Announcement

**gsgs** · September 14, 2009, 06:02 AM

Re: Sequences at Genbank!

critical mutations to watch:

deletions:
bps,segment,last byte of code, last position of deletion, no.,name

98bp,4, 548, 646, 99 >A/Colombia/08/2009/04/25
182bp,3,1229,1411, 646 >A/Luxembourg/43/2009/06/01
3bp,1, 106, 109, 955 >A/Managua/0536N/2009/06/26
1bp,8, 408, 409,1023 >A/Changsha/#05/2009/06/22
1bp,8, 465, 466,1023 >A/Changsha/#05/2009/06/22

insertions:

1bpA,7,933,934, >A/Catalonia/63/2009/04/28

only the Managua-deletion seems relevant, the others are not divisible
by 3 and thus give non-functional proteins , look like lab-errors

Code:

(F:Finkelstein,M:Mamabird,T:Tamiflu-resistance

FM-PB2,A199S GCT=A , ATT=I  : >A/NY/3566/2009/05/20
F-PB2,K702R AAG=K , AAT=N  : >A/Wisconsin/629-D01296/2009/05/03
F-PB2,K702R AAG=K , ACG=T  : >A/New Jersey/02/2009/04/

F-PA,R57Q CGG=R , CAG=Q  : >A/Nebraska/03/2009/04/27
M-PA,T129I ATA=I , TTA=L  : >A/Thailand/CU-B5/2009/06/13
F-PA,A337S GCT=A , ACT=T  : >A/Regensburg/D6/2009//
F-PA,T552S ACT=T , GCT=A  : >A/Canada-MB/RV2023/2009/05/24

HA,D160K AGC=S , GGC=G  : >A/Wisconsin/629-D02064/2009/05/22
HA,D160K AGC=S , GGC=G  : >A/Wisconsin/629-D02276/2009/05/27
HA,F251L GTA=V , ATA=I  : >A/Irkutsk/02/2009//
HA,F251L GTA=V , ATA=I  : >A/Moscow/02/2009/05/26
HA,F251L GTA=V , ATA=I  : >A/Moscow/03/2009/05/26
HA,F251L GTA=V , ATA=I  : >A/Moscow/IIV02/2009/05/26
HA,F251L GTA=V , ATA=I  : >A/Taiwan/T1821/2009/05/30
HA,Y258F ACA=T , ATA=I  : >A/Ancona/02/2009/06/11
HA,Y258F ACA=T , ATA=I  : >A/Shiga/1/2009/05/22
HA,Y258F ACA=T , ATA=I  : >A/Stockholm/29/2009/05/08
HA,Y258F ACA=T , ATA=I  : >A/Thailand/CU-H9/2009/06/17

FM-NP,G16D GGT=G , GAT=D  : >A/Canada-MB/RV2018/2009/05/29
FM-NP,G16D GGT=G , GAT=D  : >A/Texas/15/2009/04/15
M-NP,R100V GTA=V , ATA=I  : >A/Akita/1/2009/06/11
...385 in total with R100V = G298A(5) one of the 11 Cancun-markers
M-NP,R100V GTA=V , ATA=I  : >A/Zhejiang/2/2009/05/31
FM-NP,L283P CTT=L , CCT=P  : >A/South Dakota/05/2009/04/30

T-NA,E119P GAA=E , RAA=P  : >A/NY/13/2009/04/25
T-NA,H274Y TAT=Y , CAT=H  : >A/Mexico City/47/2009/05/03
T-NA,H275Y CAC=H , TAC=Y  : >A/Denmark/528/2009/06/09
T-NA,H275Y CAC=H , TAC=Y  : >A/HK/2369/2009/06/11
T-NA,H275Y CAC=H , TAC=Y  : >A/Hunan/SWL3/2009/06/13
T-NA,H275Y CAC=H , TAC=Y  : >A/Osaka/180/2009//
T-NA,H275Y CAC=H , TAC=Y  : >A/Washington/28/2009/07/14
T-NA,H275Y CAC=H , TAC=Y  : >A/Washington/29/2009/07/28
T-NA,H275Y CAC=H , TAC=Y  : >A/Yamaguchi/22/2009//

M2,C55F TTT=F , TCT=S  : >A/Sw/Alberta/OTH-33-2/2009/05/03
M2,G34E GGG=G , GAG=E  : >A/Sw/Alberta/OTH-33-23/2009/05/03
M-M2,S20N AGC=S , AAC=N  : >A/Wisconsin/629-D00978/2009/05/14
M2,V27A GTC=V , GCC=A  : >A/Catalonia/508/2009/07/03

