H5N1 Homologous Recombination in Sweden
Recombinomics Commentary 20:53
September 18, 2008

Full sequences from 12 isolates from Sweden have been released (see below).  As expected, these sequences fall into two main sub-clades.  Most of the sequences are closely related to sequences from Scotland, Denmark, and northern Germany, while two of the isolates are closely related to sequences from the Czech Republic or Slovakia.  These relationships were expected since the NS sequences from Sweden had been released earlier.

However, two of the NA sequence (one from each group - A/canada goose/Sweden/V978/2006 and A/tufted duck/Sweden/V599/2006) diverge from the other sequences over a 60 BP stretch near the 3’ end of the gene.  This region has eight polymorphisms that are shared between the two isolates from Sweden, but not found in the other isolates from the region, or any clade 2.2 isolate. However, this segment exactly matches H5N1 from the 1997 outbreak in Hong Kong (in humans and birds).  This NA sequence is quite distinct from the NA currently in circulation in H5N1.  The current version has a 20 amino acid deletion, while the 1997 sequence has a 19 amino acid deletion, which overlaps the 20 amino acid deletion, by has different start and stop positions.

The 1997 isolates largely disappeared after extensive culling in 1997, but related sequences were found in three isolates in Vietnam in 2005, and these sequences also match.  Similarly, this region is also found in H6N1 isolates in China (see list here).  Thus, this segment is present on four different genetic backgrounds, the 1997-like sequences, the H6N1 isolates in China, and two clade 2.2 backgrounds in isolates from Sweden.  The segment on four different genet backgrounds provides additional compelling data for more H5N1 homologous recombination.

A/mink/Sweden/V907/2006
A/tufted duck/Sweden/V599/2006
A/herring gull/Sweden/V1116/2006
A/tufted duck/Sweden/V526/2006
A/tufted duck/Sweden/V998/2006
A/canada goose/Sweden/V978/2006
A/smew/Sweden/V820/2006
A/goosander/Sweden/V539/2006
A/mute swan/Sweden/V827/2006
A/eagle owl/Sweden/V618/2006
A/tufted duck/Sweden/V1027/2006
A/eagle owl/Sweden/V1218/2006

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