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H7N9 snapdate: 316/317 cases by sex and week of onset/date reported

Click on image to enlarge.The dates along the bottom (x-axis) are the first Monday
of the week begging with that date. Week 1 is that in which
the first human case showed signs of disease.
A quick look shows that the proportion of recent female avian influenza A(H7N9) virus human cases is consistently sitting at or above 30%.

The overall proportion of females that have been H7N9 positive to date is 33% (316/317 cases with data). 

But over the most recent weeks, cases have often been a little more female than the 51-week average...


  • Week 44: 50%
  • Week 45: 50%
  • Week 46: 31%
  • Week 47: 33%
  • Week 48: 45%
  • Week 49: 35%
  • Week 50: 30%
  • Week 51: 39%

These weekly data are based on the week of disease onset (if known) or date reported (if disease onset unknown). Only time will tell whether the proportion of females drops back down again, or continues at higher levels than we saw in 2013. Such is the nature of an average number.

H7N9 snapdate: Zhejiang in the East, Guangdong in the South

Click on image to enlarge.
Zhejiang province is still climbing in eastern China despite market closures almost 2-weeks ago. 

Guangdong in the south surpasses 50 cases as well as Shanghai municipality and Jiangsu province, in terms of total counts.

Fujian province adds a few cases (at least some markets have been closed for disinfection) and now Hunan province is rising above the background "noise".

CIDRAP recently noted that United Nations Food and Agriculture Organization (FAO) was confident that Vietnam, on the border with Guangxi province (now at 3 cases), had not detected any "signs" (ill people, PCR positive birds..?) of H7N9 to date but intimated porous borders were a reality. And in China, market closures do not necessarily mean a halt to the purchase and household preparation of live/freshly killed poultry; they just necessitate a longer trip into the countryside to maintain spring festival meal traditions.

H7N9 snapdate: rolling average cases per day...

Click on image to enlarge.
Seriously.
This is really just an update from earlier today. My brain finally sorted out a niggling problem with the earlier version.

The chart needed to show 2013's peak season (now added to the previous version as"Rolling daily Av. Peak 2013" and shown above in green) minus the small number of cases preceding it, as I did for 2014. 

The preceding cases "dilute" down the average, giving a false impression of smaller case numbers per day than in 2014. 

I arbitrarily started this new line from the first time in 2013 that 4 H7N9 cases became ill in one day (28-March-2013; public data augmented with research literature for some). It tails off over time to join the total 2013 average, reaching 0.9 cases per day.

As you can see from the "Cases by Day" grey line; both 2013 an 2014 had 1 day with 8 case onsets (or case reported if no onset data available) in the 1 day. That is yet another benchmark to keep an eye on.

It's worth noting though that even this "enhanced" view of 2013's Case-by-Day chart, the average does not reach 2014's. The 2013 peak is 5/day whereas in 2014 the peak, so far, was 6/day but is currently at 4/day. 

Let's see what tonight holds.



H7N9 update on some trends: 2013 vs 2014

As I'd previously predicted (it was a very safe bet) and as CIDRAP's excellent coverage confirmed, H7N9 Wave 2's peak month surpassed Wave 1's in total number of cases. Quite a few more cases in Jan-204 than Apr-2013.

The total case number alone is no reason to run around like a headless chicken of course; it is what it is. It surprises me that there haven't been more cases given the live animal market culture, the number of people in the affected regions (see below for a rough population tally) and the number of times those two things intersect.

What does give me pause though is any change in the way cases are presenting. 

We are not seeing a great decline in the rate at which new cases are announced. I had expected some impact from the market closures since tomorrow (my time) represents the end of 2-weeks (a good incubation period for bird-to-human acquisitions; see my earlier post on this) since Zhejiang province markets started closing. I would had thought numbers would be declining before reaching the most distant likely incubation period. Still, we have reporting delays to account for as well. 

Of course, person-to-person spread would not be affected by market closures. If we don't see dropping average case/day numbers soon, one will have to ask more questions about market acquisitions versus human acquisitions.

Each time the World Health Organization "fine tunes" the case detail announced by FluTrackers in the preceding day(s), we see that case onsets occurred as many as 16-days prior to confirmation/announcement. So we are still seeing cases being distributed into Weeks 48 and 49 even though it is Week 51 when we hear about them.  

