Announcement

**Giuseppe** · May 6, 2009, 02:04 AM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

In Italy several antigenic variations has been observed in H3N2 strain, as reported previuosly (I ask someone to verify the substitutions in relation to above ProMed description):

Italia. SORVEGLIANZA VIROLOGICA DELL?INFLUENZA (a cura del Ministero della Sanit? / ISS - 5 febbraio 2009)

SORVEGLIANZA VIROLOGICA DELL?INFLUENZA

4 Febbraio 2009

Aggiornamento settimana 5/09

[Documento PDF originale presso il sito del Ministero della Salute. EDITATO.]

-- ITALIA

Continua la raccolta dei campioni clinici presso i Laboratori periferici della rete Influnet.

Durante questa settimana di sorveglianza sono stati raccolti 163 campioni, di cui 21 positivi al virus influenzale.

In particolare, sono stati identificati e/o isolati 19 virus di tipo A di cui 12 H3. Sono stati, inoltre, identificati 2 virus di tipo B.

Vengono segnalati, dal laboratorio dell?Universit? di Genova, 8 campioni positivi per Virus Respiratorio Sinciziale (RSV).

Nella tabella e nel grafico, di seguito riportati, vengono riassunti i dati virologici complessivi, ottenuti dall?inizio della stagione influenzale (sett. 46-08) ad oggi (sett. 5-09).

[ SETTIMANA 46 - 47 - 48 - 49 - 50 - 51 - 52 - 1 - 2 - 3 - 4 - 5 - TOTALE ]

-- FLU A - 3 - 4 - 4 - 8 - 7 - 11 - 17 - 35 - 47 - 84 - 60 - 19 - 299
-- A (non sottotipizzato) - ... - ... - ... - ... - ... - 2 - 2 - 13 - 11 - 9 - 4 - 7 - 48
-- A/H3N2 - 3 - 4 - 4 - 8 - 7 - 9 - 15 - 22 - 36 - 69 - 54 - 12 - 243
-- A/H1N1 - ... - ... - ... - ... - ... - ... - ... - ... - ... - 6 - 2 - ... - 8
-- FLU B - 0 - 0 - 2 - 0 - 1 - 1 - 0 - 1 - 0 - 0 - 2 - 2 - 9

-- TOT CAMPIONI POSITIVI - 3 - 4 - 6 - 8 - 8 - 12 - 17 - 36 - 47 - 84 - 62 - 21 - 308

N.B. Le apparenti discrepanze rispetto alla tabella della settimana scorsa sono dovute agli aggiornamenti conseguenti ad approfondimenti nelle analisi diagnostiche (tipo/sottotipo).

<table style="width: auto;"><tbody><tr><td></td></tr><tr><td style="font-family: arial,sans-serif; font-size: 11px; text-align: right;">From TABLES</td></tr></tbody></table>

<table style="width: auto;"><tbody><tr><td></td></tr><tr><td style="font-family: arial,sans-serif; font-size: 11px; text-align: right;">From TABLES</td></tr></tbody></table>

In Figura 1 vengono riportate le relazioni filogenetiche relative alla porzione HA1 della HA di virus influenzali A/H3N2 isolati in Italia nella presente stagione 2008/09, confrontati con isolati della precedente stagione. Dall?albero, risulta evidente la derivazione di questi ceppi dalla variante vaccinale A/Brisbane/10/2007, con cui condividono 2 cambiamenti aminoacidici (G50E e K140I) rispetto al vecchio ceppo A/Wisconsin/67/2005. Tuttavia, tutti i virus italiani mostrano una recente importante sostituzione (K173Q) nel sito antigenico E, rispetto al ceppo australiano, riscontrata nel ceppo di riferimento pi? recente A/Wisconsin/5/2008.

Figura 1. Relazioni filogenetiche relative al dominio HA1 della HA di recenti isolati umani A/H3N2 in Italia. L?analisi filogenetica ? stata eseguita presso l?ISS, utilizzando il metodo Kimura 2 per il calcolo delle distanze genetiche e l?algoritmo Neighbor-Joining per la costruzione dell?albero filogenetico.

-- NOTIZIE dal MONDO

- EUROPA

La circolazione dei virus influenzali nei paesi europei ? in sostenuto aumento ed i virus A/H3 sono ancora dominanti. In particolare, durante quest?ultima settimana sono stati raccolti un totale di 3779 campioni clinici: di questi 1904 (50%) sono risultati positivi ai virus influenzali.

