Recombinomics Commentary March 31, 2009

HA and NA sequences from the H5N1 outbreak in Assam, India were released at Genbank.  The two HA sequences, A/chicken/Assam/140187/2008 and A/chicken/Assam/140203/2008 were identical and clade 2.2.3, as seen previously in isolates from south Asia (India, Pakistan, Afghanistan).  However, the current sequences are the Uvs Lake strain that was initially isolated from a massive wild bird outbreak at Uvs Lake in Mongolia and the adjacent region in Siberia (Tyva) in the summer of 2006.  These sequences were subsequently found in outbreaks in South Korea and Japan at the end of 2006 / beginning of 2007.  However, another set of sequences was found in early 2007, and these sequences had acquired G743A, which was also acquired by distinct clade 2.2 isolates in Egypt, Russia, Ghana, and Nigeria in early 2007.

However, the Assam sequences do not have G743A, suggesting they originated from sequences that did not fly west to the Middle East and Europe (the sequences in Kuwait, including G743A, were subsequently reported throughout Europe, beginning in the summer of 2007.  Phylogenetic analysis also shows that the Assam sequences are on a lower branch that is distinct from the isolates with G743A.  Moreover, the newly acquired polymorphisms in the Assam sequences were not clade 2.2 sequences, but were largely polymorphisms found in other H5N1 clades circulating in Asia.

These data support migration of the H5N1 sequences from Mongolia or Russia to India via the south Asia flyway, which connects those countries.  This connect was expected, because all prior outbreaks in the region were clade 2.2, which was initially reported in countries to the north of India that were in this flyway.

However, the linkage with Uvs Lake sequences, populated with Asian polymorphisms further supports the migration of H5N1 into India via migratory birds.