Sequences at Genbank!

[gsgs]

Re: Sequences at Genbank!

(A/Israel/276/2009(H1N1))CY041965,CY041966,CY041967,CY041968,CY0 41969,CY041970,CY041971,CY041972

clickable here:

http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html

alternatively I can send it or post or PM or upload if there is interest

[pflu]

Re: Sequences at Genbank!

(A/Israel/276/2009(H1N1))CY041965,CY041966,CY041967,CY041968,CY0 41969,CY041970,CY041971,CY041972

clickable here:

http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html

alternatively I can send it or post or PM or upload if there is interest

I see them now, thanks!

I tried to search GenBank nucleotides again and still no go, I guess they can not be queried yet.

[pflu]

Re: Sequences at Genbank!

It is mutated quite a bit like A/Stockholm/28/2009.

Looks like Cancun to me, not sure how it matches to your Cancun though.

Very interesting new sequence. Must be first Israel documented case, I'll dig details, let me know what you find as well.

[HenryN]

Re: Sequences at Genbank!

I see them now, thanks!

I tried to search GenBank nucleotides again and still no go, I guess they can not be queried yet.

Sequences on the H1N1 front page usually take 1-2 days to get into the searchable database (sometimes they are in the larger database prior to the flu database).

[pflu]

Re: Sequences at Genbank!

Sequences on the H1N1 front page usually take 1-2 days to get into the searchable database (sometimes they are in the larger database prior to the flu database).

Thanks,

I thought I was going crazy because I could not find it. Makes sense now.

[gsgs]

Re: Sequences at Genbank!

the missing two segments of Arizona/01(April,22) had been released, thanks Arizona !

besides
G546A(1),(the main marker of the airplane-Newberry-Clade-I strain)
G251A(5),
C393T(6)

it has A1230G(3),A1236C(3) , just as New Jersey/04(April?), which however is clade-D

so, just one of the known markers {G546A(1)} and 5 mutations in total.
Which puts it close to the origin, but not as much as 4115 or 4487.


--------------
here they claim, Nebraska/02 were from April, 1

http://www.ncbi.nlm.nih.gov/nuccore/238015587?report=genbank

but other records from that sequence say just "April"

[Mamabird]

Re: Sequences at Genbank!

Look for some isolates from Chile shortly in GenBank. Posted to GISAID this morning. Several variants, with one (2407) showing PB1 from SC/09 and England. An isolate from Barbados (5211) has similar characteristic, not unlike Dominican Rep.

[HenryN]

Re: Sequences at Genbank!

Look for some isolates from Chile shortly in GenBank. Posted to GISAID this morning. Several variants, with one (2407) showing PB1 from SC/09 and England. An isolate from Barbados (5211) has similar characteristic, not unlike Dominican Rep.

PB1 travel log

gb|GQ385298.1| Influenza A virus (A/Toronto/0462/2009(H1N1)) ... 36.2 0.73
emb|FN401580.1| Influenza A virus (A/Regensburg/D6/2009(H1N1)... 36.2 0.73
gb|GQ365656.1| Influenza A virus (A/Bayern/62/2009(H1N1)) seg... 36.2 0.73
gb|CY041981.1| Influenza A virus (A/WRAIR/0573N/2009(H1N1)) s... 36.2 0.73
gb|CY041966.1| Influenza A virus (A/Israel/276/2009(H1N1)) se... 36.2 0.73
gb|CY041958.1| Influenza A virus (A/Santo Domingo/572N/2009(H... 36.2 0.73
gb|GQ329098.1| Influenza A virus (A/Paris/2709/2009(H1N1)) se... 36.2 0.73
gb|CY041603.1| Influenza A virus (A/New York/3177/2009(H1N1))... 36.2 0.73
gb|GQ232091.1| Influenza A virus (A/Beijing/4/2009(H1N1)) seg... 36.2 0.73
gb|CY041152.1| Influenza A virus (A/New York/3181/2009(H1N1))... 36.2 0.73
gb|GQ225371.1| Influenza A virus (A/Beijing/01/2009(H1N1)) se... 36.2 0.73
gb|GQ222425.1| Influenza A virus (A/Paris/2592/2009(H1N1)) se... 36.2 0.73
gb|GQ222421.1| Influenza A virus (A/Paris/2580/2009(H1N1)) se... 36.2 0.73
gb|CY040878.1| Influenza A virus (A/Norway/1177/2009(H1N1)) s... 36.2 0.73
gb|CY040871.1| Influenza A virus (A/Norway/1168/2009(H1N1)) s... 36.2 0.73
gb|GQ183623.1| Influenza A virus (A/Beijing/01/2009(H1N1)) se... 36.2 0.73
gb|GQ166227.1| Influenza A virus (A/Sichuan/1/2009(H1N1)) seg... 36.2 0.73
gb|GQ169306.1| Influenza A virus (A/Narita/1/2009(H1N1)) segm... 36.2 0.73
gb|GQ168854.1| Influenza A virus (A/South Carolina/09/2009(H1... 36.2 0.73
gb|GQ166655.1| Influenza A virus (A/England/195/2009(H1N1)) s... 36.2 0.73
gb|CY038244.1| Influenza A virus (A/ruddy turnstone/New Jerse... 36.2 0.73

[Mamabird]

Re: Sequences at Genbank!

