WHO Confirms Qinghai H5N1 Fatal Cluster in Lagos Nigeria
Recombinomics Commentary
February 4, 2007
The government of Nigeria has announced today the presence of A/H5N1 avian influenza virus in a 22-year-old deceased female from Lagos. The initial positive test findings from a laboratory in Nigeria were confirmed by the WHO Collaborating Centre for Reference and Research on Influenza in London
The above WHO confirmation by Mill Hill of one of the cluster members in Lagos, Nigeria was not a surprise. Samples from this patient had been tested at least four times and had been positive at least two times in Nigeria. The confirmation adds Nigeria to the WHO list of confirmed human cases. Like many countries, the first confirmation was a cluster member, and the data on the index case were lacking.
The current outbreak in Lagos and throughout Nigeria is a re-emergence of H5N1 that was identified last season. The sequences, including those from neighboring farms indicated H5N1 in Nigeria involved multiple introductions, strongly indicating the Qinghai strain of H5N1 was introduced by migratory birds.
Similar Qinghai sequences have been detected in Egypt, another country in Africa with confirmed fatal cases. The sequences in Egypt had a number of polymorphisms that are found in all or most Qinghai Egyptian sequences. Some of these polymorphisms link back to Europe, including Italy and Germany, while others link forward to western Africa, including Nigeria. Interestingly, the sequences that are most closely related to the sequences in Egypt are those from Lagos (A/chicken/Lagos.NIE/8.06/SO300/2006, A/chicken/Lagos.NIE/8.06/SO452/2006, A/chicken/Lagos.NIE/8.06/SO493/2006, A/chicken/Lagos.NIE/8.06/SO494/2006).
The HA polymorphisms shared by Egyptian and the above Nigerian sequences included G196A, G496A, C661T, C727T, A878G, C1018T, C1261T, C1686T).
Thus, the confirmation of human H5N1 in Nigeria this season is not a surprise. New cases have been identified in Egypt this season, and all confirmed cases have been fatal. The above WHO confirmed case, as well as the index case, had bird flu symptoms and died.
Release of H5N1 sequences from the confirmed case would be useful. The recent cases in Egypt included sequences from the Gharbiya cluster which had HA receptor binding domain changes (V223I and M230I) as well as NA Tamiflu resistance markers, N294S.
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