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H5N1 and H9 Bird Flu Confirmed in Afghanistan
Recombinomics Commentary
March 16, 2006
Tests conducted in Italy confirmed the outbreak of deadly subtype of H5N1 virus of avian influenza in Afghanistan, a spokesman of UN Assistance Mission in Afghanistan (UNAMA) said Thursday.
Six samples tested in Italy indicated the same results, he said, adding that the samples had been taken from different part of the country including the capital Kabul.
To become sure about the possible outbreak of the disease, the Ministry had sent 321 samples to the laboratory in Povado, Italy last week for further test. One case among them was positive against H7 subtype of influenza virus and 37 for H9.
The above comments indicate H5N1 is widespread in Afghanistan. However, the data indicate H9 is also widespread in Afghanistan. The H9 isolates are likely to be H9N2, which have been reported in the Middle East, India, and Pakistan previously.
The number of recent H9N2 sequences at GenBank is limited. Sequences from Israel contain donor sequences that can recombine with H5N1 to form S227N on HA. S227N is know to increase the affinity of H5 for human receptors and has been detected in the index case in Turkey. The H5N1 sequences from Iraq did not contain S227N. However, the sequence from a 15 year old girl did contain N186S, which is near the receptor binding domain. Donor sequences for N186S were not found in a search of the Los Alamos database, but the number of H9N2 sequences from the area is limited.
The report of H9 co-circulating with H5N1 in Afghanistan raises the possibility of recombinations in Afghanistan that would be also produce S227N.
Sequence data on current H9N2 isolates in Afghanistan, Pakistan, India, and other countries in the Middle East would be useful.
Recombinations involving H5N1 and other isolates are quite predictable, but rely on a complete and current database. Several references labs, including those from Russia, Italy, France, and Egypt have placed sequences in public database as soon as they were generated and checked for accuracy.
In contrast, labs at Weybridge and Hong Kong have placed sequences in a private database maintained by WHO. These sequences are released upon publication, which can create delays of 6-12 months. Some sequences recently deposited by St Jude were collected in the 1970’s and 1980’s. Yesterday TIGR/St Jude deposited the full sequence of WS/33, the first human influenza sequence isolated. The isolation was in 1933, so the delay in release of sequence from date of isolation was over 70 years!
Efforts to update the database via the NIAID flu blueprint are to be applauded. However there are many partial H5N1 and H9N2 sequences that are missing regions demonstrating recombination, and these sequences should also be filled in and placed in the public domain.
The sequence database is useful for predicting future evolution of H5N1, but the as noted above, many important sequences are not being released in a timely manner.
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