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Media Spin on Fujian H5N1 in South Korea
Recombinomics Commentary 03:51
May 22, 2008
According to the environmental ministry, the animal hygienic laboratory (Ibaraki prefecture Tsukuba city) when the virus which is detected with the Akita prefecture Towadako and the virus which is detected in Korean all the 羅 north road gold embankment cities are compared, base arrangement of the gene agreed 99.7% or more. The virus which is found at the total 3 place of Akita and Hokkaido understands that the result of gene analysis, it is identical.
The above translation provides more information on the H5N1 isolates from Japan and South Korea. In Japan, H5N1 was found in whooper swans at three distinct locations, Akita and two distinct sites on northeastern Hokkaido (see satellite map). Two sets of sequences from all eight gene segments have been made public, and they are virtually identical. The above translation indicates they have an identity that is 99.7% or higher with sequences in South Korea.
The sequences from Japan were reassortants. The HA sequence was closely related to clade 2.3.2 isolates from Vietnam in 2005 and most closely related to a wild bird from Hong Kong in 2007. The other seven gene segments were most closely related to clade 2.3.4 isolates, including sequences from a patient in Guangdong Province. The other closely related 2.3.4 sequences are from wild bird isolates from Hong Kong collected in 2006.
The local media in Korea is trying to claim that the isolates there have never been reported to cause a human infection, based on the clade 2.3.2 relationship for HA. However, there is little scientific data to extend this observation to the isolates in Japan or South Korea because they are mixtures and most genes are related to clade 2.3.4, which is the sub-clade associated with human infections. Moreover, H5N1 is constantly evolving, so basing human infection potential on earlier isolates has little value.
The clades of most interest are clade 1, clade 2.1, clade 2.2, and clade 2.3 All four of these sub-clades have been associated with human infections. Further subdivisions of the sub-clades are based on phylogenetic analysis and such subdivisions has not led to a loss of the ability to infect humans.
In 2004 there first human cases linked to clade 1 were in Vietnam and Thailand. Although these isolates were distinguishable, both sets of sequences cause fatal human infections.
In 2005 clade 2.1 was associated with fatal human infections in Indonesia. Most of the human cases fell into a further sub-clade with the HA cleavage site of RESRRKKR. However, the second confirmed case in Indonesia was in another sub-clade, as was the Karo cluster, so dividing up the isolates did not limit human infections to one sub-clade, although most had the novel cleavage site cited above.
The same was true for clade 2.2. One sub-clade was in Egypt, and was linked to 50 cases. However, this sub-clade could be divided into multiple smaller sub-clade, but all major subdivisions were linked to human infections. Similarly, sub-clade 2.2.3 could be subdivided and the subdivisions have cause human cases in Azerbaijan and Pakistan.
Thus, even though these sub-clades can be further divided, most of these divisions produce human infections, so claims that clade 2.3.2 does not cause human infections has little scientific support, and the H5 positive soldier in South Korea is an example of a human clade 2.3.2 infection, if the classification is limited to the HA sequence.
Thus, many sub-clades and further divisions of these sub-clades can cause human infections including the H5N1 in circulation in Japan and South Korea. This ability has been demonstrated in the soldier in South Korea who was H5 confirmed in multiple lab tests.
Recombinomics Paper at Nature Precedings