Dear Martin,

We still do not know the precise origin of Goose GD-96. There is a black hole in the data prior to this so the following is by necessity speculative but based on the best information we have.

I beleive that this virus initially emerged in geese. Goose raising in Guangdong involved a mixture of semi-intensive and extensive rearing. On one large farm I visited geese were reared in cages housing multiple geese on a farm surrounding a large dam in cages. After an initial rearing period on the farm they were sent out to graze paddies for about a month before returning to cages for final fattening – not exactly biosecure.

If we assume that this virus moved from its original wild waterfowl origin (originally as a low path virus) into geese there had to be an opportuinity for this to occur, which this type of farming provided.

Given the way poultry are sold in China and the consequent large amount of movement of live poultry, this virus would have spread through the live bird markets. It is probably in these markets where the virus acquired the genes that converted it to the 1997 strain poultry strain. Some say this happened in Hong Kong live poultry markets – it might have, but I remain sceptical on this. We will never know for sure but the Hong Kong experieince showed how these viruses could be easily propagated under the unsanitary conditions that existed in the markets then.

The original 1996-type virus persisted in geese until about year 2000 by which time it under went reassortment with other “avian” viruses of unknown origin (again presumed to be from aquatic birds) but these changes allowed the virus to multiply more readily in ducks, which was probably a key change in its genesis and further spread. It provided a much wider range of hosts, given the much larger number of ducks that are reared, and also provided the opportunity for infection of a wider range of wild birds.

Very few ducks are reared in intensive farms – they are reared on ponds, channels and paddy fields providing ample opportunity for exchange of viruses between domestic and wild birds. These ducks were sold live also providing ample opportunities for exchange of viruses between different species in the uncontrolled live bird markets in the region. What we do know is that from 1999 onwards a wide range of different reassortants arose including the Z genotype which was first recorded in Guangxi in 2001 apparently in ducks.

We don’t know exactly where all this occurred but it is likely that this involved transfer of viruses from geese to ducks to chickens and back again because the more recent viruses have features in the “N” gene that indicate adaptation to terrestrial poultry (the deletion of amino acids in the stalk of the NA protein).

My overall assessment is that the H5N1 viruses that have emerged did not originate in large industrial type farms but in semi-intensive and extensive farms and large live bird markets in which different species of poultry were mixed and housed together long enough for exchange of viruses/viral genes to occur.