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H7N9 by sex and week...are female cases on the rise?

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I tip the hat I'm not currently wearing to CIDRAP's excellent staff writer, Lisa Schnirring for the idea that led to this chart. 

Click on image to enlarge.

I've plotted 163 of the 164 lab-confirmed H7N9 cases (includes surviving and fatal cases) by the sex of the H7N9-positive person and the week in which they acquired their illness (if date of onset was noted), or else the date the case was reported to the world. 

The chart above shows that overall, male cases dominate the H7N9 landscape each week (69.5% of all cases are male)....except that among the new appearances of H7N9 in China, there seems to be a greater number of weeks in which females are equally represented among the cases. While the case numbers are low this still begs the question, as does the cause of the apparent start of the H7N9 season, what is driving these patterns?

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Middle East respiratory syndrome coronavirus (MERS-CoV) update to timeline of key events....

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Click on image to enlarge.
Feel free to use this graphic. Simply cite this blog and Dr Ian M. Mackay.

An update to my main website's MERS-CoV timeline now including the countries that have hosted their "own" cases along the top - and when the first case most likely occurred.

I'm doing a little updating across the board actually - hence the graphics!

Anything you'd like to see recorded on this timeline that I've missed?

As always, these graphics are cobbled together from various sources including public and the scientific literature. They do not represent the views or interpretations of any institution but the one in my head. They are compiled with all care and the best of intentions but may not be as comprehensive as data from the primary public health sources in the countries that are mentioned on my websites.
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H7N9 cases by Province and Municipality of origin...

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Click on image to enlarge.
H7N9 cases (surviving and fatal) by Province or
Municipality of acquisition.
This chart highlights where the human case activity was in 2013 and where it is right now.

It's based, as best I can determine, on where the person is likely to have acquired the virus rather than which hospital they were treated in or the location of the detecting laboratory.

The line to keep a very close eye on is that little tan one representing Guangdong province; it pops up in early December 2013. 

Hong Kong cases have also come from Guangdong province. 

This thin tan lane is showing all the early signs of being the next Shanghai, Zhejiang or Jiangsu as a hotspot for H7N9 cases.

Controlling the virus may well be essential for limiting H7N9's chances of getting more "comfortable" among humans in 2014. Or is it just a matter of time and chance before that happens anyway?
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H7N9 cases by week...the other bird flu is done nesting [UPDATED]

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Click on image to enlarge.
H7N9 cases by week, worldwide, from Week
beginning Monday 30.09.13 to 06.01.14.
Sources are publicly available data. 
A quick plot of case occurrence to the best of my ability given the variability in the data. Follow the left-hand column down then back up to the top of the right-hand column and down again to follow the 22 cases and 2 deaths through time.

I started with Week #33 (33rd week of H7N9; given that Week#1 starts from Feb-18; the week in which symptoms were reported for the 87-year old male index case on Feb-19 [updated]). Prior to Week #33, things were very quiet going back to April-2013. A couple of cases in July. 

These charts will change as we get more cases and more details and perhaps, more fatalities among these cases. There are between 152-158 H7N9 lab-confirmed cases, including fatalities.

The main message here is that H7N9 case numbers are on the rise again. 

It was in March and April 2013 when we saw the greatest number of H7N9 cases, but given that we now have specific PCR-tests and other assays available combined with a far greater number of "launch sites" this year, I expect we'll see increased numbers of human cases from here on in. That could change if drastic control measures are taken of course.

We have also learned from the recent case in Canada, that H5N1 is probably entrenched in areas that are not being tested/reported (see CIDRAP article). There is no doubt in my mind that H7N9 will be in the same nest, circulating in at least the 12 provinces or municipalities of mainland China from which we have seen human cases arise over the past 49-weeks. 

Speaking of which, there have been very few deaths in this approximately 15-week block. The overall proportion of fatal H7N9 cases was around 30% but among the subset of cases here, only 9.1% have died after H7N9 infection. 

Have things changed? 

I can't imagine the virus has changed since it seems most acquisitions are from poultry and there would not be evolutionary pressure in a bird to transmit more efficiently on the off-chance it was acquired by a human! So does this mean...

