H5N1 Introductions in Czech Republic Germany and Kuwait
Recombinomics Commentary
June 29, 2007
All 6 birds (swans and ducks) were from Nuremberg. We have reports, cited below, of a 2nd outbreak 180 km (about 112 mi) away. For a map of the outbreak, please see the full OIE report referenced above.
We also know it is similar to the Qinghai strain previously found in wild
birds in Europe and other places. It is time to consider 2 very important
questions:
- what is the exact nature of the connection between the 2 sites in terms
of the chronology of events? and
- where did the virus reemerge from, since the last outbreak in Germany was in August 2006? - Mod.PC
The above ProMed commentary makes the assumption that the two outbreaks in Nuremberg are related, but the public information at this time has been on the birds in Nuremberg, 1 Canada duck and 5 mute swans. The reports on this outbreak in Germany and the turkey farm in the Czech Republic indicated that there is 99.2% identity between H5N1 isolates from the two groups. Moreover, media reports indicate the Czech isolates are 99.5% identical with H5N1 from Kuwait this season.
Although none of the sequences have been made public, the level of similarity between H5N1 from the three sites indicates they were independently introduced. Although they all share a wild bird common source from the past, a recent linkage would require the level of identity to be similar to the relationship between the earlier outbreaks in Hungary and the UK. In those two outbreaks, the level of identity was 99.96%. The recent frequencies indicate all isolates are the Qinghai strain (clade 2.2), but the differences between the isolates from the three locations indicates that these are three distinct sub-clades.
Last season there was a major outbreak of H5N1 in Germany and throughout western Europe. Most of the isolates were from wild birds that died in February, 2006. The largest number of isolates came from northern Germany near the Baltic Sea. Those isolates formed sub-clade 2.2.2.1. Included were isolates from a cat and stone martin. The isolates were largely limited to northern Germany and were related to a buzzard isolate from Denmark. Another sub-clade, 2.2.2.2, was more widely detected. It was found in Germany, Italy, Slovenia, the Czech Republic, and Ukraine. A third sub-clade, 2.2.2.3 was largely limited to Germany, but included isolates from Switzerland. The sequences from most of these isolates are public and included in the phylogenetic tree displayed here.
The HA sequence from the sub-clades detected last year have a 99.0% identity between 2.2.2.1 and 2.2.2.2. The identity between 2.2.2.1 and 2.2.2.3 is 99.3%. The identity between 2.2.2.2 and 2.2.2.3 is 99.4%. These sub-clades represent independent introductions, and the percent identity is similar to the reported relationships between Nuremberg and the Czech Republic (99.2%) or the Czech Republic and Kuwait (99.5%). Moreover, the above recent frequencies indicate the relationship between Nuremberg and Kuwait may be as low as 98.7%, if reported differences between the three isolates do not overlap.
Thus, the reported identity frequencies support an independent introduction from wild birds carrying the clade 2.2 Qinghai strain. All H5N1 isolates west of China are the Qinghai strain and the various isolates collected in the same season have 98-99% identity with each other. For isolate from a recent common source, like the 2007 isolates from Hungary and UK, the identity is markedly higher (99.96%).
Media sources
Recombinomics Presentations