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2005 H5N1 Recombinant Between Vietnam and Yunnan

Recombinomics Commentary

July 4, 2005

HA and NA sequences for another H5N1 2005 isolate was deposited at Los Alamos National Labs today.  The isolate, A/Duck/Vietnam/367/2005, is from southern Vietnam (Tien Giang).  It is more recent than the 10 previous isolates, which appear to have been collected in January, 2005.  The latest isolate is from May 8, 2005 and is much like the 2004 isolates from Vietnam.

The HA sequence does not have the three nucleotide deletion and has many of the polymorphisms that distinguished the isolates from Vietnam and Thailand from the other 2004 H5N1 isolates from Asia.  However, the HA sequences is that of a recombinant, and the polymorphisms fro positions 1492 to 1568 match the four polymorphisms found in 2003 and 2004 H5N1 isolates from Yunnan Province in China (A1522G is exclusively found in Yunnan isolates, while T1492C,  A1565G and C1568T are in Yunnan isolates as well as other H5N1 isolates, mostly excluding those found in Vietnam and Thailand)..

Other than the region of recombination, the isolate looks much like the 2004 isolates in the north and south.  It matches the WHO description of human 2005 isolates.  Those from the north were missing the ARG, which was the case for the first 10 2005 isolates, including 6 from the north.  The isolates from Hanoi were somewhat different than the other earlier sequences, so these first 11 bird flu H5N1 isolates have several different features.  In the south are 2005 isolates that are similar to the 2004 isolates as well as some that have the 3 nucleotide deletion.  All isolates in the north have the deletion, but the Hanoi isolates can be distinguished from the other isolates with the 3 nucleotide deletion.

The WHO description of the human isolates indicated there was even more heterogeneity.  The human isolates from northern Vietnam have the ARG deletion, while the isolates from southern Vietnam.  Moreover one isolate is quite distinct from the pandemic strain, while another has partial resistance to Tamiflu.

The 2005 sequences at Los Alamos show additional heterogeneity. The most recent deposit is much like the 2004 isolates, except it has a recombined region in HA that is from Hunnan.  The remaining isolates have the 3 nucleotide deletion in the north and south.  Thus, in the south there are H5N1 isolates with and without the deletion.  In the north, all isolates have the deletion, but the isolates from Hanoi can be distinguished from the other northern isolates. 

There is co-circulation of two distinct genotypes in the south as well as co-circulation of two distinct genotypes in the north.  Co-circulation of distinct genotypes leads to more recombination via dual infections, which will create more new sequences and more new problems in the fall.

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