today at genbank

[gsgs]

2012.06.22 : genbank release 190.0 ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt

daily updates : ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/
2012.06.26 - US-swine 2009-2012
2012.06.27 - more US-swine , Netherland and Sweden mallards most from 2002
2012.06.28 - American H5N2 1995-2004
2012.06.29 - 222 swine H1N1 , HA1 , UK 2010.12.01 , European 1978 ,
2012.06.30 - 348 more UK-swine, same strain,date
2012.07.01 - 46 more UK-swine, same strain,date
2012.07.05 - more Singapore H1N1 Jul,Aug,2009

[gsgs]

European swine (1978) is the strain which
gave segments 6,7 to mexflu and has the HA to which we have no immunity
and which may reassort into mexflu or H3N2v and cause the next pandemic. (IMO)
So far that H1 only caused occasional mild disease in humans or even asymptomatic.
It's unusual that UK publishes swine sequences and 222 at once was never seen, AFAIR

UK had a severe early wave of Mexflu in Dec.2010, so maybe this was just
to test whether the swine would have it too - but all 222 samples were
the European swine H1N1 that went from birds to swine in the late 70s
as an entirely avian virus and since then stayed in Eurasia until 2009
when 2 segments appeared in Mexico and reassorted with 6 American swine segments
to cause the 2009 pandemic

Jun.30 : 562 UK partial HA1 swine now, all very similar , closest match at genbank is
A/Sw/England/195852/1992(H1N1)
to which is has 49 differences in 937 nucleotides = 5.2%
an earlier good match is A/Sw/France/WVL4/1985(H1N1) with 53 differences = 5.6%
88 differences to A/Sw/Germany/2/1981, one of the earliest available genomes from that strain
It's not similar to other swine sequences from Europe, so this evolved undetected
since 20 years, remembering us to mexflu for which our best match is also more
than 10 years ago. Surveillance in swine is not good.


before that there were only 295 swine H1 sequences from Europe in total

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the strain is similar to English swine strains from the mid 90s
(characterized by mutations C54T,T84C,C99T,G123A,C336T,G489A,T825C)
Showing that they succeeded to keep English swineflu viruses on the island
and continental ones outside.