Tra questi 1824 di tipo A (803 H3, 59 H1 e 962 non sotto tipizzati) e 80 di tipo B.

E? da segnalare che il 97% dei virus di sottotipo A/H1N1 analizzati ? resistente all?Oseltamivir, mentre resta sensibile allo Zanamivir ed agli inibitori della proteina M2; al contrario tutti i virus di sottotipo A/H3N2 testati risultano sensibili sia all?Oseltamivir che allo Zanamivir, seppur resistenti agli inibitori della proteina M2.

Per ulteriori informazioni ? possibile consultare i seguenti siti:

http://www.eiss.org/index.cgi

http://www.grog.org/

-- USA

La circolazione dei virus influenzali ? in aumento. Sono stati raccolti ed analizzati 3711 campioni, di cui 588 (15.8%) positivi. Tra questi, 508 di tipo A (74 H1, 14 H3, 420 non ancora sotto tipizzati). I restanti 80 appartengono al tipo B.

I virus A sono correlati alla variante vaccinale corrente.

Si riporta, inoltre, l?avvenuto passaggio di un virus suino A/H1N1 all?uomo segnalato nella settimana 3.

Per ulteriori informazioni ? possibile consultare il sito:

Influenza (Flu)

http://www.cdc.gov/flu/

Learn about flu, including symptoms, prevention methods, and treatment options.

-
-----

**kent nickell** · May 6, 2009, 04:30 AM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

Some of these changes described by Mamabird have to do with transmissibility/replication efficiency and some with virulence. Just to reiterate some of the competing views of influenza evolution....

Under the recombination view of influenza evolution, (not widely accepted), single amino acid changes such as those listed are not 'random mutations' but can be picked up by interacting with other viruses that already contain these changes. This is similar to the widely accepted reassortment mechanism where influenza viruses exchange whole gene segments (ie HA, PB2) but related to smaller subgene segments of exchange even to the point of single nucleic acids.

Under this scheme the closer two viruses are in any single gene the more likely they are to recombine to exchange these small segments of genetic information. So this widely circulating swine flu, (novel H1N1, 2009), brings new cards to the table and its human, swine and avian lineage could make it more compatible to some of the other cirulating viruses....

**AlaskaDenise** · June 1, 2009, 01:01 AM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

Based on Mamabirds list above, I found the following. It needs additional info by those of you more expert than myself.

MAMABIRD?S MOST WANTED LIST

PB2
L(F)475M - is in some human H5N1 & increases virulence by enhancing replicative efficiency (http://www.pnas.org/content/106/9/3366.long )
D567N action ?)
E627K - affects replication efficiency. The presence of lysine leads to more aggressive viral replication, overwhelming the host's defense mechanisms and resulting in high mortality rates in mice.

PB1 none (?)

PB1-F2 - appears to enhance virus-induced cell death in a cell type-dependent manner.
P28L (action ?)
D55N (action ?)
I(V)100A (action ?)
T552S - I think it?s involved in the refolding to form the active sites that are needed for the production of capped RNA primers and for the ensuing synthesis of viral mRNA.

HA multi-basic amino acids at the cleavage site (poultry infections);

NP
G16D - distinguishes human A/H1N1 from avian/swine/equine - a ?D? indicates evolutionary stability, & is associated with NP cleavage in non-avians
L283P - distinguishes human A/H1N1 from avian/swine/equine - involved in the induction of different T-cell responses by each host
F313Y - distinguishes human A/H1N1 from avian/swine/equine

MP
I15V (action ?)
K101R - changes can affect virus morphology
A166V (action ?)
N207S (?T-cell epitopes)

M2
E16G (action ?)
S20N (action ?)

NS none;

NS2 none;

NA
H274Y - confers high-level resistance to neuraminidase inhibitors
anti-viral oseltamivir
N294S - confer resistance to neuraminidase inhibitors
anti-viral oseltamivir

.

**gsgs** · June 29, 2009, 04:32 AM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

I need all these in one file, computer-readable
and nucleotide-numbering in v-flu coding region
then I can chack for any changes easily automatically...