You can see the impact of this if you compare the numbers in this post from those on 26-Jan with the latest list of cases by week below (with 2  extra weeks added on)...

  • Week 45: 6 cases
  • Week 46: 26 cases
  • Week 47: 39 cases
  • Week 48: 33 cases
  • Week 49: 28 cases
  • Week 50: 8 cases
  • Week 51: 18 cases

Week 45 and 46 have now settled (black) but all other weeks increased (in red to indicate "moving" totals). Let's look at the rate at which cases have been accruing based on date of onset (DOO) or reporting (if DOO not available)...
  • Week 42-46: 8 cases per week
  • Week 47-51: 25 cases per week
  • Week 5-9: 23 cases per week [2013 Spring peak]
Differences.

Some overall averages by day (red numbers will change)...
  • 0.9 cases per day across all 51 weeks of H7N9 human cases
  • 0.7 cases per day for all cases in 2013
  • 2.1 cases per day was the 2013 peak average, occurring on 18-April-2013
  • 4.0 cases per day for all 2014 cases to date
  • 6.0 cases per day is the 2014 peak average, occurring 01-Jan-2014
It seems a bit unfair to list 2014 only since Wave 2 was already well underway on 1-Jan, but not in 2013. But these are the numbers, yours is the interpretation.
Click on image to enlarge.

We have not seen double-digit DOO days, except 04-Feb, but I expect that day will also settle below 10 once the WHO fine-tuning data arrives.

As I've written recently and as Helen Branswell (@HelenBranswell) noted on Twitter recently, the rate at which H7N9 cases are piling up outstrips that for that other avian influenza virus, H5N1. It took 16 or 17 years to reach its 650 cases; H7N9 will likely pass halfway to that tally well within 1-year; in only 1 (admittedly huge) country.  

So let's exclude for a moment that changes to averages may simply be due to testing or reporting issues which may be affected by the following:

  • Something having changed in the type or amount of detail provided publicly 
  • Changes to the screening methods used
  • Altered screening criteria/protocols
  • Increased availability of testing
  • Media reporting impacting on parents, driving them to doctors out of increased concern for kids with less severe acute respiratory illnesses which they may not normally have visited a Doctor for
  • School holidays and changed levels of contact with poultry and older relatives
  • Season - humidity, rain, temperature
  • Prevalence of respiratory viruses with a flow-on in the changed levels of virus:virus and virus:bacteria interactions
  • Testing focus has changed to be more "family-friendly"
As I noted last night (my time), we are seeing more young children at the moment. There has also been a tiny trend away from mentioning "farmer" in the recent case posts (only 4 of the last 45 continuous cases [FT#274-#310] - see FluTracker's list for detail compared to 15 of the previous 45). 

These might just be blips that average out as more cases are announced. But it could be that within such a blip emerges an H7N9 strain with characteristics that differ somewhat. Let's hope molecular virology is also keeping track of these changes at the viral level.


Anything related to change in spread of an emerging virus should be watched, charted and discussed. After all, H7N9 was just a blip when we heard about 3-cases. Now we have 10-times as many. H10N8 has now been found in 2 human cases. I should probably start an Excel sheet on that one if I'm to practice what I preach!


Population tallies...
In millions; from Google/National bureau of Statistics, China
In provinces and municipalities reporting local acquisition of human H7N9 cases


  • Shanghai: 14
  • Anhui: 60
  • Zhejiang: 55
  • Jiangsu: 79
  • Beijing: 12
  • Henan: 94
  • Shandong: 96
  • Jiangxi: 45
  • Fujian: 37
  • Hunan: 66
  • Hebei: 72
  • Guangdong: 105
  • Guangxi: 46
TOTAL POPULATION: 781

Many thanks to Lisa Schnirring (CIDRAP) and Katherine Arden for added input and ideas.

H7N9 snapdate: age with time

Click on image to enlarge.
Age groups selected to convey clearest trends
without too many lines.
A quick look at some age bands followed each week during the course of both waves of the avian influenza A( H7N9) virus outbreak.

The interesting line to watch is that of the youngest age group (0-19-years) which has lifted to comprise 50% of cases in the week beginning 27-Jan. Also, the proportion of cases in the oldest age group (70->90-years) has dropped down in the past 2 weeks. 

