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Things I did not know #125,326...H5N1 is enzootic (=endemic in animals) in some countries...

Makes perfect sense of course, I just hadn't seen that in print in my short time looking at flu.

Helen Branswell has a piece on CTVnews about the Canadian H5N1 cases, noting that the genome will be deduced and submitted to the GISAID database.

So officially, H5N1 is considered enzootic in poultry (endemic for animals) in at least 6 countries (circulating, or epizootic, in at least 9 others):

1. Bangladesh
2. China (since 2003) 
3. Egypt
4. India
5. Indonesia
6. Vietnam

Further reading and references...

1. http://www.cdc.gov/flu/news/first-human-h5n1-americas.htm
2. http://www.cdc.gov/flu/avianflu/h5n1-animals.htm

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H7N9 age with time: is a younger adult demographic emerging this time around?

This is a big graphic - sorry for that - but I thought it best to show the distribution of age bands (this is updated from the paper I co-authored recently with Joseph Dudley) alongside the shifting age in total numbers and proportion of cases each week. The data are all publicly sourced and verified against the WHO and scientific literature whenever possible and of course, against FluTrackers excellent case list.

1 case is lacking age data.

The chart below (click on it to enlarge and see much more clearly) then some comments underneath. Keep the previous sex/week chart in mind (it's trend has not changed much with the latest cases; these charts also result from a question from CIDRAP's Lisa Schnirring last Saturday) when looking at this. Is any effect seen below due to the increased female representation?

Click on image to enlarge.
It's probably more technically correct to use a line graph for (c) 
since a linked line implies that we know what happens in between 
each data point, but bars just don't show up clearly enough.

1. The median age of all H7N9 cases (surviving and fatal) is currently at 59-years; the mode is at 54-years.
2. The median age since Week 33 (see earlier post for why this number) is 54-years whereas from Week #1 to Week #32 it was 60-years. Is this a significant lowering of the median age in wave 2 or just because we're coming into Marc-April, where things may even out?
3. 74% of all cases are aged 40-years or older (M:F 1:2.36); 48% are 60-years of older (M:F 1:2.23); 6% are 20-years or younger (M:F 9:1)
4. The age band graph (a) looks very similar to that which we published in late 2013 using 136 avian influenza A(H7N9) virus cases (not at 175 cases)
5. The total numbers in graph (b) show that patients 20-years of age or younger have not yet shown up among the new wave of H7N9 cases, and if we look at the proportion of each age band each week (c), we can see that a younger than 60-year old demographic is predominating from December, as it did back in March and April 2013.

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Helix...a show about dual use research of concern (DURC), black goo, pretty people and an absence of grounding in good virology [EDITED]

I'm not really here to critique TV shows but this one has some "virology' in it, so I'm making an exception. 

Plus, I've been yelling at people about it. So time to rant in print and get it out of my system.

I was really looking forward to this show turning up. 

Let me start by saying that I really enjoyed the tension and the creepiness of the first 3-episodes. I really liked the old school music counterpoint and the potential paleovirology which could make for a great premise for some really mystical creepy virus stories. I'm enjoying the 70s-style Arctic accommodation, somehow made made modern, and I'm a fan of Billy Campbell, Hiroyuki Sanada and Ron Moore's work. I've had many hours of enjoyment and great story telling from Lost, Contact, The X-Files, 24 and BSG. But Helix is not any of them because it doesn't convey respect for its audience.

But mainly? Dude. The "virology" is a major fail and really pulls me out of any willing-suspension-of-disbelief I'm trying (hard) to get going. I think that may also be a problem for a (majority) non virologist audience. A general audience knows what "feels" like professional science and what feels just plain flaky. 

