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Sequence Analysis of H5N1 Bird Flu in Michigan
Recombinomics Commentary

August 14, 2006

The additional testing that we're doing would include sequencing the genetic material. What is the sequence of the genes, and is that consistent with a North American strain or an Asian strain? The fact that this was compatible with our North American virus and not compatible with the Asian high path avian influenza virus that we are able to say that this is not the incursion of that Asian high path H5N1 virus.

There's also another test to determine pathogenicity or really two ways to determine pathogenicity. One is, looking at that sequence, that gene sequence. It's through that gene sequence testing that we're able to say that from a genetic standpoint this looks like a low pathogenic virus.

The above comments indicate that the H5N1 detected in two of twenty mute swans on Lake Erie in southern Michigan were LPAI (low pathogenic avian influenza.  It is likely that the full sequence will be similar top the recently releases HA sequence of H5N1 detected on British Columbia,
A/mallard/BC317/2005(H5N2), almost exactly one year ago.  However, the exact sequence can provide valuable clues about the presence of avian HPAI version of H5N1.  In wild birds, that version is most commonly the Qinghai strain.

The Qinghai strain was first identified in May of 2005 at Qinghai Lake.  It migrated into southern Siberia for the summer and caused outbreaks in Russia, Kazakhstan, and Siberia.  The strain then migrated to Europe, the Middle East, and Africa, as well as China.  Sequences of the H5N1 from mute swans in Astrakhan have North American sequences suggesting H5N1 may have already migrated to Canada last year. However, HPAI H5N1 has not been reported in Canada.

Last year young ducks were tested as part of an expanded banding program across southern Canada.  Four H5 sero-types (H5N1, H5N2, H5N3, H5N9) were identifiedH5N1 was in Manitoba, while H5N2 and H5N9 were in British Columbia.  In Manitoba, an alarmingly 24% were H5 positive.  In the testing in southern Michigan, 2 of the 20 tested birds were H5N1 positive, so the percentage in certain regions of the United States may also be alarmingly high.

The high frequency6 of H5 in wild birds is a concern because H5 can become highly pathogenic, and can acquire mammalian polymorphism.  Moreover, it can most easily recombine with H5N1 from Asia because of regions of genetic identity.

There is already evidence for both processes.  Although a large number of H5 virus was identified last year, only one sequence has been made public.  However, that sequence has polymorphisms shared by swine in Canada as well as H5N1 in Russia.

The tandem polymorphism from H1N1 Canadian swine were describe earlier.  Today 2006 HA sequences Russia were released.  A new polymorphism found in three recent isolates from Russia,
A/cat/Dagestan/87/06(H5N1), A/chickem/Krasnodar/199/06(H5N1), A/chicken/Adygea/203/06(H5N1), was also present in the H5 in British Columbia.

Analysis of the H5N1 sequence from Michigan can be used to determine of the evolution in the 2006 isolate and can be used to evaluate new polymorphism present in new Qinghai isolates.

Full sequences of the Michigan swans should be made public as soon as possible.

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