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.

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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...

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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?

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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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