I guess I'd been hoping for something more Contagion'esque; grounded in today's reality, well informed, taking itself seriously and telling interesting stories using believable characters. Having watched 3 eps, I sum it up as more Outbreak-meets-28-days-later with dual-personality-but-still-angry zombies. I reckon it needs to make the material stand apart or at least do more to improve on what's come before. We probably have enough zombie+virus variations to not need another one unless it stands out. Maybe that's what the unmoving snow-plough is for. Or maybe there are some huge twists coming that will make me look like like an idiot (or perhaps the typos have already done that). Hope so.

Some (by no means all) nerdy comments and questions follow. Spoiler alert also, if you haven't seen the 3 eps that have gone to air so far.

• What is it about this, or any retrovirus outbreak for that matter, that shouts "hey, I'm a retrovirus and I'm breaking out" to Arctic non-virologists? What retrovirus symptoms are so acute and worrying that a CDC team would have been called in? What retrovirus causes you to bleed out and die? Oh, and melts the flesh from your bones as well? How did the Arctic guys identify it was a retrovirus before asking for help?
• A "Spherical" worm virus? Clearly nothing like a retrovirus.
• "The cells are heavily damaged almost totally deformed, it's like..Armageddon down there." says senior post-doc.
                      "But no sign of a virus?" says junior whizz-kid post-doc. Ouch. C.P.E. I'ma geddin outta here.
• 15nm (?could have been 5 or 150 - was hard to hear) on an electron microscope (EM) screen...that clearly shows a scale of 8,000nm...pretty good on-the-fly size estimation young whizz-kid post-doc.
• Portable, real-time, high-magnification scanning electron microscope (SEM), adjustable with a focus knob, that can also show CG wormy virus entering cells that then instantly shrivel without the SEM killing/breaking down the cells or the virus? Also totally unlike the Helix show logo which looked more like the cell, but was black yet not shrivelled. I'm so confused.
• What's with the unofficial CDC logo - or lack of the official logo? The show is not even supported by the CDC but uses "CDC" a lot?
• "...screened for all current viral structures..", "...even icosahedrons". What are the chances that they even looked for icosahedrons??? Its not like they are a hugely common presence in the virus world or anything...Oh.
• This unknown illness caused by a "retrovirus" or whatever, is to be worked with under Biosafety Level 4 conditions (BSL4) and yet considerable work is done on open benches without any significant personal protective gear. Of course that's all after the pathogen is defined as not being capable of spreading via an airborne route. Apparently there is just one type of airborne spread and droplets and aerosols generated by a number of techniques and procedures...and gunshots...don't count.
• You take off your BSL4 suit because a mouse doesn't what? Die in a matter of minutes...perhaps hours? If wormy virus is enacting annihilation upon it's human hosts then I'd like to at least see a monkey if not some decent primary human (because that's the host we're most worried about it annihilating) cell-culture results and inflammatory marker data before I started breathing that air! We do see a (creepy, angry) monkey later, but the protective gear doesn't go back on, or ever get put on in some cases, and then in later episodes it does, then it's off again, then a non-sealing surgical mask turns up...argh! BSL4 being optional must be part of the working-without-regulations mantra up there in BigPharma Arctic world 
• In a later Ep we develop a test using green fluorescent protein. GFP is  from the jellyfish Aequorea victoria our over-sharing young whizz-kid post-doc states; although she states nothing about how this bloody rapid bedside test works nor how she produced it without any cloning at all. It gets combined with an infected patient's white blood cells. A huge volume of the GFP-containing, virus-sensitive, previously infected patient cell solution glows green (under normal light) just seconds after a huge volume of the infected patient's sample is added. 96-well plate guys? Mind you this was all developed without validation and within half an hour or so; exemplifying how great the 26-year old whizz-kid post-doc with 2 Masters degrees is in the lab. She told us she was earlier. Later we see why unvalidated tests based on poor science and rushed to market fail so spectacularly. More on that in Ep 4 I suspect.
• Hey, anyway, let's go conduct a monkey autopsy with just a face shield that is in no-way sealed to our face. And what the hell, why even bother doing up that lab coat? It would just ruin the belligerent devil-may-care researcher vibe we're aiming for. Aerosolized bits of diseased freaky-monkey tissue in your eyes/mouth/nose/lung anyone?

