Announcement

**HenryN** · July 28, 2009, 04:38 PM

Re: July San Paolo Sequence Released

LOCUS GQ414768 1701 bp cRNA linear VRL 28-JUL-2009
DEFINITION Influenza A virus (A/Sao Paulo/43812/2009(H1N1)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION GQ414768
VERSION GQ414768.1 GI:254802543
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Sao Paulo/43812/2009(H1N1))
ORGANISM Influenza A virus (A/Sao Paulo/43812/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Santos,C.L., Borges,D.D., Correa,K.O., Ishida,M.A., Benega,M.A.,
Sacchi,C.T. and de Paiva,T.M.
TITLE Human infection with novel swine H1N1 virus in Brazil
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1701)
AUTHORS Santos,C.L. and de Paiva,T.M.
TITLE Direct Submission
JOURNAL Submitted (27-JUL-2009) Respiratory Virus Section, Adolfo Lutz
Institute, Av. Dr. Arnaldo 355, Sao Paulo, SP 01246/902, Brazil
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009.
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Sao
Paulo/43812/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Sao Paulo/43812/2009"
/serotype="H1N1"
/isolation_source="postmortem blood"
/host="Homo sapiens; gender F; age 11"
/db_xref="taxon:662558"
/segment="4"
/country="Brazil"
/collection_date="03-Jul-2009"
/note="lineage: swl"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACT82516.1"
/db_xref="GI:254802544"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVL EKNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWS YIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAA CPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQ NADAYVFV
GSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLMVP RYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFHNIHPITIGKCPKYVKS TKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKS TQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAEL LVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGT YDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNG SLQCRICI"
ORIGIN
1 atgaaggcaa tactagtagt tctgctatat acatttgcaa ccgcaaatgc agacacatta
61 tgtataggtt atcatgcgaa caattcaaca gacactgtag acacagtact agaaaagaat
121 gtaacagtaa cacactctgt taaccttcta gaagacaagc ataacgggaa actatgcaaa
181 ctaagagggg tagccccatt gcatttgggt aaatgtaaca ttgctggctg gatcctggga
241 aatccagagt gtgaatcact ctccacagca agctcatggt cctacattgt ggaaacatct
301 agttcagaca atggaacgtg ttacccagga gatttcatcg attatgagga gctaagagag
361 caattgagct cagtgtcatc atttgaaagg tttgagatat tccccaagac aagttcatgg
421 cccaatcatg actcgaacaa aggtgtaacg gcagcatgtc ctcatgctgg agcaaaaagc
481 ttctacaaaa atttaatatg gctagttaaa aaaggaaatt catacccaaa gctcagcaaa
541 tcctacatta atgataaagg gaaagaagtc ctcgtgctat ggggcattca ccatccatct
601 actagtgctg accaacaaag tctctatcag aatgcagatg catatgtttt tgtggggtca
661 tcaagataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gagggatcaa
721 gaagggagaa tgaactatta ctggacacta gtagagccgg gagacaaaat aacattcgaa
781 gcaactggaa atctaatggt accgagatat gcattcgcaa tggaaagaaa tgctggatct
841 ggtattatca tttcagatac accagtccac gattgcaata caacttgtca gacacccaag
901 ggtgctataa acaccagcct cccatttcat aatatacatc cgatcacaat tggaaaatgt
961 ccaaaatatg taaaaagcac aaaattgaga ctggccacag gattgaggaa tgtcccgtct
1021 attcaatcta gaggcctatt tggggccatt gccggtttca ttgaaggggg gtggacaggg
1081 atggtagatg gatggtacgg ttatcaccat caaaatgagc aggggtcagg atatgcagcc
1141 gacctgaaga gcacacagaa tgccattgac gagattacta acaaagtaaa ttctgttatt
1201 gaaaagatga atacacagtt cacagcagta ggtaaagagt tcaaccacct ggaaaaaaga
1261 atagagaatt taaataaaaa ggttgatgat ggtttcctgg acatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggact accacgattc aaatgtgaag
1381 aacttatatg aaaaggtaag aagccagtta aaaaacaatg ccaaggaaat tggaaacggc
1441 tgctttgaat tttaccacaa atgcgataac acgtgcatgg aaagtgtcaa aaatgggact
1501 tatgactacc caaaatactc agaggaagca aaattaaaca gagaagaaat agatggggta
1561 aagctggaat caacaaggat ttaccagatt ttggcgatct attcaactgt cgccagttca
1621 ttggtactgg tagtctccct gggggcaatc agtttctgga tgtgctctaa tgggtctcta
1681 cagtgtagaa tatgtattta a

