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Novel Hong Kong H7N9 Constellation
Recombinomics Commentary 19:00
December 4, 2013

The Center for Health Protection in Hong Kong has released a full set of sequences, A/Hong Kong/5942/2013 (at GISAID), from a November 30, 2013 collection from the recently (see map) confirmed case (36F).  The CHP is to be commended for the rapid release of these important sequences.

As expected, these sequences have much in common with sequences, A/Guangdong/1/2013, from the August case in Huizhou (51F collected August 10, 2013).  That sequence was easily distinguished from the H7N9 sequences from cases in northern China (
A/Zhejiang/22/2013 and A/Zhejiang/DTID-ZJU10/2013).  Although four gene segments (H7, N9, MP, NS) were related to the northern China sequences, the other four gene segments were most closely related to H9N2 sequences circulating in southern China (mostly from poultry sequences from Hong Kong or Guangdong Province).

A/Hong Kong/5942/2013 also had same relationship with H7, N9, and MP, including the presence of Q226L in H7.  In addition, the H7 sequence had T131A, which was also uniquely found in A/Guangdong/1/2013.  Similarly, the PB2 had E627K and was closely related to the PB2 in A/Guangdong/1/2013.  However, the other three internal genes (PB1, PA, NP) were related to H9N2 sequences circulating in southern China (largely Hong Kong), but were distinct from the A/Guangdong/1/2013 sequences.

Thus, A/Hong Kong/5942/2013 represents an independent introduction into humans, which reflects a constellation circulating in southern China that is distinct from the August H7N9 from Guangdong Province.  This sequence data indicates H7N9 circulating in southern China is readily distinguished from the former and recent sequences in northern China, and there is significant heterogeneity in the southern sequences signaling widespread H7N9 in poultry in southern China.

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