  • Case management has improved?
  • Are more cases recovering and being discharged?
  • Are we still in that horrible waiting period when cases are in intensive care awaiting their fate?
  • Are we simply not getting details about deaths and discharges from China any longer? 
We were certainly missing information about which cases died towards the end of the first wave of H7N9 - my database can only identify 37 of the predicted 48 deaths. These details have not yet appeared in the scientific literature so any averages (sex, or age for example) calculated from public sources are far from perfect. I presume Chinese researchers have those data.
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Why one watches the webs for the worst of the woes...

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In an article on BAYTODAY.CA,written by @HelenBranswell, there is a fantastic quote that really defines why infectious disease bloggers, and public health professionals working through more official channels, get all fired up when they cannot have or find, information that could be used to help monitor or understand disease outbreaks. 

 "We breathe the same air. We drink the same water. We fly on the same planes. And an infectious disease outbreak anywhere is a potential risk and threat to all of us," said Dr. Martin Cetron, director of the center for global immigration and quarantine at the U.S. Centers for Disease Control in Atlanta.

"And we just have to constantly pay attention and stay vigilant."

The influenza H5N1 death in Canada has and continues to generate a huge amount of interest. It's also generating no small amount of confusion over how the infection was acquired by this late 20-something East Asian female who worked in healthcare at Red Deer Regional Hospital. Apart from that, this infection also highlighted that when many eyes focus on a case, it is very difficult to keep a patient's details, work, travel routes and trip details, secret for long. 

Does intentionally withholding any or all of age, sex, date of onset, date of hospitalization, and perhaps a few other deidentified details truly hinder a globally connected world's efforts to uncover these details? Seems not. Whether those details hinder a patient's ability to remain anonymous I cannot say; I said other things about that recently though.

In the meantime, interested and involved professionals and amateurs alike use what information they have to hand to bend their minds towards seeking answers and making comments that might help solve mysteries like this. Because they try to help. For the benefit of all of us. I suspect, regardless of the communicative devices available to them and the extent of the interconnectedness in which they abided at the time, they always have and they always will.
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H5N1: 1st fatal case in North America...[UPDATED x4-FINAL]

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An otherwise healthy resident of Alberta, Canada, died 3-Jan after contracting influenza A(H5N1) virus during a visit to Beijing ,China. The person did not leave the Beijing area and did not visit live bird market. The victim returned on Air Canada flights (according to a Tweet from @HelenBranswell), showing signs and symptoms on admission to hospital 1-Jan which included high fever and lethargy without cough or other signs of acute respiratory tract illness. The patent died of meningoencephalitis. The lab confirmed H5N1 7-Jan. 

Canadian officials will not be describing the patients age, sex or occupation. Giving the region would be enough to identify the patient given there is only 1 case.

A highly pathogenic avian influenzavirus (HPAI or "high-path) that can kill the birds it infects, H5N1 has been confirmed in 648 people across 15 countries since its identification in a 3-year old boy in Hong Kong in May 1997 (first identified in a goose in 1996). There were 38 cases identified globally in 2013, with 24 deaths. A slow-burn that seems comparable to H7N9's current spread. How often H5N1 is considered in the screening of influenza-like illness I do not know; another similarity might be under-reporting/limited prospective PCR-based screening.

As ever, these sporadic imported cases also serve to highlight that the pathogen is circulating at the source. The route of acquisition for this case is unclear at this stage. H5N1 does not readily transmit among humans requiring close contact with birds and there has been no sustained human-to-human transmission.

When a human does become infected by the virus, severe acute respiratory distress syndrome can result. This is ascribed to the availability of receptors in the deeper airways and lungs, which bind the virus and trigger the person's own immune-mediated disease via a "cytokine storm"; a large scale release of the chemicals our bodies usually employ to keep virus infections in check, but on a larger scale with more severe consequences to the host. Such a storm does not commonly occur following infection by a seasonal influenza virus (e.g. H3N2) infection, 

The WHO does not list any H5N1 cases in the area around Beijing on its 2013 map (18-Dec-2013). An out-of-date timeline of "major" H5N1 events lists human cases in Beijing in Nov-2003 and Dec-2008. Major outbreaks among birds in China have centered around Qinghai lake.