M2,31,S,N,A/N1,Adamantane,N5
M2,26,L,F,A/N1,Adamantane,L
M2,27,V,A,A/N1,Adamantane,V
M2,30,A,T,A/N1,Adamantane,A
M2,34,G,E,A/N1,Adamantane,G
NA,275,H,Y,A/N1,Oseltamivir,H5
NA,293,R,K,A/N2*,Oseltamivir,R
NA,295,N,S,A/N2*,Oseltamivir,N
NA,119,E,V,A/N2*,Oseltamivir,E
NA,119,E,G,A/N2*,Zanamivir,E
NA,119,E,A,A/N2*,Zanamivir,E
NA,119,E,N,A/N2*,Zanamivir,E
NA,152,R,K,B*,Oseltamivir,
PB1-F2,66,N,S,Virulence,Protein,
PB2,199,A,S,Transmission*,A,
PB2,627,E,K,Virulence,E,
PB2,661,A,T,Transmission*,A,
PB2,667,V,I,Transmission*,V,
PB2,701,D,N,Virulence,D,
PB2,702,K,R,Transmission*,K,
PA,409,S,N,Transmission*,N,
NP,136,L,M,Transmission*,I,
NA,??,stalk,No,19a.a.,Transmission*,No,
M2,16,A,G,Transmission*,E,
M2,55,C,F,Transmission*,F,
NS1,92,T,E,Virulence**,D,

PB2:
L475M
D567N
E627K

PB1:
P28L
D55N
I100A
T552S

NP:
G16D
L283P
F313Y

M:
I15V
K101R
A166V
N207S

M2:
E16G
S20N

NA:
H274Y
N294S

HA:
Asp160Lys
Lys189Gln
Val229Ala

PB2:
A199S;

PB1
N(T)375S; PB1-F2 P(R)48Q;

PA
T129I
S409N

HA
E190D
S221P
F251L
Y258F

NP V33I
R100V
Q357K

MP K27R
I168T
N224S

NS2
F55L

. 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.

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

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

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

keywords: mamabird ,FT 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)

--------------sorting...------------------

these 113:

Code:

PB2,A44S
PB2,M64T
PB2,Q151H
PB2,A199S
PB2,T271A
PB2,R324S
PB2,Y432H
PB2,L475M
PB2,D567N
PB2,A588I
PB2,E627K
PB2,A661T
PB2,V667I
PB2,A674T
PB2,D701N
PB2,K702R

PB1,P28L
PB1,D55N
PB1,I100A
PB1,G370A
PB1,N375S
PB1,S466F
PB1,T552S
PB1,V646M
PB1,F665S
PB1-F2,P28L
PB1-F2,P48Q
PB1-F2,D55N
PB1-F2,N66S
PB1-F2,I100A
PB1-F2,T552S

PA,P28L
PA,D55N
PA,R57Q
PA,V100A
PA,T129I
PA,S225C
PA,L268I
PA,A337S
PA,A404S
PA,S409N
PA,T552S
PA,L581M
PA,P702L

HA,I7V
HA,M8L
HA,D160K
HA,K189Q
HA,E190D
HA,N215Y
HA,S221P
HA,V229A
HA,F251L
HA,Y258F
HA,V351A

NP,G16D
NP,A29V
NP,V33I
NP,I61L
NP,R100V
NP,L136M
NP,K192E
NP,D202N
NP,T222M
NP,L283P
NP,R305K
NP,F313Y
NP,Q357K
NP,I373T
NP,Y375D

NA,G95S
NA,E96G
NA,H100Y
NA,E119A
NA,E119G
NA,E119N
NA,E119V
NA,L123S
NA,R152K
NA,H274Y
NA,H275Y
NA,R293K
NA,N294S
NA,N295S
NA,C334S

M2,A16G
M2,E16G
M2,S20N
M2,L26F
M2,V27A
M2,A30T
M2,S31N
M2,G34E
M2,C55F

M1,I15V
M1,K27R
M1,K101R
M1,V115I
M1,T121A
M1,T137A
M1,A166V
M1,I168T
M1,N207S
M1,R222H
M1,N224S

NS2,F55L
NS1,I81M
NS2,E89A
NS1,T92E
NS1,T104M
NS1,I134F
NS1,P215T
NS1,E227R

proteins enumeration

Code:


