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Nigerian H5N1 Sequences Support European Migration in 2005

Recombinomics Commentary 22:36
May 13, 2008

Sequences from all eight gene segments from isolates in Nigeria are being released at Genbank (A/chicken/Nigeria/228-5/2006, A/chicken/Nigeria/228-6/2006, A/chicken/Nigeria/228-10/2006).  These isolates were collected in early 2006, but are just now being made public.  They are closely related to previously released sequences from Lagos, Nigeria.  These sequences have a number of polymorphisms shared with isolates in Europe as well as Egypt/Gaza.  Although the sequence data is not unique, the collection dates in January and February of 2006 raise considerable doubts regarding the denials of H5N1 infections in Europe in late 2005, as well as the spread of H5N1 in Nigeria due to trade and smuggling.

After H5N1 spread to Russia and Mongolia in the summer of 2005, a further expansion of H5N1 into Europe, the Middle East, and Africa was predicted based on migration from the summer regions for the long range migratory birds.  Although H5N1 was subsequently detected in the fall of 2005 in Romania and Turkey as well as Ukraine at the end of 2005, EU countries in central and western Europe denied H5N1 infections.  Similarly, countries in the Middle East and Africa also denied H5N1 infections in 2005.  However, the subsequent detection of H5N1 in a healthy teal in the Nile Delta, which was collected in December, 2005 raised considerable doubt with regard to detection failures in Europe, since the sequences of the teal isolates were closely related to Austrian sequences, which were collected in 2006, and in the fall of 2005 the migration is from north to south.

At the beginning of 2006, human cases were reported in eastern Turkey and these clusters were followed by clusters in Iraq in late January.  After these cases were confirmed, H5N1 was widely reported in Europe, the Middle East, and Africa.  In Europe, the detection failures in 2005 were said to be linked to migration of birds in dead of winter in 2006 from eastern Europe into central and western Europe in search of open water. 

However, the sequence data from one set of isolates localized to southern Germany, Switzerland, and France, as well as another set found in northern Germany, Denmark, Sweden, and Scotland raised serious doubts about the open water explanation because the sequences were not reported in isolates form eastern Europe.

The latest sequences from southwestern Nigeria casts further doubt on the “open water” explanation of the detection failures in Europe in 2005.  The sharing of polymorphisms in Egypt/Gaza as well as isolates in the Czech Republic and Italy suggest that the isolates in Nigerian in January, 2006 had been in Europe and the Middle East in the fall of 2005.  These sequences in southwestern Nigeria also refute the claim that H5N1 in Nigeria was linked to an initial reported outbreak in northern Nigeria and was spread by trade and smuggling, since the sequences in southwestern Nigeria were easily distinguished from the sequences in the north.

Thus, the recently released sequences, which were from isolates collected over two years ago support introductions via migratory birds that were in Europe and the Middle East in the fall of 2005, and migrated to western Africa at the beginning of 2006 (these recently released sequences were from collections were in January and February, 2006)..

The two year delay in the release of this data is yet another example of the hoarding of sequences that delay the resolution of “controversies” that have impeded advances for the past two years.

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