Genetic Exchanges Between H1N1 Clade 2B and 2C
Recombinomics Commentary 12:01
October 2, 2008

Three sets of partial HA and NA sequences from Hong Kong are being released at Genbank.  All three HA sequences are Hong Kong/2562 (clade 2C) and phylogenetically map to two 2C sub-clades.  All three NA sequences have H274Y, but only two of the NA sequences are clade 2C.  The third sequence, A/HongKong/942/2008, exactly matches an earlier sequence from Hong Kong, A/Hong Kong/17/2008, as well as other clade 2B sequences from South Africa, France, England, and the United States (see list here).  Thus, this isolate is a reassortant, with a clade 2C HA sequence and a clade 2B NA sequence.

However, in addition to swapping entire genes, these isolates also have evidence of recombination between clade 2B and 2C in the HA sequences.  Although the other two HA sequence are clearly cade 2C, the are two differences between A/HongKong/1052/2008 and A/HongKong/1313/2008.  The HongKong/1313 sequence exactly matches clade 2C sequences from Korea, Northern Mariana Islands, and the United States (see list here), but one of the two differences in HongKong1052 encodes for N187S, one of the receptor binding domain changes found in five of the HA sequences from South Africa (see list here).  Thus, this rare change adjacent to the receptor binding domain is a newly acquired polymorphism in the clade 2B sequences from South Africa and the clade 2C sequences from Hong Kong.

Thus, the three sets of partial sequences from Hong Kong have evidence of genetic exchanges via reassortment and recombination between H1N1 clade 2B and clade 2C sequences.  Movement via recombination of H274Y was seen in earlier isolates as the polymorphism moved from H5N1 to clade 2C to clade 2B.  The additional examples in the Hong Kong sequences provide further support for the swapping of genetic information between the two H1N1 sub-clades.

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