**HenryN** · July 28, 2009, 04:41 PM

Re: July San Paolo Sequence Released

HA travel log

gb|GQ229293.1| Influenza A virus (A/swine/Hong Kong/NS1659/20... 30.1 0.33
gb|EU521831.1| Influenza A Virus (A/Yurimaguas/FLU4785/2006(H... 30.1 0.33
gb|EU521815.1| Influenza A Virus (A/Chanchamayo/FLU4292/2006(... 30.1 0.33
gb|EU521813.1| Influenza A Virus (A/Chanchamayo/FLU4036/2006(... 30.1 0.33
gb|EU521812.1| Influenza A Virus (A/Chanchamayo/FLU4032/2006(... 30.1 0.33
gb|EU521807.1| Influenza A virus (A/Chanchamayo/FLU3954/2006(... 30.1 0.33
gb|DQ431990.1| Influenza A virus (A/swine/Taiwan/CO935/2004(H... 30.1 0.33
gb|DQ447187.1| Influenza A virus (A/swine/Taiwan/CO935/2004(H... 30.1 0.33
gb|AY060041.1| Influenza A virus (A/SW/NE/21147/01(H1N2)) hem... 30.1 0.33
gb|CY009332.1| Influenza A virus (A/Fort Worth/50(H1N1)) segm... 30.1 0.33
gb|CY008988.1| Influenza A virus (A/Denver/57(H1N1)) segment ... 30.1 0.33
gb|AY377929.1| Influenza A virus (A/swine/Taichung/200-8/2002... 30.1 0.33
gb|AF117241.1|AF117241 Influenza A virus (A/South Carolina/1/... 30.1 0.33
dbj|D00837.1|FLA39HA Influenza A virus (A/swine/Cambridge/193... 30.1 0.33
dbj|AB043486.1| Influenza A virus (A/Saga/2/1957(H1N1)) HA ge... 30.1 0.33
dbj|AB043485.1| Influenza A virus (A/Meguro/1/1956(H1N1)) HA ... 30.1 0.33
dbj|AB043484.1| Influenza A virus (A/Yamagishi/55(H1N1)) HA g... 30.1 0.33
dbj|AB043483.1| Influenza A virus (A/Taiwan/13/1954(H1N1)) HA... 30.1 0.33
dbj|AB043482.1| Influenza A virus (A/Kojiya/1/1952(H1N1)) HA ... 30.1 0.33
gb|AF116576.1|AF116576 Influenza A virus (A/New_York/1/18(H1N... 30.1 0.33
gb|AF116575.1|AF116575 Influenza A virus (A/Brevig_Mission/1/... 30.1 0.33
gb|U04859.1|IAU04859 Influenza A virus (H1N1) A/swine/Cambrid... 30.1 0.33

**theforeigner** · July 28, 2009, 04:52 PM

Re: July San Paolo Sequence Released

Originally posted by niman View Post

HA sequence from July 3 isolate (11F) has been released at Genbank

A/Sao Paulo/43812/2009

Has acquired a polymorphism found in 1918 pandemic strain.

Dr. Niman could you please explain to us who don�t have knowledge about sequence terms ect what this means? Like, what is the consequenses ?

Is this som kind of significant mutation that make the H1N1 more virulent?

**HenryN** · July 28, 2009, 05:09 PM

Re: July San Paolo Sequence Released

Originally posted by theforeigner View Post

Dr. Niman could you please explain to us who don´t have knowledge about sequence terms ect what this means? Like, what is the consequenses ?

Is this som kind of significant mutation that make the H1N1 more virulent?

The change (V252M) was present in 1918. The isolates at the bottom of the list (South Carolina, Brevig Mission, and New York) were from dead patients from 1918 (if you click on the link you will see a full description of each isolate).
Seasonal flu (from Peru!), swine, and 1918 are a bad combination.