Where World War Z succeeded in providing a great story about a virus wanting to transmit by driving its host to infect more potential hosts, Helix fails by clubbing us over the head with a show that feels like it's leveraged science thawed from an Arctic vault constructed in the 90s. 

While I don't expect the general audience to know that centrifuging a drill core of frozen solid monkey butt will not just transform it into a homogeneous black liquid in 5-sec (or ever), I do think they will notice something is amiss. Off beat. Out of  sync. Even if it is set 5-min into the future or something.

Try making Helix smarter. I like that there is a story about DURC that may get to a wider audience. That and the suspense are probably the biggest draw-cards for me. 

This needed/needs an infectious disease expert on the advisory team. A virologist in this case. Just as disease outbreaks do in real life. Just as the movie Contagion had - and for that movie, it really paid off.

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An idiots list of influenza genetic changes..

I knew someone would have done this already! 

Many thanks to Prof Yoshihiro Kawaoka and Dr Eileen Maher who answered my email and pointed me to a massive list of the known genetic changes that determine influenza virus phenotypic characteristics of importance, in a downloadable PDF format, on the Center for Disease Control and Prevention's (CDC) website. 

http://www.cdc.gov/flu/avianflu/h5n1/inventory.htm

So I will add a fey more"key" mutations to my draft and place it on my dedicated influenza page (http://www.uq.edu.au/vdu/VDUInfluenza.htm) but I think the CDC have it all very well covered - so I no longer need to curate my own list until the day I die!

Also check out Dr Amesh A .Adalja's paper containing a Table of mutations and thanks to Robyn Hall for some additional info.

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An idiot's list of key influenza mutations...Draft 2 (please correct and contribute-updating constantly)

Okay, I admit that keeping the number-amino acid shorthand-number codes for all the influenza virus mutations out there has totally escaped me as a thing of interest so far. 

Probably because I can't remember them! 

So, like many things on VDU, I'm starting a page that may serve as a record. To start with, it will be mostly just the mutations we often see talked about in research papers and the more sciency media sources and blogs. If you are knowledgeable in this area, please spare a minute to let me know of what I'm missing.

I'd really like to list:

1. The code for the mutation e.g. Q226L or E627K ("usual" amino acid code first, mutated version last)
2. Any alternative numbering, if it exists H3 vs H5 vs H9 etc
3. What animals are involved (relates to #1 also)
4. What finding the mutation means - binding changes (upper or lower respiratory tract, stabilizes the virion, resistant to pH, antiviral resistance etc)

In return, I'll curate and maintain a webpage with that list until the day I die! Deal?

Here is the start of it...now at Draft 2...

Please click on image to enlarge. Note new post about CDC
Table of mutations for H5N1.

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H5N1 case in Canada had been diagnosed with pneumonia...testing at the source would have been helpful

And now, from a fantastically detailed post onto ProMED by Fonseca and colleagues, we see that the H5N1 case was diagnosed with pneumonia.

On 28-Dec, the patient presented to a local emergency department.

"A chest X-ray and CT scan revealed a right apical infiltrate. A diagnosis of pneumonia was made; the patient was prescribed levofloxacin and discharged home."

One sad point made in the ProMED post which supports the need for constant viral vigilance the world over, coupled with the dissemination of those surveillance data, so that patient management anywhere in the world can be armed with the best possible decision-making information...