F-M1,V115I GTG=V , ATG=M  : >A/Beijing/01/2009/05/15
F-M1,V115I GTG=V , ATG=M  : >A/Beijing/01/2009/05/16
M1,I168T ACC=T , AAC=N  : >A/Catalonia/398/2009/06/29
M1,I168T ACC=T , AAC=N  : >A/Catalonia/405/2009/06/30
M1,I168T ACC=T , AAC=N  : >A/Catalonia/412/2009/07/01
M1,N207S AAT=N , AAK=-  : >A/Wash.DC/03/2009/04/27
M1,N207S AAT=N , GAT=D  : >A/Sw/Alberta/OTH-33-3/2009/05/03
M1,N224S AGC=S , AAC=N  : >A/Catalonia/154/2009/05/02

NS1,T92E GAC=D , GGC=G  : >A/NY/3184/2009/04/28
NS1,T92E GAC=D , GGC=G  : >A/NY/3223/2009//

avian_position_human markers

PB2:A44S,M64T,A199S,T271A,L475M,D567N,A588I,E627K, A674T,K702R
PA:P28L,D55N,R57Q,V100A,S225C,L268I,A337S,A404S,S4 09N,T552S
NP:G16D,I61L,L283P,R305K,F313Y,Q357K
M1:V115I,T121A,T137A
NS1:I81M,P215T,E227R

keyword Finkelstein, diary 1600

newfluwiki2.com

http://www.newfluwiki2.com/showDiary.do?diaryId=1600

This domain may be for sale!

PB2:Q151H,R324S,Y432H
PB1:G370A,S466F,V646M,F665S
PA:L581M,P702L
HA:I7V,M8L,N215Y,V351A
NP:A29V,K192E,D202N,T222M,I373T,Y375D
NA:G95S,E96G,H100Y,L123S,C334S
M1:R222H
NS1:T104M,I134F
M2:
NS2:E89A
Alberta pig has these

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

keywords: mamabird ,FT 228987

What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping? - FluTrackers News and Information

http://www.flutrackers.com/forum/showthread.php?p=228987

PB2:A199S
PB1:N(T)375S
PB1-F2:P(R)48Q
PA:T129I,S409N
HA:E190D,S221P,F251L,Y258F
NP:V33I,R100V,Q357K
M1:K27R,I168T,N224S
NS2:F55L

PB2:L(F)475M,D567N,E627K
PB1:P28L,D55N,I(V)100A,T552S
NP:G16D,L283P,F313Y
MP:I15V,K101R,A166V,N207S
M2:E16G,S20N
NA:H274Y,N294S

joined list:

PB2:A44S,M64T,Q151H,A199S,T271A,R324S,Y432H,L475M, D567N,A588I,E627K,A674T,K702R
PB1:P28L,D55N,I100A,G370A,N375S,S466F,T552S,V646M, F665S
PB1-F2:P48Q
PA:P28L,D55N,R57Q,V100A,T129I,S225C,L268I,A337S,A4 04S,S409N,T552S,L581M,P702L
HA:I7V,M8L,E190D,N215Y,S221P,F251L,Y258F,V351A
NP:G16D,A29V,V33I,I61L,R100V,K192E,D202N,T222M,L28 3P,R305K,F313Y,Q357K,I373T,Y375D
NA:G95S,E96G,H100Y,L123S,H274Y,H275Y,N294S,N295S,C 334S
M2:E16G,S20N
M1:I15V,K27R,K101R,V115I,T121A,T137A,A166V,I168T,N 207S,R222H,N224S
NS1:I81M,T104M,I134F,P215T,E227R
NS2:F55L,E89A

