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Rapid H5N1 Evolution Via Recombination in Nigeria

Recombinomics Commentary

July 13, 2006

The H5N1 bird flu sequences from two farms in Lagos, Nigeria have been released.  As indicated in last week's Nature, the sequences were distinct from each other as well as the published sequences from northern Nigeria (see phylogenetic tree) and southern Niger.  These data indicate four separate introductions of H5N1 into the area and once again indicate wild birds have transported H5N1 into new areas.  Nigeria is at the intersection of several major flyways, including the East Atlantic flyway which links western Africa to western Europe and northeastern Canada.

However, the Lagos sequences share polymorphisms with previously released sequences from Niger and Niger, as well as Egypt, Djibouti, and Turkey. There is also evidence of recombination, as the sequences continue to diversify.  All sequences trace back to the H5N1 sequences from Qinghai Lake in China, but the Qinghai H5N1 bhird flu continues to evolve.  These newly acquired polymorphisms punctuate a Qinghai genetic background, and provide data on travel routes and recombination. 

As sequences are released from the WHO private database, patterns begin to emerge which identifies regional polymorphisms, but also provides patterns identify recombination, even when only a few polymorphisms are available. These "new" polymorphsism divide up the isolates and are powerful when couple with the time and location of the collected isolates.  The H5N1 can be viewed in real time both those generating these sequences, and at a slight delay as sequences are made public.

A/chicken/Lagos.NIE/10.06/BA209(H5N1), AM262541
A/chicken/Lagos.NIE/10.06/BA210(H5N1), AM262542
A/chicken/Lagos.NIE/10.06/BA211(H5N1), AM262543
A/chicken/Lagos.NIE/8.06/SO300(H5N1), AM262546
A/chicken/Lagos.NIE/8.06/SO452(H5N1), AM262547
A/chicken/Lagos.NIE/8.06/SO493(H5N1), AM262553
A/chicken/Lagos.NIE/8.06/SO494(H5N1), AM262572

Seven new HA sequences have been released, three from one farm and four from another.  Although both farms are near each other in Lagos, the isolates from each farm are quite distinct. On one farm, three polymorphisms, A846GG, G864A, and C1216T are in two or all three isolates, but not found in any other Qingahi sequence.  However, two more, A211G and A1459G are also found in the Niger isolate.  The sharing of polymorphisms between the Niger and other isolates indicate the Niger isolate is a recombinant with other Qinghai isolates.

Similarly, other polymorphisms, A115G, A626C, A1672G are only found on the other farm.  However, those four isolates have additional polymorphsism shared with isolates from Egypt and Djibouti.  Additional polymorphisms are shared with the three African countries, and the Czech Republic.  Other polymorphismss extend to Mongolia, Astrakhan and Denmark.  In addition, one of the Lagos isolate also has discordance within its genome, indicating it also is a recombinant with other Qinghai isolates.

The new sequences from Lagos also define additional groupings, which then indicate earlier isolates are also recombinants.  Thus, as sequences are released, the "new" polymorphisms show clear travel routes of the migratory birds distributing the H5N1, and provide compelling evidence for frequent and widespread recombination between various Qinghai strains.

These new sequences will create new problems in the fall, as H5N1 continues to expand its geographical reach and genetic diversity, and WHO continues to withhold the sequences.

There are over 75 sets of sequences of Qinghai isoaltes from Europe and the Middle East in the private WHO database.  These sequences should be released immediately.

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