Thursday 6 February 2014

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]

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

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

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