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H5 Confirmed in Sweden
Recombinomics Commentary
February 28, 2006
Agriculture Ministry spokesman Anders Gronvall would not confirm that the H5N1 strain had been detected, saying only that "it is the form people have died from, the kind we have feared."
EU spokesman Philip Tod told reporters that the European Commission was informed of an outbreak of the H5 strain in Sweden, but said it was not yet clear whether the cases found were of the deadly H5N1 strain.
Although the above comments fail to conclusive name H5N1, other media reports have indicated that the HA cleavage site matches H5N1 in China, Russia, and Nigeria. H5N1 with a cleavage site sequence of GERRRKKR has been reported in all three countries and all isolates with GERRRKKR have been HPAI H5N1.
Media reports also indicate that the species that is H5N1 positive in Sweden has been in Sweden since October. The data continues to point toward a geographical expansion of H5N1 in the fall, which included all of Europe. Although H5N1 has only recently been reported in western Europe, it is become increasing clear that the lack of early reports was not due to the absence of H5N1.
Isolating the H5N1 and depositing the sequences at a public database is important for tracking where H5N1 has been and where it is going. Russia, France, and Italy have made sequences available almost in real time. Other countries have withheld sequences or placed them in a private database available to WHO consultants. The recent comments by the WHO, indicating that the "mutations" were "random" and not predictable indicates their analysis is skewed by a view that is not held by all. Is clearly at odds with the actual data, which repeatedly shows that the polymorphisms are overlaid onto a Qinghai genetic background and the "mutations" are clearly polymorphisms from recent isolates in Asia and North America.
H5N1 in Sweden is cause for concern because of frequent detection of LPAI H5 isolates. Many of the polymorphisms in these H5 isolates found in Sweden are also in HPAI H5N1 strains.
Today a 2005 H5N2 isolate from Bavaria, A/mallard/Bavaria/1/2005(H5N2), was made available to the public. It was called "novel" and contained a number of H5N1 polymorphisms, although it had an LPAI HA cleavage site and was most closely related to LPAI H5 isolates from Sweden.
The sequence from Bavaria also suggests that the H5N1, H5N2, H5N3, and H5N9 isolates found as part of a banding experiment in Canada also have H5N1 sequences. The frequency of detection of H5 in Canada was very high. 24% of birds tested in British Columbia had H5 sequences. None of the sequences have been made available to the public.
Italy, France, and Russia are setting the bar for transparency and release of sequence data. It is time for WHO and consultants to stop hoarding the data in their "private" database and make full sequences of all eight genes available for proper analysis.
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