Recombinomics Commentary 13:29
January 29, 2010
JCVI released 50 full sequences at Genbank and almost all were from California. Included was one sample with D225A, A/California/VRDL31/2009, (as mixture with wild type) as well as two D225G and 8 D225E.  These sequences were from isolates collected over the summer and early fall.  The two isolates with D225G are distinct from each other and the many recent examples from Ukraine and Russia, representing two additional independent introductions.

A/California/VRDL27/2009 has four recently acquire polymorphisms, including A716G, which codes for D225G.  The other three polymorphisms are in a California isolate, A/California/VDLR20/2009 and a Texas isolate, A/Texas/45101424/2009.

The first polymorphism, C437T, is in several other pandemic H1N1 sequences and many swine (see list here). Another polymorphism, A1280A is widespread and in Ukraine, Russia, and Norway isolates with D225G (see list here).  The third polymorphism, G1360A is only in the three pandemic H1N1 sequences (see list here), which are the ones listed above.  The Texas isolate only has the three polymorphisms listed above, so the California isolate is the Texas sequence plus D225G, representing an independent acquisition.  Like most of the polymorphism, the other California sequence is the Texas sequences plus two other polymorphisms that are share with additional sets of pandemic isolates.


•  Cattle egrets pose threat in Serowe (Link)

•   Miscarriages, H1N1 shots ‘not linked’  (Link)

•  3 new H1N1 deaths: total now 256 (translated) (Link)

•  Four die of swine flu in Gujarat, toll rises to 229 (Link)

•  Two Children Are Bird Flu Suspects (translated) (Link)
•  Bird Flu Kills Thousands Of Chickens In East Lampung (Link)
•  2 suspect H5N1 patients (translated) (Link)

•  Romania Registers 119 Deaths, AH1N1 Infections Near 7,000 (Link)

•  1m doses of bird flu vaccine (Link)

United Kingdom
•  Inquiry in Widnes as children given adult swine flu jab  (Link)

United States
•  Rise Seen in Deaths From Pneumonia and Flu  (Link)
•  LA: 2 more die of swine flu in Louisiana (Link)

•  Avian influenza outbreak continues in many [several] provinces (Link)
•  Bird flu spreads to southern Vietnam (Link)
•  H5N1 in birds in Soc Trang province (Link)

•  MMWR – H1N1 and nursing homes (Link)

•  Some on antiviral therapy still test positive  (Link)

•  Recombinomics: H1N1 D225E Converted to D225G in Japan (Link)