Human / Avian Influenza Recombinants in Korean Swine
Recombinomics Commentary 19:39
September 12, 2008

Complete sequences for all eight gene segments from swine isolates in South Korea were recently released at Genbank (see list here).  The twenty isolates represented all three serotypes currently in circulation in seasonal flu (H3N2, H1N2, H1N1).  Like many swine sequences in circulation, including the Canadian swine sequences, all isolates had a human PB1.  In the Korea swine, the PB1 was most closely related to human isolates from the mid-nineties.  The other gene segments were swine, but five of the sequences had segments representing 1/3 to 1/2 of the gene, which were identical or closely related to avian sequences.  Many of the avian sequences matched low path isolates, but clade 2.2 H5N1 was present in one isolate, which also had regions of identity with clade 1 H5N1 also.

These regions of obvious homologous recombination represented several combinations.  Two of the isolates, A/swine/Korea/CY07/2007(H3N2) and A/swine/Korea/CY08/2007(H1N2) had the same wild bird sequence in the first half of PA.  The H1N2 isolate also had long segments of avian sequences in PB2.

However, recombination was also present in the human PB1 sequence.  One isolate, A/swine/Korea/CY09/2007(H3N2) had long regions of identity with wild bird sequences.  In contrast, the other isolates, A/swine /Korea/CAS05/2004(H3N2) had clade 2.2 H5N1 sequences in its human PB1 sequences.  In addition, there were clade 1 H5N1 sequences in PB2 for this isolate.

The examples of PB1 recombination represent the first reported human / avian recombinants, which are cause for concern.  Swine are mixing vessels that lead to reassortment and recombination.  When H5N1 emerged in humans in southeast Asia in 2004, many of the isolates had mammalian polymorphisms that would be frequently found in swine.  Some of these polymorphisms were also present in wild birds.  These recent sequences help explain both of those observations.

These recombinants also support earlier results with Canadian swine, which had examples of recombination with earlier swine sequences.  The most striking examples in the Canadian swine were in PB2 and PA, as was also seen in the Korean swine.  Similarly, sequences with clear examples of recombination were seen in isolates from live markets in Korea in 2003.

The latest recombinants highlight the role of swine as mixing vessels as well as evolution in mammalian flu genes, including the human sequences in PB1.  This extensive evolution between avian and mammalian flu sequences remain a cause for concern.

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