Although we tend to talk about H5N1 (aka `bird flu’) as if it were a single entity, in truth, the virus has continually evolved and mutated since its emergence in 1996.
You can see the evolution of the virus in the chart below, starting with Clade 0, first detected in 1996.
All of which means we are not watching just one H5N1 virus strain, we are watching at least 20 genetically separate clades of the virus, with many minor variants of each clade thrown in the mix.
Different areas of the world have seen different clades set up hen-house keeping, with clade 2.3.2 (and now 126.96.36.199) very common in South East Asia, clades 2.2.1 and 2.2 endemic in Egypt and clades 2.1.1, 2.1.2. and 2.1.3 circulating in Indonesia.
One of the more successful`new’ clades making inroads over the past few years has been 2.3.2. I wrote of the spread of this emerging clade last year in What Goes Around, Comes Around and EID Journal: H5N1 Branching Out).
In the spring of 2010 we began to see reports of poultry vaccine failures in Vietnam due to the spread of a mutated version this clade (further classified as clade 188.8.131.52), which led to this statement FAO Warns On Bird Flu.
As noted earlier, Indonesia has been dealing with 2.1 clades of the virus. but today the Director of Animal Health at the Ministry of Agriculture, in a interview for (Bahasan) Radio Australia, has indicated that clade 2.3.2 has been detected in Indonesia this year.
The following excerpt is a machine translation:
Updated on 10 December 2012
Hundreds of thousands of birds in some regions ducks died from bird flu strain recently discovered in Indonesia.
Director of Animal Health, Ministry of Agriculture, told Radio Australia Pujiatmoko explaining Ministry have detected the presence of a new type derived from bird flu since last September.
Certainty new type of bird flu virus in the world known as Avian Influenza after passing through a series of tests in a laboratory involving researchers.
The Ministry of Agriculture said the bird flu virus newly discovered variant of the H5N1 strain.
"Sub her type 2.3.2 which is a new finding in Indonesia different from AI virus that has been there, of 2.1," said Pujiatmoko.
Dr. Pujiatmoko continues to say that they don’t know if this new strain naturally evolved in Indonesia, or was introduced by wild birds or imported poultry.
The appearance of this new clade complicates an already difficult situation in Indonesia, although this article doesn’t tell us how widespread this recent arrival may be, or if clade - 184.108.40.206 which appeared in Vietnam in 2010 – has been detected as well.
The article goes on to recount recent poultry losses, and provides recommendations for culling infected birds, and the segregation of ducks (often asymptomatic carriers of H5N1) from other poultry.
The bottom line is that the H5N1 virus is a moving target, mutating and evolving, continually looking for an evolutionary advantage. That said, H5N1 remains largely an avian-adapted virus, and for now primarily a threat to poultry.
The concern, of course, is that with continual changes to the virus, one of these days it may better adapt to human or mammalian physiology.
Which is why, even after 10 years of outbreaks and no pandemic, we continue to follow developments with keen interest.