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Sequences of H5N1 from Gangcha County Qinghai China

Recombinomics Commentary
June 4, 2005

>>  The virus, which has killed more than 1000 migrating birds, is being
collected from dead birds, but scientists haven't found any similar gene
like that in the H5N1 virus that can be transmitted to humans. Jia Youling
says reports of avian influenza spreading to people in the province is
unfounded. <<

The above comments were from a media report from China dated May 27.  It would indicate that sequence data had been obtained from virus isolated form dead bird in and around Bird Island in Qinghai Lake.  Making these sequences publicly available at GenBank would be useful.  The initial 178 deaths were said to have been exclusively in bar headed geese.  These geese winter in the northern plains of India and can fly 1000 miles in 24 hours.  Thus, the geese in India are literally one flight away from Qinghai Lake which is about 1000 miles from northern India.

Therefore, it seems likely that the H5N1 actually originated in India.  Therefore, analysis of bar head geese in India would be useful.  Some of the bar headed geese continue north to southern Russia, so examination of those bar headed geese would also be useful.

The fact that the H5N1 from Qinhai doesn't match H5N1 in southeast Asia is neither surprise nor is it an indication that the H5N1 cannot kill humans.  Indeed the die-off of H5N1 bar headed geese is without precedent.  The intersection of the Central South and East Asia flyways would allow for novel recombinants which could kill birds and human.  H5N1 in southeast Asia does not usually kill ducks and geese.

However H5N1 is quite capable of killing humans with a number of genetic constellations and polymorphisms.  The initial kill in Asia was in 1997 in Hong Kong.  6 of 18 people died and the H5N1 had a 19 amino acid deletion in NA and a poly-basic HA cleavage site.  However, the internal genes were similar to H6N1 or H9N2.  Hong Kong culled all birds and that particular constellation disappeared.

However, in 2003 another H5N1 was killing people.  A Hong Kong family had traveled to Fujian province.  The daughter became sick and died.  Her brother and father returned to Hong Kong.  The father also died and H5N1 was isolated from father and son.  The constellation of genes was designated genotype Z+ because it was similar to the Z genotype, but there was no 20 amino acid deletion.

The more common genotype was Z, which has a 20 amino acid deletion in NA that overlapped the 19 amino acid deletion from 1997.  The Z genotype was widespread in Asia, but only Vietnam and Thailand had reported human cases.  These isolates however did have a number of unique polymorphism more commonly seen in mammalian isolates.  Similar "humanization" was noted in the 1997 isolates.

In 2005 there are reports of yet another version of H5N1.  In northern Vietnam and Thailand the isolates have formed a new group.  At least some are missing an ARG in the HA cleavage site, indicating they are recombinants between 2004 isolates in Vietnam and China or Japan.  The case fatality rate is lower, further supporting the fourth version of H5N1 to kill humans.

This, simply looking at the H5N1 sequences in Qinghai is not conclusive proof of the ability of the virus to kill or not kill humans.  In lab test the virus kills chickens and on Qinghai Lake it kills over 8000 water fowl, and photos suggest the number may be higher.

Clearly reports of 121 human deaths need to be thoroughly investigated, and the sequence data should be placed on deposit at GenBank as soon as possible.

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