Also check out Italy/172 and Catalonia/378. HA/NA comparable to Hong Kong/2369 except for the Tamiflu resistance marker.

Notice the P300S in HA - new marker not found in other isolates.

[gsgs]

Re: Sequences at Genbank!

more sequences from Mexico.
Seems that InDRE is redoing the early work.
No new candidates close to the origin

13551 and 13555 are the Mexico-City ("pre-Cancun",Clade L) substrain,
the other mutations are individual, so they are original Mexico (clade A)
with some mutations not seen elsewhere

                                      00000011111 0000011111111122 0000011112 00000111 00001 0000 0 00 
                                      22456613447 0388922577999901 1688944460 06778455 00241 1237 8 35 
                                      48040429054 8878515002012313 9028504907 06119027 02964 0514 8 32 
                                      52269700920 1752721618969261 3137713610 65696839 69853 7762 3 09 
-codon-position-----------------------2    2112     2       12   1 1112   22   2222121  21   2211 1  1 
---Index------------------------------AGCGGGCCGAT TTAAGTGGAAACTGTA TACGGGGACC GGAACCAA GAGTG ACGA G GG 
  1 >A/Mexico/InDRE13494/2009/04/29   ..........C ............AACC C..AA.A..T ....T... ..... .... . .. 
  2 >A/Mexico/InDRE13551/2009/04/28   .........G. .......A...A.... .....A.G.. .....T.. ..A.A ..AG . .A 
  3 >A/Mexico/InDRE13555/2009/04/29   ..T........ ...GAC....G..... .......... .....T.. T.A.A ..AG . .. 
  4 >A/Mexico/InDRE4115/2009//        G.......... ................ ..A....... ........ ..... .... . .. 
  5 >A/Mexico/InDRE4487/2009/04/14    G.......... ................ ..A....... ...G.... ..... .... . .. 
  6 >A/Mexico/InDRE4114/2009//        .A.....A... ........G....... .......... ..G....T ..... G... A .. 
  7 >A/Mexico/InDRE13547/2009/04/27   ....A...... CC.............. .......... AA....G. .TAC. .T.. . A. 
  8 >A/Mexico/InDRE13495/2009/04/29   ...A.AT.A.. ..G...A..G...... .G......T. ........ ..... .... . .. 
  9 >A/******/index/2009-02-01        ........... ................ .......... ........ ..... .... . ..

[gsgs]

Re: Sequences at Genbank!

mutation pixels of ****** sequences,
only viruses with >6500 available nucleotides are considered
each row is a virus, each column is a nucleotide-position,
each pixel is a difference to the index.
Only positions are listed where at least 2 viruses differ from the index ("markers")

so horizontal bars represent markers.E.g. you can clearly see the
11 markers of the Cancun1/St.Francis/New-York strain




I'm trying to make it larger , resize 2fold , include viruses with
>2600 nucleotides available , regrouping a bit ...

http://magictour.free.fr/panflu/mxab3b.GIF

http://magictour.free.fr/panflu/mxab3c.GIF

black: different from index
grey: matching the index
white: not available

A :early Mex
B :Northern
C :swine
D :Jersey
E :Hamburg
F :Texas
G :early US
H :airplane
I :England
J :Korea
K :Japan
L :pre-Cancun
M :Cancun

L1: Shandong,Canada

[HenryN]

Re: Sequences at Genbank!

Phylogenetic analysis provides a much cleaner picture of which isolates evolved from which isolates, as well as the number of changes in each gene segment.

[Mamabird]

Re: Sequences at Genbank!

About a dozen new full sequences from England posted today at GISAID. Should hit GenBank tomorrow perhaps.

Most are similar to England/195, but several variations in the mix as well. Didn't see anything alarming, so the problems in the UK can not be attributed to a fundamental change in the virus. It is the same variants we have all seen many times before.

[HenryN]

Re: Sequences at Genbank!

About a dozen new full sequences from England posted today at GISAID. Should hit GenBank tomorrow perhaps.

Most are similar to England/195, but several variations in the mix as well. Didn't see anything alarming, so the problems in the UK can not be attributed to a fundamental change in the virus. It is the same variants we have all seen many times before.

All of the isolates were from late April, early May and are likely travelers.

These sequences may or may not have anything to do with the current UK outbreak (and I wouldn't guarantee that they show up at GenBank).

[Mamabird]

Re: Sequences at Genbank!

Additional full sequences from Canada and Mexico posted to GISAID today.

Looks like the Canadians passed the virus on to Spain (Catalonia). Again, at first blush, no changes of significance in the virus showing up in these sequences.