Acquisition of G743A in H5N1 in Nigeria
Recombinomics Commentary 10:50
January 9, 2008
Sequences from twelve 2007 chicken isolates from Nigeria have been released at Genbank (see list below). Ten of the twelve are similar to the human HA and NA sequences released earlier. The human HA sequence had aggregated a number of regional clade 2.2 polymorphisms, and the new sequences had similar aggregation patterns, strongly suggesting that these polymorphisms were added through a series of recombinations involving a limited number of co-infections with other clade 2.2 viruses.
In addition to supporting the aggregation in HA, the NA sequences also support concurrent acquisition of G743A, which had been noted for a number of clade 2.2 genetic backgrounds. In 2006, G743A was largely limited to clade 2.2 sequences in southern Germany or northern Switzerland. However, G743A began to appear on various clade 2.2 sub-clades in early 2007. In late 2006, H5N1 sequences in Egypt were more complex than those from the prior season. Like the earlier isolates, the new sequences did not have G743A. However, beginning in February, G743A appeared on four different backgrounds. At the same time G743A was found on sequences from Russia and Ghana. These genetic backgrounds were distinct from the Egyptian sequences and were similar to earlier regional isolates in Russia or western Africa (Ivory Coast). More recently, G743A was appended onto distinct Uva Lake sequences from wild birds from three regions in Germany, as well as domestic and wild bird sequences from Krasnodar.
In the recently released sequences from Nigeria, G743A, was appended onto two of the twelve 2007 isolates, A/chicken/Nigeria/1071-10/2007
A/chicken/Nigeria/1071-22/2007, adding yet another genetic background with G743A appended onto a background that initially did not have the polymorphisms.
The appending of the same polymorphisms onto these multiple backgrounds is not easily explained by “random mutation” / selection mechanisms used to explain antigenic drift in influenza. G743A is synonymous, so it does not change the antigenicity of NA. Moreover, its concurrent appearance on multiple backgrounds significantly reduces the likelihood that the same change would be caused by independent mutations.
Thus, the new sequences from Nigeria strong support homologous recombination for the aggregation of polymorphisms from multiple donor sequences or the concurrent acquisition of the same polymorphism onto multiple genetic backgrounds.
A/chicken/Nigeria/1071-3/2007
A/chicken/Nigeria/1071-7/2007
A/chicken/Nigeria/1071-15/2007
A/chicken/Nigeria/1071-10/2007
A/chicken/Nigeria/1071-22/2007
A/chicken/Nigeria/1071-9/2007
A/chicken/Nigeria/1071-4/2007
A/chicken/Nigeria/1071-5/2007
A/chicken/Nigeria/1071-23/2007
A/chicken/Nigeria/1071-30/2007
A/chicken/Nigeria/1071-1/2007
A/chicken/Nigeria/1071-29/2007
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