A1741C(3),C1118T(5)
A0588G(3),A1741C(3),C0022A(4),C1118T(5),A0283G(6), C0738A(8)
G0799A(1),A1741C(3),G0687T(4),A0877G(4),G1173A(4), C1118T(5)
A1577G(1),A1741C(3),C1118T(5)
G1308A(1),T0450C(2),A0561C(3),G1173A(4),G1563A(4), G0522A(7),A0775G(8)
A1218G(1),G1986T(3),A1044G(6)
G0546A(1)
G0546A(1),A2030G(1),A0300G(2),A1058G(2),A0008G(3), C0145A(4),C0132T(5)
G0298A(5),G1143A(5),G0316A(6)
T1711C(1),G1945A(1),G0636A(2),T2000C(2),G0936A(3), G0298A(5),G1143A(5),G0316A(6),G0456A(8)
C1408T(4),G0298A(5),G1143A(5),G0316A(6),A0742G(6)
G2163A(1),T0658A(4),C1408T(4),G0298A(5),G1143A(5), G1248A(5),G0316A(6),A0742G(6),G0492A(7),G0600A(7), A0367G(8)

what else to watch

T128(2),A129(2),A130(2) = end-codon for PB1-F2

I223S(6) possibly linked to H275Y(6)
P453S(1) possibly linked to H275Y(6)

deletions,insertions

**vinny** · September 14, 2009, 06:12 AM

Re: Sequences at Genbank!

Are there any signs of the virus becoming more virulent,thanks.

**mixin** · September 14, 2009, 06:59 AM

Re: Sequences at Genbank!

How important is I223V in neuraminidase, which was also found in the sequences from the 2 Tamiflu resistant N. Carolina campers ?

**Mamabird** · September 14, 2009, 08:21 AM

Re: Sequences at Genbank!

Originally posted by mixin View Post

How important is I223V in neuraminidase, which was also found in the sequences from the 2 Tamiflu resistant N. Carolina campers ?

Haven't seen the NC sequences as yet, but the mutation noted above is not common.

Links to an authoritative source?

**mixin** · September 14, 2009, 08:28 AM

Re: Sequences at Genbank!

Mamabird: http://www.cdc.gov/mmwr/preview/mmwr...cid=mm5835a1_x

On August 14 and August 19, CDC detected the H275Y mutation (N1 numbering) in neuraminidase from both specimens by pyrosequencing (3,4). The H275Y mutation is associated with resistance to oseltamivir; zanamivir susceptibility is retained. A second mutation (I223V) in neuraminidase also was detected in both specimens.

**Mamabird** · September 14, 2009, 08:59 AM

Re: Sequences at Genbank!

Thanks, M. I read right passed that earlier.

A quick BLAST shows that this mutation is uncommon. Several hits to H5N1 infected chickens, and a hit to an H1N1 infected pig.

Some will tell you that this is just coincidence. But I keep seeing numerous ties of this Swine Flu to the Far East, including H5N1 sequences.

Troubling.

**AlaskaDenise** · September 14, 2009, 11:58 AM

Re: Sequences at Genbank!

How about it's connections to H9N2?

There are 31 sequences for H9N2 in Asian swine.

.

**Mamabird** · September 14, 2009, 12:30 PM

Re: Sequences at Genbank!

Originally posted by AlaskaDenise View Post

How about it's connections to H9N2?

There are 31 sequences for H9N2 in Asian swine.

.

I did not see the I223V mutation in H9 isolates with the initial BLAST, but certainly other Swine Flu mutations trace back to H9N2 isolates in the Far East.

**Mamabird** · September 15, 2009, 08:23 AM

Re: Sequences at Genbank!

Some partial HA and NA sequences posted to GISAID from Santiago, Chile.

All appear to be GS: Cancun (CDC variant iv) with collection dates from mid-June to early July.

**gsgs** · September 16, 2009, 10:04 AM

Re: Sequences at Genbank!

> Once it made the jump into people, the genes changed quickly.
> "They seemed to be evolving at something like 1.5 times the
> rate they evolved in swine," he [Worobey] said.

reuters.com

http://www.reuters.com/article/scienceNews/idUSTRE58E51G20090915?feedType=RSS&feedName=scienceNews&sp=true

and it's now back to normal mutation rates ?
It mutated 1.5 times more ? or it started earlier ?

Maybe it went from pig to human earlier (Dec.2008) and thus
had more time for mutating.
I don't see how this virus was in pics for decade(s).
More likely IMO that it formed (=reassorted) recently and
went to humans shortly afterwards

**Mamabird** · September 16, 2009, 03:16 PM

Re: Sequences at Genbank!

Nine (9) new HA sequences from Sao Paulo, collection dates from mid-June to early August.

Three are older CDC variant iii (GS: pre-Cancun) similar to Sao Paulo/43812.

The remainder are CDC variant iv (GS: Cancun).

A strange D225N change in two isolates - possibly lab error.

**AlaskaDenise** · September 16, 2009, 04:40 PM

Re: Sequences at Genbank!

