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List of Mutations

M

mixin

Well-known member
I'm searching for the amino acid, nucleotide coding and what each one does and what segment it's found in. Any help with this would be much appreciated.

Phenotype Marker from GenBank (** Panflu common markers)

Segments:
PB2(1) PB1(2) PA(3) HA(4) NP(5) NA(6) MP(7) NS(8)

Adamatane Resistance
M2: 26F
M2: 27A
M2: 30T
M2: S31N **
M2: 34E

Oseltamivir Resistance
NA: H275Y (C823T)

Enhanced Transmission
M2: A16G
M2: C55F **
NP: L136M
PA: S409N **
PB2: A199S
PB2: A661T
PB2: K702R
PB2: V667I

Increased Virulence
PB2: D701N
PB2: E627K

Severity
NS1:T92E

Polybasic HA Cleavage (gs: only for H5 and H7)
RERRRKKR

Other H1N1 mutations we are watching:
PB2: K340N (A1020T)
HA: D225N (715A), D225G (716G), D225E (717A or G)
HA: M230 730, 730, 732 ATG; M230I = AT(t,c,a?)

When cross-linked and possibly associated with mutations at 225
HA: syn413K (A1281G)
NA: syn407V (T1221C)

Segments:
PB2(1) PB1(2) PA(3) HA(4) NP(5) NA(6) MP(7) NS(8)

What group for these?: A193T, S193F, (HA in H3N2 ?)

PB2: A199S, A661T, E627K, V667I, D701N, K702R,

PB1:

PA:

HA: D225N, D225G, I324V

NP:

NA: E119V, R152K, H274Y, R292K

MP:

NS:

Further explanation about resistance: the amino acid termed E276 must rotate and bond with R224 to form a pocket for the side chain of Oseltamivir. The mutations R292K, N294S, and H274Y inhibit this rotation and prevent the pocket from forming, resulting in resistance to Oseltamivir. An E119V mutation also interferes only with oseltamivir binding, possibly because a water molecule can fit between oseltamivir and valine at the active site but cannot insinuate itself between zanamivir and valine at residue 119.
http://priory.com/pharmacy/oseltamivir_tamiflu.htm
 
Re: List of Mutations

Here are the amino acids:

A: GCT, GCC, GCA, GCG (Alanine,Ala)
R: CGT, CGC, CGA, CGG, AGA, AGG (Arginine,Arg)
N: AAT, AAC (Asparagine,Asn)
D: GAT, GAC (Aspartic Acid,Asp)
C: TGT, TGC (Cysteine,Cys)
E: GAA,GAG (GlutamicAcid,Glu)
Q: CAA,CAG (Glutamine,Gln)
G: GGT, GGC, GGA, GGG (Glycine,Gly)
H: CAT, CAC (Histidine,His)
I: ATT, ATC, ATA (Isoleucine,Ile)
L: TTA, TTG, CTT, CTC, CTA, CTG (Leucine,Leu)
K: AAA, AAG (Lysine,Lys)
M: ATG (Methionine,Met)
F: TTT, TTC (Phenylalanine,Phe)
P: CCT, CCC, CCA, CCG (Proline,Pro)
S: TCT, TCC, TCA, TCG, AGT, AGC (Serine,Ser)
T: ACT, ACC, ACA, ACG (Threonine,Thr)
W: TGG (Tryptophan,Trp)
Y: TAT, TAC (Tyrosine,Tyr)
V: GTT, GTC, GTA, GTG (Valine,Val)

STOP,Sto,}: TAG, TGA, TAA
hydrophobic: GAVLIMFWP
hydrophilic: STCYNQ,DE,KRH

ATG, ATT, ATC, ATA, AAA, AAG, AAT, AAC, ACT, ACC, ACA, ACG, AGA, AGG, AGT, AGC
CAA, CAG, CAT, CAC, CCT, CCC, CCA, CCG, CGT, CGC, CGA, CGG, CTT, CTC, CTA, CTG
GCT, GCC, GCA, GCG, GAT, GAC, GAA, GAG, GGT, GGC, GGA, GGG, GTT, GTC, GTA, GTG
TAT, TAC, TGT, TGC, TTA, TTG, TTT, TTC, TCT, TCC, TCA, TCG, TGG, TAG, TGA, TAA
 
Re: List of Mutations

glycosylation positions:
21, 33, 63, 81, 94, 129, 158, 163, 271, 289, 154

receptor binding sites
98,134-138,153-155,184-196,216-230 (H3)

Here's the list of mutations Gs made; it can also be updated.