There have been a rash of children in recent announcements; 8 of the last 45 cases have been <10-years of age. For a virus with a median case age sitting at 58-years, this is quite a departure. 


Is this due to an increase in familial clusters? Does it herald a shift in the way the virus is spreading? Intrafamilial transmission may provide a hint at increasing transmission efficiency. It might also be a sign of increased testing augmenting clinical observation of close contacts of ill family members. 


It bears watching closely whatever is happening because its different for some reason. Also worth watching is the downward creeping age. In 2013 the median age was 55.5-years and in 2014 it is 53.5-years. Among the past 45 cases it sits at 52.0-years


Tonight we have 310 H7N9 cases ( a third in Guangxi province bordering Vietnam has just popped up while I was writing this paragraph and I've altered the numbers above), with at least 50 deaths (that can be accounted for using public data).

Middle East respiratory syndrome coronavirus (MERS-CoV): summing up 100 weeks

We stand at 182 cases with 78 deaths. The proportion of fatal cases (PFC) stands at 43%.

  • Median age of all cases, including deaths, sits at 53-years (missing data on 13 cases); median age of fatal cases is 60-years
  • 47% of all MERS cases with data are >55-years of age; 36% are >60-years
  • 65% of cases are male (missing data on 18 cases)
  • Underlying comorbidities feature in most severe disease MERS cases
  • Approximately 18% of MERS-CoV cases are in healthcare workers; 2.7% of all fatal MERS cases are HCWs
  • 81% of case are from the Kingdom of Saudi Arabia (KSA); the Arabian peninsula is the zone of case origin
  • Reliable real-time reverse transcription polymerase chain reaction (RT-rtPCR) assays exist for detection, confirmation and genotyping
  • Camels have been found on multiple occasions at multiple sites in the region to have antibodies to an antigenically similar virus to the MERS-CoV and nasal swabs have been found to be MERS-CoV RNA positive, as have humans in contact with the same camels (infection direction unknown). 
  • Camel, goat, monkey, alpaca and human cells lines efficiently replicate MERS-CoV (multiple intermediate sources?)
  • 1 diagnostic sequence of MERS-CoV RNA has been identified in a Taphozus perforatus bat (origin of animal other infections?)
  • MERS-CoV uses DPP4 (CD26) as its receptor on host cells, a molecule found on some cell lines and epithelial cells of kidney, small intestine, liver and prostate. DPP4 has a standard role in hormone and chemokine activation
  • No viable antiviral therapy or cocktail exists to treat infection. No vaccine exists.
  • MERS-CoV replicates well in the lower respiratory tract of lab-infected macaques
  • Person-to-person (p2p) transmission of MERS-CoV is sporadic
  • Genetic variation among MERS-CoV genomes suggests multiple insertions into humans from the source(s)
  • Fever, cough and shortness of breath in >70% of 47 cases in KSA; runny nose in 4%; abnormal chest X-Ray in 100%
  • Sample often, sample lower respiratory tract to increase chance of successful RT-PCR result 
  • Testing 5,065 hospitalized patients, healthcare worker contacts and family contacts found 2% (n=106) positivity over 12-months, in Saudi Arabia 
  • MERS-CoV has circulated in KSA during several mass gatherings (2x Hajj pilgrimages and Umrah) providing ample opportunity for p2p transmission. There has been no evidence for an uptick in p2p transmission. We are nowhere near the verge of a pandemic.

Monkey magic: Vero cells make more MERS-CoV RNA than any other animal's...

Apart from camel, goat, bat and human cells which draw the eye in studies on the source of MERS-CoV, did anyone notice the Vero cells? 

These cells are derived in the dim dark ages from African green monkey kidney (Cercopithecus aethiops). After infection, these monkey cells were shown to make more MERS-CoV RNA than any other cell line tested and the second greatest quantity of viral particles (after goat cells).

Check out Eckerle et al. over at the CDC's Emerging Infectious Diseases journal for a very nice graphic.

This may be an artefact of the adapted cell-line....but let's not forget to test those baboons hmm?

