Note: I will be updating this post through the day, as I play with the sequences in my spare time.  (Right now I have to get the kids up and get them ready for school.)  Don’t expect to learn anything particularly new from this, since I’m no influenza expert; but since I’m going to be doing this for my own curiosity I may as well save others the time.
Update: Also see my Wednesday post for more info.

For those playing along at home, some of the swine flu genomes are now available.  Only one of them has a complete genome, and these are the California and Texas cases — now we really want to compare them to the Mexico strain to see if the mortality is associated with strain variation or not.

I haven’t looked at the sequences much yet.  I did run some quick alignments of the HA gene; nothing unexpected.  These are all the same strain, but not identical (as you expect from influenza).  It’s significantly different from the HA of the H1N1 strain that was circulating this year (A/Brisbane/59/2007) (I think that was the circulating strain, it’s close anyway).   If you’re interested you can check:
Alignment compared to A/Brisbane/59/2007
Alignment of the 7 swine flu HA proteins
Alignment of the 6 complete swine flu HA proteins

The closest matches to the HA in GenBank are from A/swine/Minnesota/1192/2001(H1N2) and several other swine flu strains, which are ~ 94% identical.  I haven’t compared the other genomic fragments yet to see what other strains got into the mix.

Update 1. I’ve run the segments of the most complete new virus (A/California/04/2009(H1N1)) to see what viruses this looks most like.  The only remarkable thing I see is how unremarkable it is.  It’s pretty much a generic swine flu top to bottom, with close matches only to other strains of swine flu.  Since those other strains didn’t jump into people, that’s just another indicator of how much we have to learn about molecular determinants of virulence in viruses.

Quick results, showing only the first few matches (there are many!):

PB1 matches
Accession Strain Pct identity
AF342823.1 A/Wisconsin/10/98 (H1N1) 96%
AF250130.1 A/Swine/Indiana/9K035/99 (H1N2) 96%
CY033790.1 A/mallard duck/South Dakota/Sg-00125/2007(H3N2) 96%
PB2 matches
Accession Strain Pct identity
EU301177.2 A/swine/Korea/JNS06/2004(H3N2) 96%
AF455734.1 A/Swine/Minnesota/55551/00 (H1N2) 96%
CY033794.1 A/mallard duck/South Dakota/Sg-00128/2007 96%
PA matches
Accession Strain Pct identity
AF455722.1 A/Swine/Illinois/100084/01 (H1N2) 96%
AF251433.1 A/Swine/Minnesota/593/99 (H3N2) 96%
F251425.1 A/Swine/Iowa/569/99 (H3N2) 96%
HA matches
Accession Strain Pct identity
AF455680.1 A/Swine/Indiana/P12439/00 (H1N2) 95%
AF250124.1 A/Swine/Indiana/9K035/99 (H1N2) 95%
AY038014.1 A/Turkey/MO/24093/99(H1N2) 95%
NP matches
Accession Strain Pct identity
AF251415.2 A/Swine/Iowa/533/99 (H3N2) 96%
EU798854.1 A/swine/Korea/CY05/2007(H3N2) 96%
EU798853.1 A/swine/Korea/CY04/2007(H3N2) 96%
NA matches
Accession Strain Pct identity
AF250366.2 A/Swine/England/195852/92 (H1N1) 94%
CY038009.1 A/swine/England/WVL7/1992(H1N1) 94%
Y038001.1 A/swine/Spain/WVL6/1991(H1N1) 94%
M matches
Accession Strain Pct identity
AY363575.1 A/swine/Hong Kong/5212/99(H3N2) 97%
AY363574.1 A/swine/Hong Kong/5200/99(H3N2) 97%
AY363573.1 A/swine/Hong Kong/5190/99(H3N2) 97%
NS1/NS2  matches
Accession Strain Pct identity
AF153262.1 A/Swine/Minnesota/9088-2/98 (H3N2) 96%
AF153261.1 A/Swine/Texas/4199-2/98 (H3N2) 96%
AF153263.1 A/Swine/Iowa/8548-1/98 96%