Human H5N1 in Sudan?
Recombinomics Commentary
November 20, 2006
Authorities in southern Sudan announced in September that they had found the H5N1 strain in chicken and in the owner of an affected farm. The farmer was hospitalised with avian flu symptoms and later tested positive, prompting the World Health Organization to send a team into the impoverished country.
The above comments indicate H5N1 bird flu has been detected in a farmer in southern Sudan. WHO issued a report on the H5N1 outbreaks in poultry in Sudan. The report indicated that all human tests were negative, include a 50F who was hospitalized. However, there was no indication that the 50F was a farmer, so the relationship between the two hospitalized patients remains unclear.
The Sudan and Egypt had H5N1 outbreaks in poultry in February and sequences have been released. Although all sequences were the Qinghai strain, the Egyptian sequences were similar to the H5N1 from a patient in Djibouti as well as patients in Egypt. There were no reported human cases in Sudan, but the H5N1 in poultry had a novel HA cleavage site and was readily distinguished from isolates in neighboring Egypt and Djibouti.
Recently, additional outbreaks were reported in Egypt and southern Sudan. The Egyptian outbreak was associated with a confirmed fatal case as well as additional suspect cases, including three siblings and a neighbor who were hospitalized last week.
The sequence from the recent confirmed case in Egypt and it contained a novel change at position 230, involving an M-->I change (M230I). This change created a match with all three human seasonal strains, H1N1, H3N2, and influenza B. The influenza B match covered positions 226-230 (QSGRI). This region encompasses the receptor binding domain, and raises concerns over an increase in human-to-human transmission.
The recent Nature report also described additional changes (N186K and Q196R) which were also reported to be present in human H5N1 isolates from Azerbaijan and Iraq, from earlier outbreaks, Moreover, another human H5N1 isolate from Iraq has N186S. N186K also matches influenza B, while N186S matches early human H3N2 isolates. These additional matches raise concern, because these changes may synergize.
S227N has also been detected in Turkey and Egypt and these changes may be in a subset of H5N1 in an individual patients, and detection of these changes can be impacted by isolation procedures, especially if isolation uses chicken eggs as the isolation medium.
More information on the patient in Sudan would be useful.
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