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Since 28-Jan-1997

The latest avian influenzavirus strain added to

the list of agents causing "bird flu" is called

avian influenza A(H7N9) virus - a colourfully

exciting reference to its key surface proteins (see influenza background). H7N9 is

considered a low pathogenic avian influenza virus (LPAIV)...at least in its feathered

hosts. Avian influenza A(H7N9) virus (which I may shorten to H7N9 to save my

fingers) was once considered a relatively rare cause of infection although how

extensively and

routinely it was

looked for in the

past is unclear.

Avian influenza

A(H7N9) virus is

similar to its closer

cousins, H7N2,

H7N3 and H7N7

and its more

distant cousin

H5N1 in that they

are all IFAVs and

they usually infect

birds. However,

they are each quite

distinct and made up

of different genes.

Avian influenza A(H7N9) virus is an IFAV (see the adjacent schematic) that has evolved in birds. The virus has 8 single-stranded RNA segments that encode 11 proteins. However, when cases of infection by it were reported for the first time in humans (China, March 2013; very general locations of confirmed cases to date are shown in the adjacent chart), it was linked to its first two deaths10 in this host(an 87 year old male [87M, sick 19.02, died 04.03; 2 family member(s) also reported ill12 with pneumonia but H7N9 negative] and a 27 year old male butcher [27M, sick 27.02 and died 10.03], both in Shanghai, China) or critical illness (35F in Chuzhou city). Since then, cases slowly but continuously climb, at an increasing rate. Because there is a delay between illness onset and laboratory confirmation of 10-13 days, the newest cases started have illness onset dates some way back making it is still hard to judge the impact of control measures like live animal market closures and animal culling, on interrupting transmission. A timeline of the early cases is shown above but much more info on precise placement of the cases can be found using this excellent map. The chart to the abovedivides the H7N9 outbreak during Wave 1 into fatalities per notification week. Public notifications started from March 31st (Chinese CDC notified WHO), so this chart does not include approximately 4 deaths that occurred before this date. It shows each week's H7N9-positive fatalities as a proportion of the total fatalities. In the graph of the accumulating confirmed cases below (red, as per chart below, includes fatalities), fatalities (red) and the rolling proportion of fatal cases (PFC; grey), we can see that the total proportion of fatal cases (PFC) sits around 30%. Please don't go nuts and draw any major conclusions based on extrapolating the CFR to the global population - this figure is solely meant to show you the numbers and trends. What it does show us is how the outbreak came to be noticed - fatalities. The PFC has remained fairly steady, although its calculation is at the mercy of the availabilty and extent of public data. Big hat tip to Eli Perencevich for his version of graph. For an update on the most recent epidemiology, please visit my blog, virologydownunder.blogspot.com.au and use the search box to find recent “H7N9” posts. The various H7N9-positive municipalities (Shanghai and Beijing) and provinces (e.g. Henan, Anhui, Zhejiang, Giuangdong, Jiangxi, Hebei, Fujian, Hunan and Jiangsu) in southeastern China have had different numbers of cases reported and the reports started at different times. The first cases were confirmed from Shanghai on March 30th and included the first case who showed signs darting back to February 19th. Jiangsu's first confirmed cases occurred 30-March-2013 (although they were not announced until 2-April-2013) then Anhui province followed (confirmed on 31-March-2013) then Zhejiang province (1st April-2013), Henan province (11- April-2013) and Beijing reported its first case 13-April- 2013. Guangdong province confirmed its first case 6- August-2013; Fujian province, 26-April-2013; Hebei province, 20-Jul-2013; Shandong province, 22-Apr-2013; Guangxi province 29-Jan-2014; Jilin reported its first detection, 21-Feb-2014. Most cases in Wave 1 were from Zhejiang province which was also a major site of virus activity in Wave 2, along with Guangdong province.

The denominator problem...

You may remember from your early maths classes that fractions have both a numerator (the number on on top or before a slash/line, that represents a portion of the whole) and a denominator (the non-zero number on the bottom or after the line that represents all the parts of the whole).  avian influenza H7N9 flu cases by area of China The avian influenza A(H7N9) virus outbreak in March-May 2013 mostly manifested as severe disease - those people being admitted to hospital needing help to breathe (requiring oxygen or mechanical ventilation) - and we did not see many mild or asymptomatic cases (virus positive but no obvious feelings of signs of illness). This might be because there were no mild cases (although a couple popped up in children and adults) or because only the worst cases were tested. In favour of the former hypothesis, enhanced surveillance in China found few H7N9-positive cases of mild disease - the most notable being children. Many milder respiratory diseases look the same based on signs and symptoms but can be caused (and I use that word with caution) by many, many different respiratory viruses. There may be cases of respiratory infection going around in China that are H7N9-positive but not severe enough to warrant a admission to hospital or even a trip to the Doctor. Until we know more about this part of the H7N9 story, we won't know the total number of avian influenza A(H7N9) virus infections that are occurring, so we can't calculate the true denominator. More info on this in a recent article. Obviously, if the denominator is small (like it is now with so few H7N9-positive cases and those being from mostly severe illness or deaths, then we see a high proportion (percentage) as our Proportion of Fatal Cases (x severe cases over a small number of total cases is a high proportion). If there are mild cases of avian influenza A(H7N9) virus infection out there (as we saw earley examples of 15-Apr-13) and they are in large numbers, that denominator could be much larger and the severe disease cases will be "diluted" down to a smaller proportion (x severe cases over a large number of mild and severe total cases is a low proportion).
Order Family Genera Species Influenzavirus taxonomy Genome Genes & Proteins  Unassigned  Orthomyxoviridae  Influenzavirus A, Influenzavirus B, Influenzavirus C  Influenza A virus, Influenza B virus, Influenza C virus Virion (-)ssRNA, 7 (IFCV)- 8 (IFAV/IFBV) segments (~14kb total length)  PB2, PB1 [Pol & PB1-F2], PA, HA, NP, NA, M [M1 & M2], NS [NS1 & NEP]   Enveloped, approximately spherical, 80-120nm

Avian influenza A(H7N9) virus

Last Updated 30-March-2014

Written by Ian M. Mackay, PhD on his personal time. All opinions are his own and do not represent medical advice or the views of any other institution. Graphics are compiled for general interest.Please use freely, citing this website and me.
A time line of important H7N9 events starting with the date of illness onset for the first laboratory confirmed case. It will be updated as events unfold so stay tuned. These data are compiled for general interest, from multiple sources including interested parties and official organizations. This chart may not have every relevant case because of difficulties in obtaining complete data from these sources. They are compil
H7N9 Fataliaties by week. Use images freely but please cite www.virologydownunder.blogspot.co m.au and Dr. Ian M Mackay as their source. Click on image to enlarge.
H7N9 Timeline of events. Use images freely but please cite www.virologydownunder.blogspot.com.au and Dr. Ian M Mackay as their source. Click on image to enlarge.                  
Structure of an influenzavirus virion. Use images freely but please cite www.virologydownunder.blogspot.com.au and Dr. Ian M Mackay as their source. Click on image to enlarge.                  
Accumulating confirmed H7N9 cases and proportion of deaths. Use images freely but please cite www.virologydownunder.blogspot.com.au and Dr. Ian M Mackay as their source. Click on image to enlarge.