Rhiza Labs FluTracker Forum

OK, I made a picture :

http://magictour.free.fr/panflu/h3_tt6c.GIF

some(~300) "old" viruses most from early 2007,
Wisconsin/05 -like were removed.
The index is almost Brisbane/10/2007

it ignores mutations that occur only once in the list, as usual

it just considers changes to the index, 3 or more different
nucleotides at one position are treated as 2 different
(--> some "bias", sigh) to make it easier
------edit----hmm, I should use another color for these

it would be useful to include GISAID sequences here (agreed ?)
but this is forbidden by their terms of use
if you have registered (agreed ?)
and presumably not supported, since you would have to
download all their H3-sequences and build my database.
So, I think it doesn't exist and we can only get this from genbank.

_________________
no patents on genes, publish the GISAID sequences !

here is the mutation table:
http://magictour.free.fr/panflu/H3_TT.L6Z
compressed with gzip

I only had a brief look at it and noted indication for
recombination or lab-error in

A/Cheongju/H471/2008/02/28 + A/Cheongju/H473/2008/04/15
with parents
A/Cheongju/H380/2007/09/19 + A/Cheongju/H383/2007/10/10
and
A/Boston/44/2008/02/19 + many similars



here is an example how "polymorphism jumping"
should look in the pictures:


two ligtning-like black vertical lines A,B such that
some horizontal lines are intersected by A
some by B
and some by both

_________________
no patents on genes, publish the GISAID sequences !

each line is a virus (HA only)
each column is one position in the HA-genetical segment
each black dot is a difference of that virus at that position
from the index (here ~Brisbane-H3N2-flu)
so the vertical black lines show common mutations, "markers"

to the right of each HA a dot is added to show the sampling date,
the more right the more recent (2010) the more left
the older (2007)

the viruses (HA-segments only) = lines are sotted
so to group them by the 20 most common markers.
These are shown at the bottom.
The lengths of the vertical bars in the bottom box give
their ranking in how often that mutation=marker occurred
the nucleotide-position is attached to the left or right
of the top of the bar (or below for 522,540,1548)

green dot = matches with the index at that position
orange dot = not available (partial sequence)

----------------------------

I should mark the antigenically important regions
and the mutations that result in amino-acid changes,
since these are those that are important for the vaccine-match.

mybe I can do it later

as a rule of thumb: positions above 1000 and positions
divisible by 3 are usually not important for the vax.
But they still show how the virus spreads.

another column at the right should indicate the country
or continent in a later version... (those with mutation
at 297 are from Spain)

_________________
no patents on genes, publish the GISAID sequences !

31 H3s from Kenya , June 2010 at genbank.
All are Kenya/Egypt/Iowa - like, but not the new Pennsylvania/02 strain

_________________
no patents on genes, publish the GISAID sequences !

CDC has released a new series of H3N2 isolates at GISAID from around the world. Updated travel log for A108G, one of many newly emerging polymorphisms which you have erased from your analysis.

EPI279991 A/Hong Kong/3685/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279988 A/Mexico/4056/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279979 A/Barbados/170/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279976 A/Chile/8196/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279967 A/Pennsylvania/08/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279964 A/Colombia/6722/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279961 A/Florida/11/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279958 A/Ohio/01/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279955 A/Wyoming/04/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279883 A/Hong Kong/2146/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279881 A/Hong Kong/2121/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279879 A/Hong Kong/2097/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279177 A/CAMBODIA/1/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279174 A/SOUTH AUCKLAND/15/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278815 A/Panama/307149/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278808 A/Alabama/05/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278805 A/Alabama/05/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278790 A/Chile/6927/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278787 A/Chile/6380/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278784 A/Chile/6278/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278781 A/Chile/6096/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278778 A/Chile/5845/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278772 A/Hong Kong/2183/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278769 A/Hong Kong/2152/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278766 A/Dominican Republic/4319/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278763 A/Texas/04/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278760 A/Panama/307149/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI278633 A/Norway/780/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI276906 A/PERTH/10/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI276774 A/Peru/WRAIR1508P/2007 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI276248 A/Alabama/AF2156/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI270344 A/Kansas/06/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI265949 A/Stockholm/1/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI254610 A/Pennsylvania/02/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI254241 A/Jeju/705/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI249466 A/Nagasaki/N109/2007 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI234931 A/Texas/TX-AC22291/2003 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI234923 A/Texas/TX-78105/2003 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI226819 A/TOKYO/10709/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI224925 A/YAMAGATA/74/2006 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI224792 A/TOKYO/51672/2006 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI215091 A/Torino/14/2008 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI175211 A/Massachusetts/13/2008 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI168419 A/Sendai-H/F355/2006 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI161952 A/Xinjing/Tulufan540/2008 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI161160 A/Hong Kong/CUHK50563/2004 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI157961 A/Mexico/2656/2003 (A/H3) segment 4 (HA) 52.8 0.00000
EPI157677 A/Hong Kong/1052/2003 (A/H3) segment 4 (HA) 52.8 0.00000
EPI157570 A/Egypt/900525/2003 (A/H3) segment 4 (HA) 52.8 0.00000
EPI155157 A/Argentina/631/2006 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI154203 A/Texas/05/2008 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI153043 A/Sri Lanka/23/2007 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI146354 A/Argentina/AG-R631-06/2006 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI146091 A/Mexico/MX-2656/2003 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI146010 A/Egypt/EG-2003900525/2003 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145954 A/Arkansas/AR-V-3083/2003 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145777 A/ISHIKAWA/25/2006 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145681 A/YAMANASHI/81/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145680 A/YAMANASHI/80/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145679 A/YAMANASHI/74/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145678 A/YAMANASHI/73/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145677 A/YAMANASHI/61/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145603 A/SHIZUOKA/790/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI145558 A/NAGANO/1248/2005 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI115995 A/Texas/42/2003 (A/H3) segment 4 (HA) 52.8 0.00000
EPI115976 A/Texas/33/2003 (A/H3) segment 4 (HA) 52.8 0.00000
EPI115857 A/Arkansas/1/2003 (A/H3) segment 4 (HA) 52.8 0.00000
EPI96751 A/Memphis/7/1990 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI53030 A/New York/51/2003 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI3039 A/Aichi/198/2006 (A/H3N2) segment 4 (HA) 52.8 0.00000

_________________
www.twitter.com/hniman

New sequences with T264C. Almost all were collected in late July and August. Hong Kong was August 22.

EPI279991 A/Hong Kong/3685/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279988 A/Mexico/4056/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279979 A/Barbados/170/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279976 A/Chile/8196/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279967 A/Pennsylvania/08/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279964 A/Colombia/6722/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279961 A/Florida/11/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279958 A/Ohio/01/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000
EPI279955 A/Wyoming/04/2010 (A/H3N2) segment 4 (HA) 52.8 0.00000

_________________
www.twitter.com/hniman

Has H3N2 picked up D225G and Tamiflu resistance at all?

H3N2 has D225N. Tamiflu resistance is EXTREMELY rare in H3N2 in the past several years.

_________________
www.twitter.com/hniman

Thanks

N2 does not "pick up" mutations from N1

_________________
no patents on genes, publish the GISAID sequences !