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H5N1 Clade 2.2.3 Migrates Into Nigeria
Recombinomics Commentary 12:06
August 11, 2008
A strain of Highly Pathogenic Avian Influenza previously not recorded in sub-Saharan Africa has been detected in Nigeria for the first time, FAO said today.
The new strain has never been reported before in Africa; it is more similar to strains previously identified in Europe (Italy), Asia (Afghanistan) and the Middle East (Iran) in 2007.
The above comments describe the migration of clade 2.2.3 into Africa. This is not unexpected. Almost exactly one year ago, clade 2.2.3 was detected in the heart of Europe (Czech Republic, Germany, and France). The vast majority of the outbreaks were in wild birds, even though migration in Europe in the middle of the summer is minimal. The widespread outbreaks indicated H5N1 had become endemic in wild birds and the reservoir in resident birds lead to the outbreaks in domestic poultry.
Clade 2.2.3 then expanded in the fall and winter. All reported isolates in Europe were clade 2.2.3 and the vast majority, including those detected over the summer, were the Uvs Lake strain.
Therefore it is likely that the clade 2.2.3 in Nigeria is also the Uvs Lake strain, although that is not clear from the description above. However, the isolates cited were from the Capua lab, who did the sequencing of the 2008 isolates in Nigeria, and the failure to mention Uvs Lake isolates is likely more linked to what the Capua lab has sequenced previously, rather than the closest match with public sequences, which were from northern Europe, the Middle East, Uvs Lake, and South Korea / Japan.
Although clade 2.2.3 has not been reported previously in Egypt, the most recent isolates were acquiring clade 2.2.3 polymorphisms via homologous recombination.
Recombinomics Paper at Nature Precedings