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Swine to Human H5N1Transmission in Indonesia?

Recombinomics Commentary

May 17, 2006

Among the confirmed deaths on Wednesday was a 38-year-old catering businesswoman from Surabaya who had dealt with live pigs and pork meat before she died last week.

The above comments on a confirmed death in Surabaya are cause for concern.  Last year H5N1 infected swine were identified in Surabaya.  Reports indicated that all eight genes had been sequenced in Japan, and the sequence included a polybasic cleavage site.  Although the sequence was generated over a year ago, it has not been made public via deposition at the public database at GenBank or Los Alamos.  Instead it is almost certainly being withheld in the WHO private database.

Only one human H5N1 sequence has been deposited from Indonesia.  That sequences has a novel HA cleavage site of RESRRKKR, which is not found in any sequence at GenBank.  However, a recent report suggested that the novel sequence was in human isolates from Indonesia as well as a cat isolate from Indonesia.

Novel sequences are common in swine H5N1, in part because there are a limited number of such sequences.  All public swine H5N1 sequences have come from China, and most have novel HA cleavage site. The common H5N1 sequence is RERRRKKR.   Two of the swine sequences, A/swine/Guangdong/1/2003(H5N1) and A/swine/Shandong/2/03(H5N1), but even in these cases the nucleotide sequence that encodes the cleavage site is relatively rare.  It is unique for the Guangdong sequence and shared with a few wild bird isolates in the Shandong sequence.

Several of the swine isolates,  A/swine/Fujian/F1/2001(H5N1), A/swine/Fujian/1/2003(H5N1), A/swine/Guangdong/2/2003(H5N1), A/swine/Guangdong/4/2003(H5N1, A/swine/Guangdong/5/2003(H5N1) have the REIRRKKR sequence which is shared with a small number of waterfowl including Guangxi ducks, and A/swine/Anhui/2004(H5N1), which has REGRRKKR which is also found in a small number of waterfowl.

These small number of isolates in these swine H5N1 sequences raise the possibility that the novel sequence in the human isolates in Indonesia also come from swine.  In any event, the human and swine sequences from Indonesia should be released, and the source of the novel HA cleavage site should be determined.

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