>A/******/index/2009-02-01
PB2,759,MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMRYPITADKRIMDMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLAITKEKKEELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTGSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRAAVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAIGLRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIESIDNVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN}
PB1,757,MDVNPTLLFLKIPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMESMNKEEIEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRGYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTEISFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNILSMAPIMFSNKMARLGKGYMFESKRMKIRTQIPAEMLASIDLKYFNESTKKKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTIYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYGFVANFSMELPSFGVSGVNESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRSFELKKLWDQTQSKVGLLVSDGGPNLYNIRNLHIPEVCLKWELMDDDYRGRLCNPLNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARVDFESGRIKKEEFSEIMKICSTIEELRRQK}
PA ,716,MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERGESIIVESGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGEETIEEKFEITGTMRKLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNAKIEPFLRTTPRPLRLPDGPLCHQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLMAWKQVLAELQDIENEEKIPRTKNMKRTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPEPRSLASWVQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGESPRGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALK}
HA ,566,MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI}
NP ,498,MASQGTKRSYEQMETGGERQDATEIRASVGRMIGGIGRFYIQMCTELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGKKVIPRGKLSTRGVQIASNENVETMDSNTLELRSRYWAIRTRSGGNTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEVIRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAEEYDS}
NA ,469,MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQNQIETCNQSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK}
PB1-F2,90,MEQEQDTPWTQ}TEHTNTQKRESGRQTQRLVHPSSTRLMDHYLRIMNQVGMHKQTVF}RLWLSLKNPTQEYLRIHALKQWKLFNKQG}IN}
M1 ,252,MSLLTEVETYVLSIIPSGPLKAEIAQRLESVFAGKNTDLEALMEWLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLYKKLKREITFHGAKEVSLSYSTGALASCMGLIYNRMGTVTTEAAFGLVCATCEQIADSQHRSHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAAEAMEVANQTRQMVHAMRTIGTHPSSSAGLKDDLLENLQAYQKRMGVQMQRFK}
M2 , 97,MSLLTEVET PTRSEWECRCSDSSDPLVIAANIIGILHLILWITDRLFFKCIYRRFKYGLKRGPSTEGVPESMREEYQQEQQSAVDVDDGHFVNIELE}
NS1,219,MDSNTMSSFQVDCFLWHIRKRFADNGLGDAPFLDRLRRDQKSLKGRGNTLGLDIETATLVGKQIVEWILKEESSETLRMTIASVPTSRYLSDMTLEEMSRDWFMLMPRQKIIGPLCVRLDQAIMEKNIVLKANFSVIFNRLETLILLRAFTEEGAIVGEISPLPSLPGHTYEDVKNAVGVLIGGLEWNGNTVRVSENIQRFAWRNCDENGRPSLPPEQK}
NS2,121,MDSNTMSSFQ DILMRMSKMQLGSSSEDLNGMVTRFESLKIYRDSLGETVMRMGDLHYLQSRNEKWREQLGQKFEEIRWLIEEMRHRLKATENSFEQITFMQALQLLLEVEQEIRAFSFQLI}

.....now nucleotides...

delete 0,0,0,0,0,0,94,0,688,0,478 nucleotides from the head to align to the
correct reading frame for PB2,PB1,PA,HA,NP,NA,PB1F2,M1,M2,NS1,NS2

**gsgs** · June 29, 2009, 07:56 AM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

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

**AlaskaDenise** · August 27, 2009, 06:13 PM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

bump this since there is renewed interest in potential mutations.

.

**gsgs** · August 28, 2009, 12:03 AM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

bumping makes less sense now that I get too many new posts
in the morning to even read the headlines.

I think I'll have to restrict to certain subforums
or subscribe to threads.

**Toaster2** · August 28, 2009, 01:36 AM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

Originally posted by Mamabird View Post

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.

HA I219K should be associated with increased transmission by droplets

**Toaster2** · August 28, 2009, 01:38 AM

Re: What's on the genetic menu for New A/H1N1 and seasonal A/H1N1 & A/H3N2 swapping?

Originally posted by gsgs View Post

bumping makes less sense now that I get too many new posts
in the morning to even read the headlines.

I think I'll have to restrict to certain subforums
or subscribe to threads.

I agree, its getting harder and harder to keep up. Where we used to have a global discussion, it is getting more regional I guess due to time differences and volume of new posts.

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

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