Why have a case definition that seems designed to miss transmission events? [UPDATED]

v2 24APR2015. Modified figure to exclude erroneous "uninfected" person

FluTrackers just tweeted a link to a story they have posted from Korea which I've excerpted below. 

I don't usually excerpt, so take it as a measure of my complete dismay about this.
Asymptomatic Carriers of AI Confirmed in S. Korea 2014-02-04

..The Korea Centers for Disease Control and Prevention confirmed that ten people who had participated in culling birds during the outbreaks of bird flu in 2003 and 2006 had antibodies for the H5N1 strain of avian influenza....
...The agency said that it had announced before that there were no human infection cases as asymptomatic carriers are not regarded as patients under the World Health Organization standards.
What? Seriously? You cannot be listed as a Case unless you are symptomatic?! 

I can understand that a symptomatic Case will require medical care and resources and is a priority in counting the true human toll from an infectious agent spreading among people, but to be excluded from any Case counts when you are still a viable piece in the transmission chain puzzle (see image below)? That makes no sense to me at all. Unless there is concern that the laboratory is at fault or that the test is untrustworthy. But there are no mentions of those issues.

I've pasted below the most up-to-date H5N1 Case Definition (CD) I could locate on the World Health Organizations's (WHO) website. It's from 2006 but there does not seem to be anything more contemporary (at least on H5N1 CDs) at WHO.

Confirmed H5N1 case (notify WHO)
A person meeting the criteria for a suspected or probable case

AND

One of the following positive results conducted in a national, regional or international influenza laboratory whose H5N1 test results are accepted by WHO as confirmatory:
a. Isolation of an H5N1 virus;

b. Positive H5 PCR results from tests using two different PCR targets, e.g. primers specific for influenza A and H5 HA;
c. A fourfold or greater rise in neutralization antibody titer for H5N1 based on testing of an acute serum specimen (collected 7 days or less after symptom onset) and a convalescent serum specimen. The convalescent neutralizing antibody titer must also be 1:80 or higher;

d. A microneutralization antibody titer for H5N1 of 1:80 or greater in a single serum specimen collected at day 14 or later after symptom onset and a positive result using a different serological assay, for example, a horse red blood cell haemagglutination inhibition titer of 1:160 or greater or an H5-specific western blot positive result.

So Korea's CDC had lab results (the stuff after the "AND"). What else does a person "meeting the criteria for a suspected or probable case" have to be diagnosed with for them to be a confirmed case? See the relevant section below with my highlighting (read the entire thing, in its intended order here)

Suspected H5N1 case
A person presenting with unexplained acute lower respiratory illness with fever (>38 �C ) and cough, shortness of breath or difficulty breathing.
AND
One or more of the following exposures in the 7 days prior to symptom onset:
a. Close contact (within 1 metre) with a person (e.g. caring for, speaking with, or touching) who is a suspected, probable, or confirmed H5N1 case;
b. Exposure (e.g. handling, slaughtering, defeathering, butchering, preparation for consumption) to poultry or wild birds or their remains or to environments contaminated by their faeces in an area where H5N1 infections in animals or humans have been suspected or confirmed in the last month;
c. Consumption of raw or undercooked poultry products in an area where H5N1 infections in animals or humans have been suspected or confirmed in the last month;
d. Close contact with a confirmed H5N1 infected animal other than poultry or wild birds (e.g. cat or pig);
e. Handling samples (animal or human) suspected of containing H5N1 virus in a laboratory or other setting.
Probable definition 1:A person meeting the criteria for a suspected case
AND
One of the following additional criteria: 
a. infiltrates or evidence of an acute pneumonia on chest radiograph plus evidence of respiratory failure (hypoxemia, severe tachypnea)
OR 
b. positive laboratory confirmation of an influenza A infection but insufficient laboratory evidence for H5N1 infection. 
Probable definition 2:
A person dying of an unexplained acute respiratory illness who is considered to be epidemiologically linked by time, place, and exposure to a probable or confirmed H5N1 case.
Korea's CDC had no choice but to exclude what appear to be retrospectively confirmed, real avian influenza A(H5N1) virus cases of infection because they adhered to the letter of the CD. 
Click on image to enlarge.
Excluding cases from official reporting & tallies
because they are asymptomatic or don't meet the 
"AND" and "OR" extra criteria may make tracking
infections to their source that much more difficult. 
In doing so, they omitted reporting cases that could have held vital epidemiological information; these cases may have linked 1 severe case to another otherwise sporadic case via an asymptomatic link. The linkage might explain how a case "popped up" or it might better define person-to-person spread. They may not have done any of this too. I have no idea of the history of these 10 cases nor any of their contacts nor any H5N1 cases that may have occurred around the same time. 

