Aggregation of H5N1 Single Nucleotide Polymorphisms in Nigeria
Recombinomics Commentary 02:30
January 9, 2008
Twelve complete sequences of H5N1 from Nigeria were released at Genbank (see list below). Ten of the twelve HA sequences were similar to the HA sequence from the first confirmed human case in Nigeria. The HA sequence was unusual because it had aggregated single nucleotide polymorphisms that were region markers for clade 2.2 (Qinghai strain). This type of aggregation is most easily explained by homologous recombination.
Analysis of the newly released 2007 sequences indicate that similar aggregation was present on these additional isolates, indicting the recombination was stable and widespread in isolates in Nigeria in 2007. The additional sequences also confirm a high level of recombination in Nigeria, which leads to rapid evolution of H5N1.
Recombination is also supported by the appending of NA G743A onto another genetic background. Two of the twelve NA sequences have acquired G743A.
The dominant sequences circulating in Europe are the Uva Lake strain, which is migrating into western Africa. These sequences should provide additional donor sequences for more rapid evolution of H5N1 in western Africa, which is cause for concern.
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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