**HenryN** · July 28, 2009, 05:11 PM

Re: July San Paolo Sequence Released

Second travel log

gb|GQ402203.1| Influenza A virus (A/Canada-MB/RV1982/2009(H1N... 35.6 0.008
gb|GQ392029.1| Influenza A virus (A/Italy/127/2009(H1N1)) seg... 35.6 0.008
gb|GQ368664.1| Influenza A virus (A/Sao Paulo/2233/2009(H1N1)... 35.6 0.008
gb|GQ330653.1| Influenza A virus (A/Italy/56/2009(H1N1)) segm... 35.6 0.008
gb|GQ329076.1| Influenza A virus (A/Paris/2722/2009(H1N1)) se... 35.6 0.008
gb|CY041830.1| Influenza A virus (A/New York/3348/2009(H1N1))... 35.6 0.008
gb|CY041822.1| Influenza A virus (A/New York/3352/2009(H1N1))... 35.6 0.008
gb|CY041782.1| Influenza A virus (A/New York/3337/2009(H1N1))... 35.6 0.008
gb|GQ323551.1| Influenza A virus (A/Massachusetts/08/2009(H1N... 35.6 0.008
gb|GQ323451.1| Influenza A virus (A/Rhode Island/03/2009(H1N1... 35.6 0.008
gb|GQ323446.1| Influenza A virus (A/Maine/03/2009(H1N1)) segm... 35.6 0.008
gb|GQ287625.1| Influenza A virus (A/Tokushima/1/2009(H1N1)) s... 35.6 0.008
gb|GQ283493.1| Influenza A virus (A/Finland/555/2009(H1N1)) s... 35.6 0.008
gb|GQ232044.1| Influenza A virus (A/Rhode Island/02/2009(H1N1... 35.6 0.008
gb|GQ232007.1| Influenza A virus (A/Vermont/03/2009(H1N1)) se... 35.6 0.008
gb|GQ200287.1| Influenza A virus (A/Shandong/1/2009(H1N1)) se... 35.6 0.008
gb|GQ166222.1| Influenza A virus (A/Italy/07/2009(H1N1)) segm... 35.6 0.008

**HenryN** · July 28, 2009, 05:16 PM

Re: July San Paolo Sequence Released

Third polymorphism (serious mixing and matching)

gb|GQ377095.1| Influenza A virus (A/California/24/2009(H1N1))... 31.9 0.093
gb|GQ359765.1| Influenza A virus (A/Stockholm/31/2009(H1N1)) ... 31.9 0.093
gb|GQ292961.1| Influenza A virus (A/Mexico City/22/2009(H1N1)... 31.9 0.093
gb|GQ229293.1| Influenza A virus (A/swine/Hong Kong/NS1659/20... 31.9 0.093
gb|GQ232085.1| Influenza A virus (A/Guangdong/02/2009(H1N1)) ... 31.9 0.093
gb|GQ223435.1| Influenza A virus (A/Guangdong/05/2009(H1N1)) ... 31.9 0.093
gb|GQ132144.1| Influenza A virus (A/Canada-ON/RV1529/2009(H1N... 31.9 0.093

**Rwilmer** · July 28, 2009, 05:18 PM

Re: July San Paolo Sequence Released

So does this mean that swine has a much higher virulence as a result, Dr. Niman? What is V252M associated with, virulence, transmissability? I was reading up on this a little and found that seasonal flu also has this mutation, is that correct? http://synapse.koreamed.org/Synapse/...jbv-39-125.pdf

**Jeremy** · July 28, 2009, 05:19 PM

Re: July San Paolo Sequence Released

Niman,

Would these mutations have an effect on the vaccine currently being produced?

**theforeigner** · July 28, 2009, 05:35 PM

Re: July San Paolo Sequence Released

Originally posted by niman View Post

The change (V252M) was present in 1918. The isolates at the bottom of the list (South Carolina, Brevig Mission, and New York) were from dead patients from 1918 (if you click on the link you will see a full description of each isolate).
Seasonal flu (from Peru!), swine, and 1918 are a bad combination.

Thanks for trying to explain Niman but I still don�t understand

. The thing is I have no clue concerning sequenses ect, so what I am asking for is your bid, in plain english, what the consequeses are? is this a mutation making the H1N1 more virulent?

I belive we are MANY who wish that thise newsreports on sequenses would always be followed by a short explanation, in plain english, because we dont have knowledge about the issue.

**Sally Furniss** · July 28, 2009, 05:56 PM

Re: July San Paolo Sequence Released

Mention of V252M here

http://www.flutrackers.com/forum/showthread.php?t=18292

**HenryN** · July 28, 2009, 06:04 PM

Re: July San Paolo Sequence Released

Originally posted by Rwilmer View Post

So does this mean that swine has a much higher virulence as a result, Dr. Niman? What is V252M associated with, virulence, transmissability? I was reading up on this a little and found that seasonal flu also has this mutation, is that correct? http://synapse.koreamed.org/Synapse/...jbv-39-125.pdf

I don't follow influenza B very closely, and am not sure if numbering corresponds. Position 252 is based on H3 numbering.

**hawkeye** · July 28, 2009, 06:15 PM

Re: July San Paolo Sequence Released

So the San Paolo Sequence is not of the same Novel H1N1 source?

**HenryN** · July 28, 2009, 06:18 PM

Re: July San Paolo Sequence Released

Originally posted by Jeremy View Post

Niman,

Would these mutations have an effect on the vaccine currently being produced?

V252M in influenza B helps the virus evade the seasonal flu vaccine (but I still need to check to so if the H3 numbering applies in influenza B).

**Rwilmer** · July 28, 2009, 06:18 PM

Re: July San Paolo Sequence Released

Dr. Niman, what does this mutation mean? More virulence? Will the vaccine still work?

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July San Paolo Sequence Released

July San Paolo Sequence Released

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