- 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.
- © 2006 Recombinomics. All