Recombinomics: Identical H5N1 Deletion In Indonesia Egypt and China

Recombinomics Commentary 15:00
July 25, 2011
James Cook University in Australia has recently released five HA H5N1 sequences from Indonesia (clade 2.1). All five had a 3 base pair deletion, S133del (H3 numbering), which exact matched 3 BP deletions described in Egypt (clade 2.2) and China (clade 7). Four of the sequences (A/chicken/Indonesia/Timika_10/2006, A/chicken/Indonesia/Tanggerang_10/2007, A/chicken/Indonesia/Sukabumi_3/2007, A/chicken/Indonesia/Sukabumi_10/2007) are virtually identical and are closely related to previously released sequences from Western Java (A/chicken/West Java/SMI-CSLK-EB/2006, A/Chicken/West Java/SMI-PAT/2006, A/Chicken/West Java/SMI-CSLK-EC/2006, A/Chicken/West Java/PWT-WIJ/2006), which did not have the deletion indicating the deletion was appended onto this background.

The fifth sequence, A/chicken/Indonesia/Tanggerang_1/2007, is distinct and maps to another branch, supporting acquisition by recombination., which is also supported by the acquisition of the same S133del on three distinct genetic backgrounds (clade 2.1, clade, 2.2, clade 7).

Recombination is also supported by additional markers in the four closely related Indonesia sequences, which have T321C. This marker is in the earlier West Java sequences, but is also in the Egyptian sequences with S133del (see list here), indicating it was an early acquisition in Egypt, and spread by clonal expansion. S133del on an Egyptian clade 2.2 background is associated with a receptor binding profile similar to seasonal H1N1. It is present in all public human H5N1 sequences since mid-2009, as well as the mild H5N1 in Egyptian toddlers in early 2009.

In addition, T500C (encoding I155T), is also in the four related Indonesian sequences, as well as the Egyptian sequences with S133del (see list here) strongly supporting homologous recombination between Egyptian and Indonesian sequences.