"The index of suspicion was low as travel was to an area in China where there have been no recent reports of the circulation of this virus, and coupled with no obvious exposure to poultry, the diagnostic work-up and consideration for A(H5N1) infection was very low"

As a recent J Virology article by Yu and colleagues highlights, when a sensitive testing method like the polymerase chain reaction (PCR; in this case RT-PCR because influenza viruses all have an RNA genome, not a DNA one) is applied to the search for a virus, it yields the kind of data that can:

1. Explain from where a virus emerges
2. Inform the search for disease aetiology - where are human cases getting infected from and if a zoonotic infection (from animals to humans), which animal(s) is the culprit?
3. Alert the world to any risks of infection when travelling to a certain area(s)
4. Allow the local health departments to mitigate the risk of their population acquiring infection by instigating controls (like live bird market closures). This has implications for the world since respiratory viruses have the potential (thankfully not realized for H7N9 or H5N1 to date) to spread more rapidly and efficiently that blood-borne or mosquito-borne or sexually transmitted viruses.
5. Permit understanding of how widespread (over what geographic area is it detected) a novel or emerging virus may be and how entrenched (is the same site repeatedly positive) it is

Not doing such testing, or using less sensitive methods will not yield this information. 

In Yu's study, testing of 12 poultry markets, mostly urban, and local farms linked to 10 human infections in Hangzhou, Zhejiang province around 4th to 20th April 2013 yielded signs of H9N2, H7N9 and/or H5N1 viruses in all markets. Poultry were often positive for H7N9 and H9N2 (this finding from individual RT-PCRs was confirmed using next generation sequencing), whereas human specimens were not. These levels hadn't been turned up when 899,000 bird were tested in 2013 using (perhaps) less sensitive methods.

I think with influenza, it may be safer to presume its everywhere until that presumption can be discounted. Clearly the conditions for influenza viruses to swap gene segments and sort themselves into new subtypes and variants are commonplace and frequent; these aren't just chance occurrences of different birds passing in the night via overlapping flyways. These feathered vectors are co-infected by 2 or more viruses at a time. Luck and the constraints of viral fitness are presumably the only things keeping H7N1, H5N9, H7N2 cases from dialing up in humans? What seems to be lacking is more molecular testing at the farms supplying the markets. Not just in Zhejiang, but all over the region.

As the authors noted, 100,000s of people visit these live bird markets each day and very few influenza cases seem to be due to them. Long may that last. But it's a tinderbox for which matches are already being struck; if the viruses should bud of that one-in-a-million variant that is enabled to readily spread from person-to-person, whooshka. 

More testing guys, keep testing.

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Adjustment to dates....

Got myself confused didn't I?!

I mentioned in a post last week that..

I started within Week #35 (given that Week#1 starts from Feb-5; the week in which symptoms were reported for the index case on Feb-11). Prior to Week #35, things were very quiet going back to April-2013. A couple of cases in July.

That date, Feb-11, is in fact when the son of the confirmed index case was ill. The son was never able to be confirmed (despite me thinking I'd seen a paper that showed antibody results for him) so he remains as a "probable" case. 

The 87-year old father became ill 19-Feb-2013. I've also adjusted my Week numbering to start on the Monday of the week of interest. So Week #1 of the H7N9 outbreak, based on the week in which illness onset was identified in the first lab-confirmed case, begins 18-Feb-2013.

What does this mean? Not a lot really. In those charts with a date scale on the x-axis (the bottom line), the beginning will have shifted, and the comment from last week's blog has been updated to say that I started from Week #33.

Welcome to Week #48 (the beginning of the 48th week) of known human influenza cases due to avian influenza A(H7N9) virus.

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H7N9 by area of case acquisition...

This is another way of looking at the sites of origin of avian influenza A(H7N9) virus cases in southern and eastern China. After adding in the most recent 7-cases today, Guangdong province now comprises 9.9% of cases. 

Females dropped a little from yesterdays post, but remain a more frequent presence than we saw in 2013 or overall on average numbers.

I know if I go to bed now, the next batch of cases may well arrive but such is life in the southern hemisphere.

There is talk of more live bird markets closing soon. Given that most cases still list some contact with poultry (feels like there might be more without contact in recent notifications?), more closures cannot come soon enough in my opinion. 

Whilst these numbers are small given the population sizes involved and can in no way be confused with a seasonal influenza epidemic, they are gaining on that "other" bird flu, H5N1, at an increasing rate.

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