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H7N9 In Avian Markets In Shanghai
Recombinomics Commentary 13:00
April 6, 2013

Huhuai agricultural products wholesale market, Songjiang, Shanghai, SHANGHAI
A pigeon for consumption in a wholesale market. 7 samples from chickens and 1 sample from the environment

Outbreak 1 Fengzhuang market, Minhang, Shanghai, SHANGHAI
2 samples from chickens, 2 samples from pigeons and 4 samples from the environment

Outbreak 2 Jingchuan market, Minhang, Shanghai, SHANGHAI
1 sample from chicken and 1 sample from the environment

The above comments are from April 4 and April 5 OIE reports citing locations and samples positive for H7N9 bird flu.  The locations are near the initial H7N9 cases.  The Jingchuan market is approximately 2000 feet from the Fifth Peoples Hospital (see map), where the first two confirmed H7N9 cases died, and the two brothers of the first confirmed case were also treated.  Moreover, local media reports described additional cases treated at the same hospital (see map).

The bird cases have been PCR confirmed and sequencing was cited in the OIE reports.  Media reports cited the Agriculture Department noting a close similarity between the H7N9 in birds and those identified in the initial cases.

The WHO Chinese Influenza Research Center released full sequences from the first three confirmed cases (A/Shanghai/1/2013, A/Shanghai/2/2013, A/Anhui/1/2013).  All three were closely related and had PB2 E627K, signaling mammalian adaptation, and a 5 amino acid deletion in the N9 stalk, signaling poultry adaptation.  However, the two more recent cases had evolved away from A/Shanghai/1/2013 and had Q226L, signaling human adaptation.

More recently, the Hangzhou Center for Disease Control and Prevention released sequences from H7, N9, and MP from a March 24 sample from a fatal case, A/Hangzhou/1/2013, which was most closely related to the more recent sequences above, but H7 position 226 evolved further to L226I, signaling additional human adaptation.  This rapid evolution is similar to changes driven by ferret passage in H5N1 bird flu transmission experiments.

The changes at H7 position 226 match season initial flu sequences from the 1957 and 1968 pandemics, while the most recent change matches current seasonal H3N2.

Therefore, release of sequences from the avian isolates are critical to determine the relationship between the avian sequences and the most recent human sequences, which have clear evidence of human adaptation.

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