There is no H5N1 component in the current seasonal influenza vaccine, but then there is no significant risk to the Canadian public health from H5N1.

The current WHO phase of pandemic alert for H5N1 is ALERT:
This is the phase when influenza caused by a new subtype has been identified in humans. Increased vigilance and careful risk assessment, at local, national and global levels, are characteristic of this phase. If the risk assessments indicate that the new virus is not developing into a pandemic strain, a de-escalation of activities towards those in the interpandemic phase may occur.

As the Public Heath Agency Canada recommend, Think-Tell-Test....
THINK
  • implement best practices for triage, infection control and patient management as indicated
TELL
  • Consult your local Public Health for assistance in SRI/severe ILI patients with the following:
    • Recent travel or contact with travelers to an affected area with confirmed H5N1 activity in humans and/or domestic poultry
TEST
  • Consult your local Public Health for guidance on appropriate testing, recommended procedures and prioritization for H5N1 investigation IF significant exposure history has been established which may include:
    • Close contact (within 1 metre, i.e. touching distance) with a confirmed human case of H5N1 or
    • Close contact with sick or dead domestic poultry or wild birds

Other news and related information sources include...
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From birds to humans....

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Reports indicate 2 new cases of human infection with influenza A H7N9 in Guangdong. The 47-year-old (Foshan) and 71-year-old (Yangjiang) males are both hospitalized and in bad condition.

It was only a matter of time since the market testing has been revealing signs of H7N9 circulating.

For 47M...
"The Guangdong health authorities have on patients 60 close contacts under medical surveillance, not currently found exception."

For 71M...
"The Guangdong health authorities have on patients 65 close contacts under medical surveillance, not currently found exception."

So the contacts are under surveillance but I strongly suspect that if that surveillance was to extend to actual RT-PCR testing, then we would likely see some detections amongst those cases. Symptoms alone do not the full story tell.

My source was Twitter via @pandemic_news and associated blog post here.
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H7N9 in Guangdong; Market #2

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As the tally of H7N9 cases passes 150 (n=151 since Feb-19-2014, 321-days), crofsbogs has picked up on an environmental sample from a second live bird market (Nanchao market) that has been confirmed as positive for H7N9 by Center of Disease Control and Prevention (CDCP).

This time we learn that nucleic acids were detected so RT-PCR methods are in use, at least in Zhuhai city, a prefecture-level (between less populated than a Province but more than a County) city on the coast of Guangdong province bordering with Macau. 

Was RT-PCR in use during those huge poultry screening events last year? Tracking back to a post on some of the vast numbers of animals tested (hundred's of thousands) earlier in 2013 it looks like the testing back then was virological (trying to grow virus I presume) and serological (detecting antibody to recent infection by the virus) rather than molecular (PCR-based). I stand to be corrected on that.

Just thinking out loud, but it seems to me that 800,000+ birds had been tested using RT-PCR then we would have had a much better idea of the extent to which H7N9 was distributed across China.

As an aside, the 3 most recent human cases also read like a who's-who of 2013's H7N9 hotspots; Jiangsu province, Shanghai municipality and Zhejiang province. 

I'm making some more lines available on my Excel sheet.
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Editor's Note #13: 2014 thoughts...

Virology Down Under.
What does Virology Down Under's (VDU) blog stand for? 

First off, a little background.

The idea of VDU the website, was to provide some useful info on viruses; the type of info that could be used to help less expert people get an idea of what they are and what they do to us. It had its beginnings in 1996 as the website for the Sir Albert Sakzewski Virus Research Centre (SASVRC), my workplace. It then accrued enough mutations that it evolved into VDU.


That endeavor truly started online in 1997; 16-years, 11-months and 9-days ago. Last year VDU spawned a blog. This. 