PB2(1) PB1(2) PA(3) HA(4) NP(5) NA(6) MP(7) NS(8)

PB2: G0546A, G0799A, A1218G, G1308A, A1577G, T1711C, G1945A, A2030G, G2163A
PB1: A0300G, T0450C, G0636A, A1058G, T2000C
PA: A0008G, A0561C, A0588G, G0936A, A1741C, G1986T,
HA: C0022A, C0145A, T0658A, G0687T, A0877G, G1173A, C1408T, G1563A
NP: C0132T, G0298A, C1118T, G1143A, G1248A,
NA: A0283G, G0316A, A0742G, A1044G
MP: G0492A, G0522A, G0600A,
NS: A0367G, G0658A, C0738A, A0775G

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

their S224P in PA is my T670C(3)
M582L in PA is A1741C(3)
S91P in HA is T298C(4)
S206T in HA is T658A(4)
V323I in HA is G1012A(4)
V100I in NP is G298A(5)
T373I in NP is C1118T(5)
V106I in NA is G316A(6)
N247D in NA is A742G(6)


so their variant i is my "early Mex"
their variant ii is my "Northern"
their varint iii is my "pre-Cancun"
their variant iv is my "Cancun"
their variant v is my "early US" (they don't include Texas/15 here)
 
Re: List of Mutations

As provided by Mamabird here:

Provided in 1, below are the problem amino acids associated with the currently circulating Swine Flu. These are generally found in every pandemic virus and most seasonal flu viruses, and some relate to sensitivity to antivirals, etc. All the available Swine Flu virus gene sequences have these human/problem characteristics.

1. PB2: A199S; PB1 N(T)375S; PB1-F2 P(R)48Q; PA T129I and S409N; HA E190D, S221P, F251L and Y258F; NP V33I, R100V and Q357K; MP K27R, I168T and N224S; M2 none; NS2 F55L; NA none.

Provided in 2, below are those amino acids that this bug has not yet obtained, but if obtained, could be problematic. Some are more important that others. None of the Swine Flu viruses have these characteristics as far as I know, but we should all keep an eye out for them>

2. PB2 L(F)475M, D567N and E627K; PB1 none; PB1-F2 P28L, D55N, I(V)100A and T552S; HA multi-basic amino acids at the clevage site (usually associated only with poultry infections); NP G16D, L283P and F313Y; MP I15V, K101R, A166V and N207S; M2 E16G and S20N; NS none; NS2 none; NA H274Y and N294S.

In other words, the Swine Flu virus has about half of the problem amino acids already in its tool box. The only other viruses even close to this are some H9N2 viruses circulating widely in Hong Kong and H7N7 in the Netherlands. As to the wild type avian viruses, only the North American variety come close.

Take away: This is a problem virus that bears watching closely. Reassortment with seasonal flu or H5N1 could be interesting.

.
 
Re: List of Mutations

the 1918-virus had 46=8+7+10+9+7+5 amino-acid mutations in the
inner 6 segments away rom the bird-index.

(to compare: 1930 swine had 116,1933 human had 115,1977 swine had 180,
pan1957 had 123,pan1968 had 147,H3N2(2007)had 249,H1N1(2007) had 194,
US-swine triple-reassortant(1998) ha 107=12+15+10+26+10+34
pan2009 had 147=17+23+17+28+16+46, (+5+8+7+2+--+--+12 since triple-)

here are those 46 with a count, how often they were maintained
in my database of 52 viruses, mainly early human and swine:

