Recombinomics: Novel Clade 7 H5N1 Cleavage Sites Raise China Concerns

Recombinomics Commentary 21:19
March 30, 2009

The novel HA cleavage sites in the recently released H5N1 clade 7 sequences from northern Vietnam are cause for concern. The isolates from Vietnam are most closely related to clade 7 sequences from Shanxi and Hunan in China. All have the same basic cleavage site REGGRRKR. However, the two isolates from Vietnam have added an R to produce a cleavage site that is REGGRRRKR. This additional basic amino acid may make the H5N1 more virulent and expanded tissue tropism, because the cleavage is facilitated by tissue specific proteases and the extended cleavage site may offer additional specificities. Moreover, the most recently released sequence, A/chicken/Vietnam/NCVD-03/2008 has duplicated the firts two positions to produce an even larger cleavage site, REREGGRRRKR, which may be linked to even greater virulence and tissue tropism. This isolate also has an upstream 3 BP deletion, although neither recent isolate from Vietnam has the 3 BP deletion identified in the clade 7 isolates from Hunan and Shanxi.

This increase in genetic instability is likely linked to recombination driven by vaccine escape. The latest WHO update on vaccine targets notes that the two isolates from Vietnam were antigenically distinct and both were chosen as clade 7 vaccine targets, even though both came from 2008 Vietnam isolates. Selection of clade 7 vaccine targets is limited by the withholding of clade 7 sequences. China has yet to release sequences from the January cases, even though the sequence of A/Beijing/1/2009 was discussed in media reports in January. The WHO update was glaringly silent on this case, which was the first in the series of nine confirmed cases in China in January, which abruptly stopped in February.

China has acknowledged that the poultry outbreak in December, 2008 was clade 7, which created vaccine resistance problems, leading to new vaccinations in adjacent areas. However, the human cases were widespread throughout China, raising concerns that vaccine resistant H5N1 extended beyond provinces adjacent to Jiangsu. This is supported by the recent clade 7 sequences from Vietnam, which have a large number of non-synonymous changes that would compromise prior vaccines. Moreover, it is not clear that clade 7 is included in vaccines in Vietnam, which would facilitate H5N1 spread and instability.

Release of recent H5N1 sequences from patients and poultry in China and Vietnam would be useful.