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H5N1 in Suffolk England Match Wild Bird Sequences

Recombinomics Commentary
November 13, 2007

Mr Landeg's statement that the initial sequence data (of the current H5N1 strain) suggests close relatedness to outbreaks in the Czech Republic and Germany, deserves attention. A very high similarity (99.96 percent) at the whole genome level was revealed in February
(2007) between the H5N1 viruses found in Suffolk and the Hungarian outbreaks.

The relatively short distance between the 2 foci in Suffolk is intriguing; it will be interesting to obtain information on the similarity level between the H5N1 strains isolated from them. The possible involvement of wild avians -- to which Mr Landeg referred --
deserves further investigation.

The above remarks in a ProMed commentary are curious, because the issue of related has already been addressed by public sequences coupled with statements from the agencies sequencing H5N1 in Germany and England.  These comments suggest the recent H5N1 infections in England were related to the sequences in Germany and the Czech Republic, which were easily distinguished from the H5N1 sequences from the earlier outbreaks in England and Hungary (the sequences in Hungary and England were 99.96% identical)

All of the H5N1 linked to wild birds west of China have been the Qinghai strain (clade 2.2).  However, these sequences have multiple markers that allow the isolates to be placed into sub-clades based on phylogenetic analysis, which is quite straight forward.

This type of analysis generated a number of Qinghai (clade 2.2) sub-clades based on sequences from infections in the 2005/2006 season.  Most of the Europen isolates were from fatal wild bird infections in early 2006,  In Germany there were three sub-clades.  One was in northern Germany and closely related to H5N1 from Denmark.  Another was in Bavaria and closely related to H5N1 from Switzerland.  A third sub-clade was in southern Germany and most closely related to sequences from Italy, Austria, and Ukraine.

In 2007 there was an outbreak in Hungary which was distinct from the 2006 isolates.  The earlier outbreak in England was 99.96% identical, raising the possibility that the relationship was due to transport of the H5N1 sequences to England by a company that had facilities in both countries.

In the summer of 2007, outbreaks were reported in wild birds in the Czech Republic and Germany.  Although each location had slightly different versions of H5N1, all were distinct from the prior isolates in Europe.  Instead, the sequences were most closely related to 2006 isolates from Tyva/Mongolia.  These sequences were from a massive outbreak there in the spring/summer of 2006.  The size of the outbreak was similar to the outbreak at Qinghai Lake in 2005 and raised the possibility that the Tyva/Mongolia strain would appear in Europe in late 2006 / early 2007.  However, although H5N1 was reported in Russia, the Middle East, and Africa, there was little H5N1 reported in Europe.

The detection of H5N1 in large numbers of wild birds in summer suggested that H5N1 had become endemic in Europe because long range migration was minimal over the summer, and many of the wild birds were resident birds.

However, in early 2007 there were many versions of H5N1 emerging that had evolved from the 2006 isolates.  Isolates in Moscow, Egypt, and Ghana had the same change, NA G743A, suggesting a common source was circulating undetected.

Recently a full sequence from Krasnodar was published.  Like the German and Czech sequences, it was also most closely related to the Tyva/Mongolia sequences, and it had G743A, suggesting these sequences were circulating undetected in late 2006/early 2007 and went undetected until the summer of 2007.

The presence of similar sequences in Germany, the Czech Republic, and Krasnodar suggested that similar sequences would appear in Europe because the sequence was widespread in wild bird populations.

The detection of similar sequences in the recent isolates from England further supports introduction by wild birds and endemic H5N1 in Europe.

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