A199S(1),50
C241Y(3),49
D209N(8),48
D55N(3),44
D567N(1),41
E227K(8),2
E268G(7),44
E382D(3),47
E383D(2),46
E627K(1),50
E70K(8),43
F313Y(5),41
G16D(5),41
G266E(7),51
I178V(8),27
I322V(3),38
I539V(1),11
K270R(7),50
K312R(3),40
K54R(2),36
K702R(1),42
K716R(3),41
L136M(5),44
L234I(7),2
L283P(5),38
L475M(1),50
L576I(2),47
N375S(2),31
N473S(5),28
P28L(3),37
Q330K(7),38
Q357K(5),39
R100I(5),10
S272N(7),49
S297N(8),49
S400L(3),41
S654N(2),38
T108A(1),2
T121A(7),50
T552S(3),41
V100A(3),41
V105M(5),41
V114I(1),46
V33I(5),48
V473L(2),47
V645M(2),31


seasonal H1N1 from 2007 still had 31 of these 46 mutations from 1918,
******=pan2009 has 10 of these 46 mutations:

N375S(2),E382D(3),V33I(5),V105M(5),Q357K(5),G266E(7),K270R(7)
E70K(8),I178V(8),D209N(8)

N375S(2),E382D(3),G266E(7),K270R(7) are coincidence, since these
segments do not come from 1918
 
Re: List of Mutations

seasonal H1N1 from 2007 still had 31 of these 46 mutations from 1918,
******=pan2009 has 10 of these 46 mutations:

N375S(2),E382D(3),V33I(5),V105M(5),Q357K(5),G266E( 7),K270R(7)
E70K(8),I178V(8),D209N(8)
Click to expand...

That's amazing that those mutations survived for over 100 years (if I'm understanding correctly). Can we assume they are important ones for survival of the flu?

N375S(2),E382D(3),G266E(7),K270R(7) are coincidence, since these segments do not come from 1918
Click to expand...

1918 had those mutations but they came from somewhere else? Where did they come from then?
 
Re: List of Mutations

some mutations will survive statistically.
31 from 46 is a lot, fewer in the classical swine-lineage (22 until 1977),
but the swine-viruses do not descend so directly from 1918-flu.

Some mutations were acquired by pan1918 and pan2009(tripl1998)
independently

new introductions into mammals had these distances from the bird-
index in the inner segments:

1918:8+7+10+9+7+5 human,North America
1957:-+5+-+-+-+- human,China
1968:-+4+-+-+-+- human,China
1979:8+5+14+5+3+9 swine,Europe
1998:12+-+10+-+-+- swine,USA
1963:8+12+14+15+1+10 equine,Miami
1956:54+45+42+30+36+69 equine,Prague
 
Re: List of Mutations

pan1957,segment 2:V114I(000100),E172I(000000),N375S(0,0,17,36,29,0),A401V(000100),R430K(0,0,0,14,2,0)
pan1968,segment 2:K121R(010000),L212V(000000),R327K(000200),N375S(0,0,17,36,29,0)

in parentheses, how often that mutation occurs in my database
of 245 avian segment2s collected before 1985 in continents
(Africa:3,Asia:19,Europe:33,North-America:158,Ozeania:32,South-America:0)

N375S is in all 3 pans
 
Re: List of Mutations

before the "invention" of the bird-index, we didn't know
that these were "mutations" , it could have been the standard

the equine(H3N8) virus from 1963 also had N375S, but not the European Swine(H1N1) from ~1978

sw78(2):N105T,I517V,R584H,A587T,N642S
eq63(2):G154D,A157S,D175N,K214R,R215K,S261R,N275S,E383D,R386K,K429R,R430K,N642S


I think 375S is still in seasonal H3N2 while H1N1 mutated back to 375N in the 40s or 50s
 
Re: List of Mutations

From a recent USAF update, reporting on 45 samples they sequenced:
http://www.flutrackers.com/forum/showthread.php?t=139400

All 45 specimens differ from the vaccine strain by an amino acid change at position 83 (proline to serine); 44 of 45 possess additional changes at positions 203 (serine to threonine) and 321 (isoleucine to valine).
Parallel Non-synonymous mutations have been recorded from the ancestral aspartic acid at position 86 (aspartic acid to asparagine/glycine) and at position 128 (serine to proline/leucine).
Click to expand...

Is there any way to know what segment a mutation is in?
 