But the possibility exists that they could have had a role in improving understanding of the spread of a new or newly identified virus. Could this particular CD discourage more comprehensive testing of less ill groups? That would be unfortunate. There  is already far too much that we don't know about the spread of influenza, let alone all the other respiratory viruses.

Take a look at the US Center for Disease Control and Prevention's CD advice for H5N1 and for H7N9; it leaves out the need for symptomatic illness in defining a confirmed case. However it does retain "illness compatible with influenza", which clearly implies a symptomatic event, as a prerequisite for a "case under investigation".

What is also very informative to this debate though, is that the WHO's much more contemporary CD for reporting MERS-CoV infection does take into account asymptomatic cases..

Asymptomatic cases: The demonstration of asymptomatic infection is useful for epidemiological investigations and should be pursued as part of case investigations, however, the burden of proof must be higher due to the risk misclassification because of false positive tests due to laboratory contamination. Generally, in most viral infections, an immunological response such as development of specific antibodies would be expected even with mild or asymptomatic infection and as such serological testing may be useful as additional confirmation of the diagnosis. Additional steps to reconfirm asymptomatic cases, or any case in which the diagnosis is suspect, could include re-extraction of RNA from the original clinical specimen and testing for different virus target genes, ideally in an independent laboratory.
This may mean that the H5N1 definition was just out of date and is in dire need of modernisation. 

One implication from the Korean statement, to my mind at least, is that an absence of symptoms has been taken to mean an absence of importance in the chain of transmission because that person was not registered as a Case. I suspect that the simple act of listing a person carries significant weight. I just can't see how leaving even 1 lab-confirmed but asymptomatic person off such a list benefits the search for an answer to how an emerging virus is spreads. At least, I haven't read a convincing case for any such benefit (pun intended).

[UPDATE] Reply from WHO's Gregory H�rtl (@HaertlG)





One Health Initiative is alive and well among Australian influenza specialists...

It struck me as really quite impressive how much influenza researchers (and a non-fluey ring-in like me) are already well aware of, and in some cases working on, the importance of animals in virus spread to humans. 

Admittedly, I'm a rhinovirus guy (or a metapneumovirus guy, or coronavirus guy, or an enterovirus guy, Saffold virus guy, parainfluenza virus 4 guy, a PCR guy...) not a flu guy, but 2/5 talks on Day 1 of the Influenza Specialist Group (ISG) Annual Scientific Meeting (ASM) this afternoon included plenty of focus on poultry, wild and song birds, camels and even penguins! I did not know that penguins had H11N2 and the the nearest genetic matches were 50-years old!

And judging from the questions on my MERS-CoV and H7N9 talk (of which there were many - thanks to all!), its plain to the many experts in that room tonight that we still have a lot of data holes to plug in the story of H7N9 and MERS-CoV. Both virological and clinical gaps.

Also plain to me, was that I need to do some more reading about viral loads and clicnial outcomes in MERS and think a little more about whether our own hospital systems enhance the spread of viruses, as they may have done during SARS. Did the West see more of it because of its highly structured intensive care units concentrating cases ad funnelling infection at healthcare workers, or was it just that less developed nations didn't detect it's entry? Many interesting discussions tonight. Like the one about what to do you do with a problem like the rhinoviruses? Lots of detections in influenza-like illness (on a par or surpassing those due to influenza and respiratory syncytial virus), but also a chunk in controls. I know that you can't write off the 200 or so RVs as passengers just because they occur across the entire disease spectrum; all viruses do, its just that there are far fewer distinct members of any other given respiratory virus species you'd like to name. 

Really great to speak in front of a room full of people who already have their "spare time" filled with real research, still show an interest in how this sort of platform (the one you're reading now) can bring the message of influenza, or viruses in general, to others. 


  1. Influenza Specialists Group
    http://www.isg.org.au/

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