Zhejiang province: then and now in H7N9 town

Click on image to enlarge.
The data are plotted as number of cases (y-axis)
vs. week of illness onset (or date reported if
onset data was not reported). The time span is
the same for both graphs (2-months) and the
number of cases is fixed at a 50-cases on
the y-axis of both so that the slopes can be
compared.

A quick look at what life was like in Zhejiang province, the current H7N9 hotzone, over a 2-month period (top) when cases really took off in 2013 compared to the past 2-month period this year.

The current slopes is less steep and the case tally is a little lower, but it is not hard to see that both will increase if the current rate of cases continues; of the last 18 H7N9 cases, 12 (67% or two-thirds) were from this province.

H7N9 snapdate: cumulative case chart by region

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In this update - a mere 2 or 3 days after the last, Zhejiang province continues to stand-out as the place to acquire a severe H7N9 infection. Shanghai and Guangdong province have slowed. Apart from most recent cases being in severe or critical condition, most have contact with poultry.

The WHO confirmations have ~15 cases yet to list (see FluTracker's list for the latest figures)- there data include dates of onset which are great to have and may change some of the placements of those data slightly. 

Just out of interest, H7N9 Week#46 and #47 yielded (to date) 25 and 21 cases, respectively.  This is currently Week #49, by my counter.

H7N9 snapdate: cumulative case chart

Click on image to enlarge.

This is a new idea for VDU's blog: the snapdate or "snap update". It covers those times when I have little more to say beyond what a chart conveys yet still more words than a Tweet can cover.

This is a snapdate of 205 avian influenza A(H7N9) virus cases.

That Zhejiang slope looks eerily familiar. I know 205 is only 6 more than 199, but crossing a multiple of 100 is "a thing" for me. 

Something I tweeted yesterday that I thought was interesting when comparing the earlier "bird flu" to (one of many of) the latest...

• >200 H7N9 cases in <1-year
• >645 H5N1 cases in >15-years

Despite all the papers and press, it still feels like the fluff over H7N9 has been less all-encompassing than that for H5N1 was/is, even though H7N9 reached its first 100 cases in fewer than 2-months.

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

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..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.

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.

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

Click on image to enlarge.

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.

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

Click on image to enlarge.

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

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

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

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

Which brings me to a whinge. 

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

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

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

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

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

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

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

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

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

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

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