Re: List of Mutations

vaccine is (almost) always HA

CA/07 had two mutations, they should have chosen another strain
for vaccine. But the mutations are probably not so important.

So, all "normal" strains don't have these mutations, thus differ from
the vaccine strain.

The middle "mutation" (203) is S220T(H1)=T658A(4) ,
one of the 11 Cancun-markers
 
Re: List of Mutations

I just read today from that report:
NYMC X181A A/California/07/2009: refers to a recombinant strain that four of five manufacturers are using for vaccine that contains three mutations not present in the A/California/7/2009/pH1N1 reference strain
Click to expand...
I didn't realize that all the vax was from the same strain except for MedImmune's.

None of the 44 sequences are public (at least I can't find them).

Tell me again the math that takes us from "(203) is S220T(H1)=T658A(4)"?
 
Re: List of Mutations

I can't figure out the enumeration yet
what I have so far:

Code: 
kalign:
-------
>A/Udorn/307/72(H3N2)
MKTI-IALSYIFCLVLGQDFPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILDGI------DCTLIDALLGDPHCDGFQN-ETWDLFVERSKA-FSNCYPYDVPDYASLRSLVASSGTLE---FISEGFTWTGVTQNGG-SNACKRGPDSGFFSRLNWLYKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTDQEQTSLYVQASGRVTVSTKRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDILVINSNGNLIAPRGYFKM-RTGKSSIMRSDAPIGTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFI-MWACQKGNIRCNICI
          0         0         0         0         0         0         0               0         0          1          1         1         1            1         1          1         1         1         1         2         2         2         2         2         2         2         2          2         2         3         3         3         3         3         3         3         3         3         3         4         4         4         4         4         4         4         4         4         4         5         5         5         5         5         5          5      
          1         2         3         4         5         6         7               8         9          0          1         2         3            4         5          6         7         8         9         0         1         2         3         4         5         6         7          8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5          6      
          0         0         0         0         0         0         0               0         0          0          0         0         0            0         0          0         0         0         0         0         0         0         0         0         0         0         0          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0          0      

>A/******/index/2009-02-01
MKAILVVLLYTFA----------TANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK-----LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI
         0                   0         0         0         0         0              0         0         0         1         1         1         1         1         1         1         1         1         1         2         2         2         2         2         2         2         2         2         2         3         3         3         3         3         3         3         3         3         3         4         4         4         4         4         4         4         4         4         4         5         5         5         5         5         5         5      
         1                   2         3         4         5         6              7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6      
         0                   0         0         0         0         0              0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0      


MAFFT:
------
>A/Udorn/307/72(H3N2)
MKTI-IALSYIFCLVLGQDFPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILDGI------DCTLIDALLGDPHCDGFQN-ETWDLFVERSKA-FSNCYPYDVPDYASLR---SLVASSGTLEFISEGFTWTGVTQNGG-SNACKRGPDSGFFSRLNWLYKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTDQEQTSLYVQASGRVTVSTKRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDILVINSNGNLIAPRGYFKM-RTGKSSIMRSDAPIGTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFI-MWACQKGNIRCNICI
          0         0         0         0         0         0         0               0         0          1          1         1            1         1         1          1         1         1         1         2         2         2         2         2         2         2         2          2         2         3         3         3         3         3         3         3         3         3         3         4         4         4         4         4         4         4         4         4         4         5         5         5         5         5         5          5      
          1         2         3         4         5         6         7               8         9          0          1         2            3         4         5          6         7         8         9         0         1         2         3         4         5         6         7          8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5          6      
          0         0         0         0         0         0         0               0         0          0          0         0            0         0         0          0         0         0         0         0         0         0         0         0         0         0         0          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0          0      
>A/******/index/2009-02-01
MKAILVVLLYTFATA----------NADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK-----LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI
         0                   0         0         0         0         0              0         0         0         1         1         1         1         1         1         1         1         1         1         2         2         2         2         2         2         2         2         2         2         3         3         3         3         3         3         3         3         3         3         4         4         4         4         4         4         4         4         4         4         5         5         5         5         5         5         5      
         1                   2         3         4         5         6              7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6      
         0                   0         0         0         0         0              0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0


