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Avian Genes In Clade H5N1 Guangdong China Isolate
Recombinomics Commentary 22:15
June 6, 2012

Further tests conducted by the Public Health Laboratory Services Branch of the CHP on the Influenza A virus isolate from the nasopharyngeal aspirate taken from the boy showed that the H5 gene of the isolate belonged to clade, which is the same clade as the isolates from wild birds detected in 2011 and 2012 and in the imported human infection case in late 2010. So far all the genes characterised belong to avian origin
The above comments name the sub-clade of the latest human H5N1 case from China, but fail to describe H5 changes that are associated with adaptation to humans, such as those described in recent and upcoming H5N1 transmission in ferrets.  The two published papers included gene segments that were not avian, but such acquisitions have not been reported previously in H5N1 isolates from Asia.  The closest example of a natural H5N1 isolates with non-avian genes was the PB2 gene from a chicken in Qalubiya, Egypt, A/chicken/Egypt/Q1182/2010, which had recombined sequences largely from seasonal H1N1 and H1N1pdm09.

The recent transmission study by Kawaoka, published in Nature, placed a clade 1 H5 on an H1N1pdm09 genetic background and obtained droplet transmission in a subset of ferrets, while Donis obtained similar transmission with an H5 placed on a clade 1 genetic background as well as an N2 from seasonal H3N2.

However, the Kawaoka studies identified an initial H5 change N158D in a subset of the ferrets, which was also likely in similar studies by Fouchier which will soon be published in Science.  As noted, N158D and associated loss of the glycosylation at position 160, is widespread in clade 2.2 in the Middle East.  However, N158D is also widespread in wild bird clade sequences, including the published sequence from the prior case in Guangdong, A/Shenzhen/1/2011, from late 2011.

Those sequences also had receptor binding domain changes V223I and M230I, which have been fixed in clade 

Therefore, release of sequences from the case described above would be useful.

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