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Analysis of Uva Lake H5N1 Sequences in England
Recombinomics Commentary 01:11
January 11, 2008
The source of this outbreak is to be sought in wild birds; ornithological assessment is anticipated. It will be also of great interest to obtain information on the strain involved, particularly its sequencing results highlighting its genetic profile and its relationship with other recent isolates in the UK, in other European countries, and elsewhere. - Mod.AS
The above ProMed commentary is welcome news. Sequence data can precisely define the H5N1 in the recent wild bird outbreak, as well as the early outbreak in free range turkeys in Engaland. The sequence will almost certainly be the Uva Lake strain, like every reported H5N1 outbreak in Europe since the summer, but these sequences have regional markers, which allow for further subdivisions.
This was easily seen in the early Qinghai Lake strain. The sequence from the whooper swan from the shores of Scotland was closely related to 2006 H5N1 sequences from Denmark, Sweden, and northern Germany. Germany actually had three groupings. In the south, one group matched H5N1 from Switzerland, while a second group was close to isolates from Italy and the Ukraine.
This year, although all are the Uva Lake strain, which link back to a wild bird outbreak at Uva Lake in the summer of 2006, the current series can be readily broken dozen into separate groupings. Three sequences were released from the summer outbreaks in Germany, and each is distinct. Sequences from Krasnodar have also been released and the whooper swan and chicken HA sequences were exact matches. Krasnodar released full sequences of all eight gene segments, and the chicken and whooper swan were 99.95% identical. Recently, Uva Lake HA sequences from Romania were released from three species (chicken, duck, cat) from the late November, 2007 outbreak, and all three sequences were identical.
The sequences from England will be most informative if the other Uva Lake sequences are released from Kuwait, Czech Republic, France, England, Poland, northeastern Germany, Rostov, Saudi Arabia, Egypt, Israel, India, Pakistan, Afghanistan, Bangladesh are released. Those in Europe are almost certainly Uva Lake, while those in south Asia are very likely the Uva Lake strain. The recent sequences from South Korea, collected at the end of 2006, were also Uva Lake, and quite distinct from the European sequences (but closer to the European sequences than any H5N1 other than the original Uva Lake sequences).
The sequences precisely map out transport and transmission routes, and the time for release of these sequences, (as well as 2005 and 2006 H5N1 sequences still being hoarded) has long since passed.
Recombinomics Paper at Nature Precedings