Code: 
http://vir.sgmjournals.org/cgi/reprint/68/4/1205.pdf
                                                                                                                                                                                                                                             227
                                                                                                                                                                                                                                              |
>A/Taiwan/01/1986(H1N1)                                                                                                                                                                                                                       |
Winter et.al:  10        20        30        40        50         60        70         80        90        100       110       120          130        140       150       160       170       180       190       200       210       220    |  230       240       250       260        270       280       290       300
MKAKLLVLLCAFTATDADTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGNCSIAGWILGNPECESLFSKKSWSYIAETPNSENGTCYPGYFADYEELREQLSSVSSFERFEIFPKESSWPNHTVTKGVTASCSHKGKSSFYRNLLWLTEKNGSYPTLSKSYVNNKEKEVLVLWGVHHPSNIGDQRAIYHTENAYVSVVSSHYNRRFTPEIAKRPKVRGQEGRINYYWTLLEPGDTIIFEANGNLIAPWYAFALSRGFGSGIITSNASMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSTKLRMVTGLRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNNECMESVKNGTYDYPKYSEESKLNREKIDGVKLESMGVYQILAIYSTVASSLVLLVSLGAISFWMCSNGSLQCRICI}
real:    10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230      |240
                                                                                                                                                                                                                                              |
                                                                                                                                                                                                                                              |
>A/******/index/2009-02-01                                                                                                                                                                                                 x S220T            x D225G=D222G
MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI}
>A/******/Cancun-NY/Index/2009-04-15
MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGTSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI}-


keywords

Winter
Fields
Brownlee
1981
h3-numbering
h1-numbering
hemagglutinin
influenza
 
Re: List of Mutations

http://peds.oxfordjournals.org/cgi/content/full/gzp027

refers to two papers from 1981,1991 which are not available



others also refer to Winter,Fields,Brownlee 1981
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC54066/?page=3

but that article is not availale online and I can't find the
numbering convention described


with the mutations from the airforce pdf:


Code: 
V19I K22R V30I P83S D86N,G D97N E112K V114I S128P,L N129D S157L A197S S203T A261V N276S T277A K283E I295V L312M I321V


kalign:
-------
>A/Udorn/307/72(H3N2)
MKTI-IALSYIFCLVLGQDFPGNDNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILDGI------DCTLIDALLGDPHCDGFQN-ETWDLFVERSKA-FSNCYPYDVPDYASLRSLVASSGTLE---FISEGFTWTGVTQNGG-SNACKRGPDSGFFSRLNWLYKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTDQEQTSLYVQASGRVTVSTKRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDILVINSNGNLIAPRGYFKM-RTGKSSIMRSDAPIGTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFI-MWACQKGNIRCNICI
          0         0         0         0         0         0         0               0         0          1          1         1         1            1         1          1         1         1         1         2         2         2         2         2         2         2         2          2         2         3         3         3         3         3         3         3         3         3         3         4         4         4         4         4         4         4         4         4         4         5         5         5         5         5         5          5      
          1         2         3         4         5         6         7               8         9          0          1         2         3            4         5          6         7         8         9         0         1         2         3         4         5         6         7          8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5          6      
          0         0         0         0         0         0         0               0         0          0          0         0         0            0         0          0         0         0         0         0         0         0         0         0         0         0         0          0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0          0      

                                                                                                                                                                129                         157                                                                                                                     277
>A/******/index/2009-02-01 1                 19 22      30        .              .         .         .         .  83 86         97             112             128         .         .         .         .         .         .      197   203    .         .         .         .         .         .261      .     276 .  283    .    295  |         . 312     .321
MKAILVVLLYTFA----------TANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK-----LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI
         0                   0         0         0         0         0              0         0         0         1         1         1         1         1         1         1         1         1         1         2         2         2         2         2         2         2         2         2         2         3         3         3         3         3         3         3         3         3         3         4         4         4         4         4         4         4         4         4         4         5         5         5         5         5         5         5      
         1                   2         3         4         5         6              7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6         7         8         9         0         1         2         3         4         5         6      
         0                   0         0         0         0         0              0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0         0
 
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