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Qinghai H5N1 in Shantou China
Recombinomics Commentary
October 29, 2006

Recent H5N1 sequences released at Genbank included 404 H5N1 isolates from China deposited by Hong Kong University and collaborators.  Although many of the HA sequences were partial sequences, most included the HA cleavage site and the vast majority have the novel HA cleavage site, PLRERRRK_R found in the recently reported Fujian strain.  However, a Guinea fowl isolate from Shantou, A/Guinea fowl/Shantou/1341/2006(H5N1), had the characteristic Qinghai cleavage site, PQGERRRKKR.  Although this strain was initially isolated from waterfowl at Qinghai Lake in Qinghai Province, subsequent Qinghai isolates have been limited to regions to the north and west of Qinghai Lake including Mongolia, Russia, Kazakhstan, India, Afghanistan, Europe, the Middle East, and Africa,

The Shantou is the first Qinghai isolate which have a number of defining polymorphisms, including PB2 E627K.  The HA and PB2 sequences from the Shantou isolate were made public, and the characteristic polymorphisms were present in both sequences, including E627K.

The number of Qinghai sequences outside of China continues to increase and these sequences have a number of polymorphisms shared with a subset of Qinghai isolate.  In HA, the Shantou isolate had C1261T (see list here), but several additional polymorphisms were not found in other Qinghai isolates, but were in H5N1 isolates from eastern China and Vietnam.  Similar polymorphism sharing was in PB2 also.

H5N1 evolves via acquisitions of polymorphisms by homologous recombination in dually infected hosts.  The profile of newly acquire polymorphisms in the Shantou isolate indicate the Qinghai strain is evolving via dual infections in eastern and southeastern China. 

The limited detection in China may be related to vaccination efforts or natural immunity which may have suppressed levels of the Qinghai strain, but increased levels of the Fujian strain.  Alternatively, current surveillance methods may select against detection of the Qinghai strain

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