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H5N1 Evolution Via Recombination in India

Recombinomics Commentary

July 15, 2006

Two partial HA H5N1 bird flu sequences (A/chicken/Jaigaon MH/8842/2006 and A/chicken/Nandurbar MH/7972?2--6) from Maharashtra, India have been published.  The two sequences have a number of unique polymorphisms, but are most closely related to each other. 

As expected, both are the Qinghai strain and have a number of polymorphisms shared with other Qinghai isolates. G536A, A539G, and C868T are in both isolates from India, as well as A/swan/iran/754/2006, A/chicken/Afghanistan/1207/2006, and A/whooping swan/Mongolia/244/2005. 

However, two additional polymorphisms, G1252A and A1708G are discordant, indicating the Indian isolates are recombinants.  A1252A is shared with A/bar headed goose/Qinghai/5/2005 and A/duck/Niger/914/2006, while A1708G is shared with A/chicken/Kurgan3/2005 and A/chicken/Nigeria/641/2006.

As additional sequences are made public, the examples of recombination increase.  The Qinghai strain of H5N1 has migrated into a number of countries which are reporting H5N1 for the first time.  The polymorphisms punctuating the Qinghai genetic background create discordance within the Qinghai genomes, indicating these isolates are recombining with each other and creating new combinations of polymorphisms.

Over 100 additional Qinghai sequences remain sequesters in the WHO private database.  These sequences should be released immediately.

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