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Diversity in Human WSN/33 Sequences in Swine in Korea in 2005

Recombinomics Commentary

April 29, 2005

Nine 2005 H1 sequences have been determined for two H1N1 isolates and seven lung samples from fatal infections in swine in three provinces of South Korea.  Like the two 2004 H1 swine sequences at GenBank, the nine new sequences are greater than 99% homologous to the human 1933 lab flu strain, WSN/33.  All nine sequences are unique (the earlier report indicating two sequences were identical was in error - the two identical sequences were an initial and final sequence of the same sample).

The 2005 sequences reveal much more genetic instability than the two 2004 isolates.  In this region of approximately 600 bp there were 5 polymorphisms that were unique to WSN/33.  These 5 polymorphisms were also in the two 2004 swine isolates and all nine 2005 sequences.  In addition WSN/33, S175, and S10 each had one unique polymorphism.  The one unique polymorphism in S175 was present in eight of the nine 2005 sequences.  The only 2005 sequence that was wild type at this position was PCR sequence YG.  Although the YG sequence had nine polymorphisms, all nine were unique. 

In contrast, the remaining eight 2005 sequences had four polymorphisms that were found in four or more of the 2005 sequences.  One was in all eight sequences, while another was in both viral isolates as well as four of the six PCR sequences.  The other two polymorphisms were only in the PCR sequences, but each was in four of the six sequences.

Three of the six PCR sequences had all four polymorphisms, but the three sequences were from lung samples from swine in each of the three provinces.  Thus, these three were the most diverse and were found in all three provinces.  In addition to the four 2005 polymorphisms that were in four or more sequences, there were nine unique polymorphisms in the YG sequence as well as 15 more unique polymorphisms in the eight other sequences.

The nine 2005 sequences define 21 polymorphisms that are unique to the 2005 isolates.  In contrast there were only three 2004 polymorphisms in the two 2004 isolates.  Although the large number of 2005 polymorphisms is related to the larger number of sequences, which include seven PCR sequences from lung samples, the sequences are clearly rapidly acquiring new polymorphisms.  This added heterogeneity virtually eliminates the possibility that the 11 WSN/33 - like H1 sequences in swine in Korea are due to "lab error".

These eleven WSN/33 sequences from swine in Korea raise serious issues about efforts to detect these sequences.  The association of these genes with H9N2 bird flu genes raises questions about the origin of the WSN/33 sequences.

The spread of human 1933 H1N1 in swine in Korea and around the world is cause for concern.

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