The VDU website, while in need of sprucing up (still), exists more as a fixed point in time while the blog aims to keep readers abreast of some of the goings on in virology. The blog's focus is on respiratory virology because that's what I know most about, but other things get dropped in on occasion. The focus is also on my take on things, hopefully with some humour thrown in. I initially commented in April 2013 that I'd stay away from blather and keep the opinion related to hard data. That's still my intent, but opinion being what it is I may rant on occasion, I may drift away from citable evidence and I may collect thoughts in a way that cannot be verified by any one single study. Hopefully I'll make that clear but it will all be part of VDU's DNA...probably RNA given its focus on respiratory viruses...and nerdy little comments like that will continue to pop up too!

I've noticed during my short time in "flublogia" (I think that's a hard 'g') that each blog/site/newsboard has a distinct personality. Apart from spending a large slice of their own time collecting, collating and writing about infectious diseases for a largely intangible audience; page hits and comments being key proof-of-life beyond the keyboard. Some key authors I have learned from in 2013 produce a "vibe" through their blogs. I often read the same new piece of information but on multiple sites to see a wide range of interpretations - each one telling me something different, each a specialized cell contributing to the tissue. 

Crawford Kilian emphasizes the human cost to infections, Mike Coston emphasizes ways to personally protect yourself from infection and manages to place new news in superb context thanks to his blog's back-catalogue of posts while FluTrackers emphasize the spotting of information before it even occurs (yes, they are that fast!) and lays the groundwork for trends that are often only visible after their subject matter has emerged. If I want to actually be interested in what's happening in the world of not-viruses, I'll go to Maryn McKenna's Superbug because it's the only bacterial text I enjoy reading (and she posts funny Tweets). There are others but correcting all these typos means that I write slowly and this has already taken a while.

So what about VDU's blog? It aims to identify, define and add opinion to patterns seen during virus infections, epidemics and outbreaks. It's a part-time thing so I post when I can. My opinion may not be bleeding-edge expert or informed by decades of specific literature and research (sometimes it is)- virology has many, many aspects to it and I don't claim to be across them all - but I am most happy to be educated so please do leave comments here or on Twitter, LinkedIn, ResearchGate or anywhere else I've left an avenue for contact.

Another of the VDU blog's intentions is present its data pictorially and certainly to create a reference of somewhat "softened" science for you and also for me; it now serves me as a literature review repository and I hope some of its graphics can also be useful to you in your talks, blogs or whatever. VDU's images remain free to use - I just ask that you link back to the blog.

I won't dwell on the misery caused by virus infections (and there is much), in fact I deliberately keep VDU faceless and focus on the virus rather than the host. Others do a much better job of conveying the human cost than I can anyway. It's not because I don't care (I have written on this topic previously) so I apologize if it all seems a little devoid of humanity.

The VDU blog is not yet 1-year old; still an infant in human terms. It's been crawling along okay so far but it's still got a lot to learn and hopefully some more readers to pick up as it grows. In its 1st year VDU's blog has driven 2 publications, been cited in the scientific literature, under-pinned a lot of interviews with the media and been the reason for few local and interstate seminars (another coming up next month). More than I could have possibly imagined. It has also  created a lot of new links to good people both in science research and in science writing. I have learned much thanks to the help and mentoring these people have provided.

I hope that gives you an idea of what to expect from the blog in 2014. All the best for the New Year.

IanM


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H7N9 in the water and the goose stalls, in Guangzhou

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Via Twitter, Xinhuanet posted a story this evening that tests have identified influenza A(H7N9) virus in 2 poultry booths selling goose meat and an environmental sample of sewage water in a wet market in Zengcheng, Guangzhou, Guangdong Province. 

The nature of the testing, reported bye the local Center of Disease Control and Prevention (CDCP) is not specified so whether live virus was detected or viral nucleic acid is unclear. Finding influenza virus nucleic acids in the water of a live bird market in the current climate is not hard to believe - PCR being so sensitive and all - but whether it came from geese is not clear without more information.

There doesn't seem to be anything about this on the Animal Health's OIE latest disease alert list.

Disinfection of the market has been carried out and there is a suggestion that slaughtering of birds will occur soon.

Of course, FluTrackers had this a day ago!
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