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July San Paolo Sequence Released

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  • Rwilmer
    replied
    Re: July San Paolo Sequence Released

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

    Leave a comment:


  • HenryN
    replied
    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).

    Leave a comment:


  • hawkeye
    replied
    Re: July San Paolo Sequence Released

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

    Leave a comment:


  • HenryN
    replied
    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.

    Leave a comment:


  • Sally Furniss
    replied
    Re: July San Paolo Sequence Released

    Mention of V252M here

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

    Leave a comment:


  • theforeigner
    replied
    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 donīt 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.

    Leave a comment:


  • Jeremy
    replied
    Re: July San Paolo Sequence Released

    Niman,

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

    Leave a comment:


  • Rwilmer
    replied
    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

    Leave a comment:


  • HenryN
    replied
    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

    Leave a comment:


  • HenryN
    replied
    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

    Leave a comment:


  • HenryN
    replied
    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.

    Leave a comment:


  • theforeigner
    replied
    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 donīt 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?

    Leave a comment:


  • HenryN
    replied
    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

    Leave a comment:


  • HenryN
    replied
    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

    Leave a comment:


  • HenryN
    started a topic July San Paolo Sequence Released

    July San Paolo Sequence Released

    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.
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