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H5N1 Migration into Nigeria and Niger

Recombinomics Commentary

July 6, 2006

After analysing samples from infected birds on two farms in south-western Nigeria they found the viruses were genetically distinct from each other and from H5N1 found in the north of the country.
So rather than one strain spreading through the country, different strains had been introduced on separate occasions, which could make controlling the spread of the virus more difficult."It strongly suggests that the virus in the north and the virus in these two southern farms have been independently introduced into Nigeria

The above comments summarize the data presented in today's Nature, which describes two versions of the Qinghai strain in Lagos, which are distinct from the H5N1 in northern Nigeria.  Similarly, the H5N1 in neighboring Niger is also distinct from northern Nigeria.

The northern Nigeria strain was the first reported outbreak in Nigeria and some media reports and wildlife conservation groups suggested that H5N1 was introduced into the area via trade.  However, media reports indicated wild birds in Nigeria had been dying for weeks or months prior to the reported outbreak on the farm.  This pattern continued as new outbreaks were confirmed, including Lagos..  Media reports of deaths in wild and domestic bird preceded confirmed outbreaks, pointed toward a poor surveillance system.

This poor surveillance was common throughout Africa.  Many neighboring countries continue to claim to be free of H5N1 bird flu, but positive data in neighboring or surrounding countries raise significant doubts on the negative data.  Those doubts extended to reports of wildlife groups that failed to find H5N1 in any wild bird in Africa.  In many countries the failure to detect H5N1 extended to low pathogenic avian influenza, which is widespread in wild birds, indicating fatal flaws in collection and testing procedures.

The sequence data in Nigeria and neighboring Niger clearly showed that the H5N1 was the Qinghia strain and was introduced independently into the country.  These independent entries had been documented elsewhere and the recent history of H5N1 spread to the west of China leaves little doubt that the primary vector is wild birds.  Trade plays a minor role at best.

Prior to the H5N1 outbreak at Qinghai Lake in May, 2005, reported cases of H5N1 were limited to China and countries to the east or south.  Although the Asian version of H5N1 was first identified in 1996 in a goose from Guangdong, the distribution of H5N1 was limited.  Reports of H5N1 exploded in 2004 in eastern Asia, but this explosion in reported cases did not lead to H5N1 to the west.

The reports of H5N1 migration to the west began shortly after the May, 2005 outbreak and followed well established migratory pathway.  In the summer of 2005 Russia. Kazakhstan, and Mongolia reported H5N1 infections fro the first time.  These infections were in wild birds or farms adjacent to ponds shared by migratory birds.  The largest outbreak was at Chany Lake a nature reserve frequented by migratory waterfowl.  Similarly, initial outbreaks in Mongolia were at another nature reserve, Erhel Lake.

In the fall the H5N1 was initially reported in nature reserves in the Volga Delta and Danube Delta.  H5N1 then spread to Europe, the Middle East, and Africa.  In Europe, where surveillance is more robust, many countries have reported H5N1 in wild birds, but have yet to report cases on farms.

Sequences from these isolates are beginning to released, and all are the Qinghai strain.  However, there are many version of the strain due to recombination with other influenza viruses, which are also largely H5N1 in Asia.  These new polymorphism punctuate a Qinghai genetic background and create distinguishing polymorphism reflecting travel histories of the isolates.  These have been displayed for isolates in Nigeria, Niger, Astrakhan and other Qinghai isolates. 

These differences can also be seen in phylogenetic trees.  The tree of Qinghai isolates in Europe has multiple branches due to independent introductions via migrating birds.  The same type of diversity is seen in trees of Qinghai isolates in Russia and China as well as trees showing the isolates from Nigeria.

These multiple introductions creates the potential for more genetic diversity as the H5N1's co-infect birds and recombine further.  These recombination are now stating again in Siberia as H5N1 infected birds from Europe, the Middle East, and Africa summer in these northern regions and create new Qinghai strains which will create new problems in the fall, as these birds with new H5N1 recombinants migrate again to the south.

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