MERS-CoV: another emerging virus that just...stopped emerging?

Click on image to enlarge.
Data are plotted using sites of acquisition of MERS-CoV
infection. Dates are of illness onset when reported, 
otherwise the date the case was announced

Two charts by way of an update on cases of infection by the Middle East respiratory syndrome coronavirus (MERS-CoV)...which shows that there is not much to update from my last charts on Jan-17 here and here.

Click on image to enlarge.
Same accumulation graph (green) together with the
accumulated fatal cases and the proportion of fatal cases (PFC)

The main feature of these two charts is that cases have plateaued. There has been little recent reporting of new MERS-CoV infections...from anywhere.. for some weeks.

Has something been done within the Kingdom of Saudi Arabia (KSA) to interrupt the transmission chain between whatever the MERS-CoV source(s) was(were) and humans? 

We have not heard of any measures and of course no-one is generously offering to clarify this obvious and abrupt change in epidemiology. As has always been the case with the MERS story, this new turn of events leaves one unsure of what to think about this apparent sudden decline of case announcements. 

I'm wondering if reporting has simply ceased. Two reasons for this personal view:

1. The most recent MERS-CoV case was a 55-year old male healthcare worker (HCW; Bangladeshi surgeon working at Prince Salman Hospital) who died 15-Jan in Riyadh. Now sure, he may have acquired MERS from an animal source (camel, bat, mouse, or cow, we don't know) but the odds, to my mind and with the MERS-CoV picture to date, it seem much more likely that he was caring for someone afflicted with MERS-CoV, which would mean 1 or more other cases exist but have not been reported.
2.  The level of communication from the KSA about many aspects of MERS-CoV has not been of the quality that could foster any trust. It often appears that free communication of has been stifled or strangled rather than nurtured or nourished. The specifics to support that opinion can be found in browsing through my posts on MERS-CoV this past year or so.

So its impossible to say more about what's happening with MERS-CoV infections beyond the fact that they have not spread, noticeably, beyond the bounds of the Arabian peninsula.

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Zhejiang live bird market closures and enhanced monitoring of farms, wild bird habitats and parks...

Crawford Kilian is always on top of the market closure announcements, and Xinhua in general. His recent blog post is particularly welcome; halting of live bird trading in Hangzhou's markets (on Friday 24th). Markets in 6 districts will be closed and disinfected and some/more monitoring of birds (hopefully not just for H7N9) will be launched on supplying farms and in wetlands and parks. I hope that's all RT-PCR-based.

Hangzhou is the largest (2.5-million people), and capital city of Zhejiang province, a region that has served as H7N9's playground over the past few weeks. 

This action comes on top of 2 other districts (1 in Hangzhou and one in Jinhua) already having closed their markets.

Shanghai closes up 31-Jan to 30-Apr, for the Spring Festival. 

The Xinhua story quotes Li Lanjuan of the Chinese Academy of Engineering and director of State Key Laboratory for Diagnosis and Treatment of Infectious Diseases as predicting that...

"China will see more human H7N9 cases in the future as the virus tends to become more active during winter and spring"

...or at least, human cases appear more often then.

References...

1. Crof's H5N1 blohg
   http://crofsblogs.typepad.com/h5n1/2014/01/h7n9-hangzhou-halts-live-poultry-trading-shanghai-reports-2-deaths.html
2. Xinhua article
   http://news.xinhuanet.com/english/china/2014-01/24/c_133069407.htm

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Influenza in Queensland, Australia...

Image adapted from Geoscience Australia,
The Australian Government.
http://www-a.ga.gov.au/web_temp/1531782/61756.pdf

Hot, humid and sunny are the conditions here just now. Although some rain around too-stormy rain with big dumps of water an flash flooding. Must be summer.

In the previous week's Queensland Health Statewide Communicable Disease Surveillance Report it looks as though we have a slight uptick in laboratory confirmed influenza cases so far this year (this is in total numbers, not proportions of samples tested, so take the value with a grain of NaCl) compared to the year-to-date totals for 2013 and 2012 in Queensland Australia.

As of the the 13-Jan update (data from 12.1.2014)

• 106 case notifications in 2014
• 73 cases by this time in 2013
• 41 cases by this time in 2012
• 144 cases by this time in 2011
• 21 cases by this time in 2010
• 12 cases by this time in 2009

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Pre-existing antibody reactive to avian influenza A(H7N9) virus did not predict better survival

Freeman and Cowling comment in the Journal of Infectious Diseases on a paper last year by Yang and colleagues (I made a note about that one here). They also re-analysed one of the conclusion and found that, for this dataset at least, having H7N9 antibodies did not afford a reduced risk of death. 

Freeman and Cowling conclude that this doesn't negate using convalescent sera (the bit of blood, minus the cells and the clotting factors, that contain proteins, water and the antibodies we make against an infection we've had) as a treatment option. But from the data in Yang's paper, the pre-infection existence of higher levels of antibodies that react with H7N9, did not improve chances for survival. 

More study is needed.

