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Email from Dr Ruth Watkins Feb 13 2007

I was rung up by radio 4 tonight and interviewed by Robin Lustig last night 12 Feb and they edited my interview a little.  It was on the reopening of slaughter and packing at Holton of UK birds, Matthews having agreed to suspend imports from Hungary at the moment. And that was the essence of the questions put to me having heard what Miliband had recorded earlier.
My points were
1.  I assumed that the cutting and packing plant had also been cleaned as well as the slaughter house (worryingly comments this morning suggested this may not have been the case, if not vital evidence may not have been collected)
2. In my opinion opening was premature as issues of breakdown in safe food handling and biosecurity had not been addressed.  Review required of protocols and procedures and retraining of staff and possibly structural alterations needed e.g. a wall between the turkey sheds to prevent persons going from processing to bird rearing facilities.  It was clear that at least some staff did not understand about H5N1 as one worker employed in rounding up turkeys had said on TV that he felt safety was OK as he was wearing a suit and nothing touched his skin.  He seemed unaware that the risk of infection to humans was by inspiration and I hoped he had been wearing a respirator (the comment on this workers interview was cut)  
3.  The assumption made that the clean up was complete, every last turkey carcass cleared away etc ought not to be assumed and it would be better to allow more time to elapse to permit natural decay of the virus e.g 30 days.  This was a very serious outbreak.
4. The problem of spread of this pathogenic H5N1 virus worldwide by industrial farming and international trade had not been addressed and had not gone away.  Thus I doubted that the turkey rearing houses at Holton should ever be reopened.  This latter comment about never reopening the rearing facilities on a site where produce imported into UK was processed was cut from the broadcast, but not the point about international trade spreading the virus.
(I was asked about the virus being brought over on lorry wheels and I said I had given it some thought- there ought to be a trail and as there was not it was very unlikely and it was more likely the virus had been packed up and loaded in Hungary and unpacked at Holton.)
Today's news on the Hungarian virus and its very near identity to the Holton virus is I am sure made by the laboratory at Weybridge based on sequencing information on many viruses and its analysis.  This type of forensic matching has been done over the last 20 years in human virology and becomes ever more sophisticated as there are more viruses sequenced and longer segments if not the whole genome sequenced,  and this is combined with greater mathematical power of the analysis programmes.  There may even be a unique signature change in the sequence, a duplication or deletion that points the finger even more strongly than nucleotide sequence matching alone. It has to be accepted whatever the Hungarian government says about all the paper work being above board that the virus outbreak in Hungary and that in the UK are linked.
If there were no Matthews turkey farms in Hungary and no importing of any products from Hungary to Holton it would indeed be a mystery but nevertheless linked all the same.  However raw turkey carcasses were imported from Hungary and at least some had been slaughtered at that plant near the outbreak on the two geese farms.  No further elucidation is ever likely to emerge of how the virus boarded the lorries in Hungary.  That does not change the fact that this is what must in all probability have occurred.
The basis of transmission linkage by sequence analysis rests upon  the ever changing nucleotide sequences of replicating virus particularly RNA viruses.  Many changes are of redundant or non coding nucleotides or ones which change an amino acid but have no effect on the protein function.  There are constraints on what can change and many changes are not compatible with producing a replication competent virus and such a virus plays no further role in virus transmission.  However changes to a virus slowly accumulate as time passes and the virus passes through many hosts.  From the number of virus samples that Weybridge have received the similarity between Holton 2007 and Hungary 2007 is striking and significant and I expect they have tested it thoroughly and checked their work looking at several of the eight genome segments of influenza virus.
In human virology one can detect transmission pairs, HIV for example needlestick donor and recipient or mother baby, or transmission groups such as an HBV positive surgeon and the patients he has infected and exclude extraneous or prior infection on sequence analysis.  In the case of a lesser degree of sequence similarity one can distinguish the continent or country from where the measles virus or polio virus isolated in a UK case originated, for example.  One can also confirm whether infection is by a current wild virus strain or a live vaccine strain in the case of measles or polio virus again as examples.  By sequence analysis one can detect whether a historical virus emerged from a stored site, in the case of H1N1 human influenza virus reemerged in the human population in 1977 when this same sequence had last been recorded in 1957 I believe. 
Its a lot for David Milliband and the Hungarian ambassador to get their heads round!
best wishes Ruth



































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