Originally posted by Mamabird View Post

.........
A strange D225N change in two isolates - possibly lab error.

Compare to:

ACA33732 [Influenza A virus (A/Texas/70/2007(H1N1))]
ACH69227 [Influenza A virus (A/Nevada/AF1946/2008(H1N1))]

They have the same D225N change.

.

**Mamabird** · September 16, 2009, 06:54 PM

Re: Sequences at Genbank!

Originally posted by AlaskaDenise View Post

Compare to:

ACA33732 [Influenza A virus (A/Texas/70/2007(H1N1))]
ACH69227 [Influenza A virus (A/Nevada/AF1946/2008(H1N1))]

They have the same D225N change.

.

Yes, and again, probably some type of lab error. Very rare.

The "D" is the human marker at 225. The "E" is the avian marker. And the "G" is considered the swine marker. I have no idea what an "N" signifies, except "Whoops".

**AlaskaDenise** · September 16, 2009, 08:00 PM

Re: Sequences at Genbank!

Maybe it got donated from a pika.

Since the US isn't testing them - they may have donated a surprise gene to the mix.

.

**gsgs** · September 16, 2009, 10:10 PM

Re: Sequences at Genbank!

G930T(4) = Q310H(amino)
A4G(4)=K2E(amino)

****** HAs from South America:

Code:

                                              0000001  
                                              0167794  
                                              0451130  
                                              4585608  
-codon-position-------------------------------11112 1  
---Index--------------------------------------ACTGAGC  
 20 >A/Cancun-NY/Index/2009/04/15             ..A...T  
  7 >A/Sao Paulo/54392/2009/08/01             ..A...T  
  8 >A/Santiago/3827/2009/07/07               --A...-  
  9 >A/Sao Paulo/2056/2009/05/20              ..A...T  
 10 >A/Sao Paulo/53206/2009/07/19             ..A.G.T  
 11 >A/Sao Paulo/53225/2009/08/01             ..A.G.T  
 12 >A/Sao Paulo/2261/2009/05/29              ..A...T  
 13 >A/Sao Paulo/55312/2009/08/05             ..A...T  
 14 >A/Distrito Federal/2611/2009/06/05       ..A...T  
 15 >A/Sao Paulo/55115/2009/08/05             ..A...T  
 16 >A/Sao Paulo/2193/2009/05/29              ..A...T  
 17 >A/Bogota/0466N/2009/06/25                ..A...T  
 18 >A/Sao Paulo/2275/2009/05/29              ..A...T  
 19 >A/Sao Paulo/53845/2009/08/02             ..AA..T  
 21 >A/Puerto Montt/Bio87/2009/06/19          ..A...T  
 22 >A/Chile/8886/2009/05/18                  ..A...-  
 23 >A/Santiago/2009/2009/06/18               -.A...-  
 24 >A/Chile/8947/2009/05/17                  ..A...-  
 25 >A/Castro/JXP/2009/06/11                  ..A...T  
 26 >A/Tk/Chile/28317-6504-3/2009/08/17       ..A...T  
 27 >A/Chile/8949/2009/05/18                  ..A...-  
 28 >A/Mato Grosso/2329/2009/05/28            ..A...T  
 29 >A/Santiago/3221/2009/06/30               -.A...-  

 36 >A/Sao Paulo/1454/2009/04/29              ......T  
  5 >A/Sao Paulo/2303/2009/06/01              ......T  
 31 >A/Sao Paulo/53823/2009/08/01             G....TT  
 32 >A/Sao Paulo/57831/2009/08/09             G....TT  
 33 >A/Sao Paulo/53838/2009/08/01             G..A.TT  
 34 >A/Sao Paulo/2233/2009/05/27              G....TT  
 35 >A/Sao Paulo/43812/2009/07/03             .....TT  

  6 >A/Chile/9113/2009/05/19                  .A....-  
  2 >A/Colombia/08/2009/04/25                 -A....-  
 30 >A/Colombia/450/2009/05/06                -.-----  
  1 >A/Colombia/450/2009//                    --....-  
  3 >A/Bogota/176/2009/04/27                  --....-  
  4 >A/Bogota/224/2009/04/25                  --....-  
 37 >A/Colombia/213/2009/04/30                --....-  
 38 >A/******/index/2009/02/01                .......

Announcement

Sequences at Genbank!

Comment

Comment

Comment

Comment

Comment

Comment

Comment

Comment

Comment

Comment

Comment

Comment

Comment

Comment

Comment