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Market sampling: H7N9, sensitive testing, market closures and small numbers

A World Health Organization Western Pacific Region update on influenza A (H7N9) virus has a few interesting bits of information that pulls together a recent flurry of reports. This is the situation as of 22-Jan...

• 18/200 (9.0%) "pathological samples" from markets (listed below) in Zhejiang province, presumably using PCR-based methods, were H7N9 positive  
• Sanliting Agriculture Products Market (6 oral/cloacal swabs, 2 environmental faecal swabs)
• Central Agriculture Products Market (2 oral/cloacal swabs, 1 environmental faecal swab) 
• Fenghuangshan Agriculture Products Market (1 oral/cloacal swab)
• Guoqing Poultry Wholesale Market (3 oral/cloacal swabs, 3 environmental faecal swabs).
• 2/2,521 (0.08%) pathological samples were H7N9 positive in Guangdong province
• Pathology specimens from the provinces of Jiangxi, Liaoning, Jilin, Heilongjiang, Jiangsu, Fujian, Shandong, Hubei, Hunan, Guangxi, Yunnan, Qinghai, Xinjiang Provinces and Chongqing and Shanghai Cities were H7N9-negative
• 7-Jan, H7N9 RNA was also reported  in 3/17 samples collected from the kitchen of a restaurant in Haizhu District, Guangzhou City, from the chopping board and sewage water. 
•  Meanwhile H7N9 RNA was identified in 8 out of 34 environmental monitoring samples collected from the Guangdong's Longbei Market, Jinping District, Shantou City.
• Ningbo city (Zhejiang Province) has stopped commercial live birds entering the city
• Shanghai city will suspend live bird trade all over the city from 31-Jan to 30-Apr. Live poultry from other provinces will not be allowed into the city except for transport to a centralized slaughterhouse.

It's great to see some data from other provinces and municipalities that have not reported any human H7N9 cases to date.  I do wonder about the relatively small numbers of market samples though. Some of these samples pale in comparison to what was tested in 2013; which reacted earlier than this, the second time around. While 2,00 samples is not an easy day in the lab, we saw >800,000 bird samples tested by "virological" (?culture) and serological methods in 2013 (see other thoughts on the use of PCR in birds here).

So what have we learned here? 

1. Further confirmation that live bird markets house H7N9-positive birds. With most human cases this year having come into contact with poultry, the transmission chain is in place. Market closures seem the most effective way to stop transmission abruptly and they have a precedent for this in 2013. This is happening. Will it be enough? What  about the market-supplying farms?
2. RT-PCR testing is more likely to uncover influenza in birds than culture methods and is better than antibody testing (although how much better is hard to judge from the information provided). Added bonus: RT-PCR is more likely to tell you what's circulating now rather than a little while ago...although no-one really responds to the lab results that quickly anyway.

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H7N9 snapdate: cases per week and cumulative cases

Click on image to enlarge.

This "snap update" is about the H7N9 epidemic curve. It reveals that the second wave of H7N9 human cases are really piling up this winter. As I sit here at 9:30pm (7:30pm in Shenzen), I've just added another 7 from Zhejiang (n=5), Shanghai (n=1) and Guangdong province (n=1) for today. 

It's also worth noting that we did not know of H7N9 in humans this time last year; we are still a few weeks away from the 1st anniversary of H7N9's discovery. WHO was notified 31-March-2013, but onset of first illness due to H7N9 was 18-Feb-2013). Its case numbers suggest a slow rise compared to a seasonal human influenza epidemic (H1N1 or H3N2 viruses for example), but it is a rapid rate for an avian flu in humans.

Tallies have hit 25, 26, 7 and 12 cases (=70 so far) per week for the past 4-weeks (beginning 30-Dec, 6-Jan, 13-Jan and 20-Jan respectively). These tallies will change if/as new case announcements continue and are assigned to dates of onset that sit in among these weeks.

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H7N9 infection of women is not on the rise....

Click on image to enlarge.

A bit over a week ago I posted a chart showing that the proportion of females with avian influenza A(H7N9) virus may be rising.

We've had a lot of cases since then so is that trend still holding? 

[By the way, you are forgiven for  thinking this is the "H7N9 Down Under" blog!]

The new chart shows that the proportion of females has dropped back to something looking a little more like it did in 2013. The earlier data seems to have been a blip after all. 

With the addition of new cases to the dataset and with the shifting and re-sorting of cases into this or that week as onset data firm (WHO have recently been doing a fantastic job filling in the data gaps from Chinese reports), we can see that the proportion of females has been 40% or (often much) less each week for 10 of the past 14 (71.4%) weeks.  

In summary...

• The current proportion of female confirmed H7N9 cases overall is 29.5% (219/220 cases with data) 
• In 2013, females comprised 29.7% of cases
• In 2014 females comprise 29.5%. No difference to speak of.

So males dominate among the mostly severe human cases of H7N9 infection; business as usual for H7N9. 

Also, sustained person-to-person transmission (infected person passing to another  person, (1st round; = sporadic transmission) who passes it to another person (2nd round) and so on...is not happening.

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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.

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H7N9 snapdate: cumulative case chart by region

Click on image to enlarge.

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.

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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.

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