Rhiza Labs FluTracker Forum

The recently released sequence, A/swine/Iowa/03032/2010,

http://www.ncbi.nlm.nih.gov/sites/entre ... dl=GenBank

has duplicated G158E as part of a 2 aa insertion. Thus, instead of wild type going from KKGN to KKEN, this sequence has gone to KKEKEN. Moroever, it has acquire polymorphism found in virtually all pandemic H1N1 sequences. The recombinant moves have striking parallels with the evolution of the 1918 virus and are a major concern. This is the most recent H1N1 sequence at GISAID or Genbank.

_________________
www.twitter.com/hniman

LOCUS HM585495 1713 bp cRNA linear VRL 03-JUL-2010
DEFINITION Influenza A virus (A/swine/Iowa/03032/2010(H1N1)) hemagglutinin
(HA) gene, complete cds.
ACCESSION HM585495
VERSION HM585495.1 GI:299766147
KEYWORDS .
SOURCE Influenza A virus (A/swine/Iowa/03032/2010(H1N1))
ORGANISM Influenza A virus (A/swine/Iowa/03032/2010(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1713)
AUTHORS Gramer,M., Juleen,K., Foss,A., Wees,C., Raymond,L., Leiferman,M.
and Otterson,T.
TITLE Direct Submission
JOURNAL Submitted (24-JUN-2010) Veterinary Diagnostic Laboratory,
University of Minnesota, 1333 Gortner Ave, St. Paul, MN 55108, USA
FEATURES Location/Qualifiers
source 1..1713
/organism="Influenza A virus
(A/swine/Iowa/03032/2010(H1N1))"
/mol_type="viral cRNA"
/strain="A/swine/Iowa/03032/2010"
/serotype="H1N1"
/host="swine"
/db_xref="taxon:858219"
/segment="4"
/country="USA"
/collection_date="04-Jun-2010"
gene 1..1707
/gene="HA"
CDS 1..1707
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADJ38088.1"
/db_xref="GI:299766148"
/translation="MKTILVVLLYTFTTADADTLCIGYHANNSTDTIDTVLEKNVTVT
HSVNLLENRHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTAGSWSYIVETSNS
DNGTCYPGDFINYEELRELLSSVSSFEKFEIFPKTSSWPNHDTNRGVTAACPHDGAKS
FYRNLLWLVKKEKENSYPMINKSYTNNKGKEVLVLWAIHHPATSADQQSLYKNANTYV
FVGSSKYSKKFEPEIAARPKVRDQAGRMNYYWTLVEPGDNITFEATGNLVVPIYAFAL
KRNSGSGIIISDTPVHNCDTTCQTPNGAINTSLPFQNIHPVTIGECPKYVKSTKLRMA
TGLRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADLKSTQNAID
GITNKVNSVIEKMNTQFTAVGKEFNHLERRIENLNKKVDDGFLDIWTYNAELLVLLEN
ERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDDTCMESVKNGTYDYPKY
SEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRI
CI"
ORIGIN
1 atgaagacaa tactagtagt cctgctatat acatttacaa ctgcagatgc cgacacatta
61 tgtataggat atcatgcgaa caattcaact gacaccatag acacagtact agaaaagaat
121 gtaacagtaa cacactctgt caaccttcta gaaaacaggc ataatgggaa actatgtaaa
181 ctaagagggg tagctccatt gcatttgggt aaatgtaaca ttgctggctg gatcctggga
241 aatccagagt gcgaatcact ctccacagca ggctcatggt cctacattgt ggaaacatct
301 aattcagaca atgggacgtg ttacccggga gatttcatca attatgagga gctaagagag
361 ctattgagct cagtgtcatc atttgaaaaa tttgagatat tccccaagac aagttcatgg
421 cccaatcatg acacgaacag aggtgtgacg gcagcatgtc ctcatgatgg ggcaaaaagc
481 ttctacagaa atttattatg gctggtcaaa aaagaaaagg aaaattcata cccaatgatc
541 aacaaatcct acactaacaa taaagggaag gaagttctcg tgctatgggc cattcaccat
601 ccagctacca gtgccgacca acaaagtctc tacaaaaatg caaataccta tgtttttgtg
661 gggtcatcca aatacagcaa gaaattcgag ccagaaatag cagcaagacc caaggtgagg
721 gatcaagcag ggagaatgaa ctattactgg acactagtag agcctggaga caatataaca
781 ttcgaagcaa ccggaaatct agtggtaccg atatatgcct tcgcattgaa aagaaattct
841 ggatctggta ttatcatttc agatacacca gtccacaatt gtgatacgac ttgtcagaca
901 cccaatggtg ctataaacac cagcctccca tttcaaaata tacatccggt cacaattgga
961 gaatgtccaa aatatgtaaa aagtactaaa ctgagaatgg ccacaggatt aaggaatatc
1021 ccgtctattc aatccagagg cctgtttggg gccattgccg gctttattga agggggctgg
1081 acaggaatga tagatggatg gtacggttat caccatcaaa atgagcaggg atcaggatat
1141 gcagccgacc tgaaaagcac acagaatgcc attgacggaa tcactaacaa ggtaaattct
1201 gttattgaaa agatgaacac acaattcaca gcagtaggta aagagttcaa ccacttggaa
1261 agaagaatag agaatttaaa taaaaaggtt gatgatgggt ttctagacat ttggacttac
1321 aatgccgaac tgttggttct gttggaaaat gaaagaactt tggattacca cgactcaaat
1381 gtgaaaaact tatatgaaaa agtaagaagc caactaaaaa acaatgccaa ggaaattgga
1441 aatggatgct ttgaatttta ccataaatgt gatgacacgt gcatggaaag cgtcaaaaat
1501 gggacttatg attacccaaa atactcagag gaagcaaaac taaacagaga ggaaatagat
1561 ggggtgaagt tggaatcaac aaggatttac caaattttgg cgatctattc aactgtcgcc
1621 agttcattag tactggtagt ctccctgggg gcaatcagtt tctggatgtg ctctaatggg
1681 tcgctacagt gcagaatatg tatttaacat tag

_________________
www.twitter.com/hniman

Perhaps I have grown rusty and forgotten, since things have been so quiet for so long, but what, if known, does G158E affect?

_________________
I am not a doctor, virologist, or any of type of medical/life sciences professional.

I am a layman with a background in the physical sciences.

Produces LOW REACTORS. Positions 156-159 is a MAJOR immunological site and with two G158E's this virus can ignore prior immune responses.

Parallel H1N1 pandemics is a real posibility. This H1N1 is NOT pandemic H1N1.

_________________
www.twitter.com/hniman

_________________
www.twitter.com/hniman

_________________
www.twitter.com/hniman

Related to

LOCUS FJ986621 1701 bp cRNA linear VRL 08-MAY-2009
DEFINITION Influenza A virus (A/Ohio/02/2007(H1N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION FJ986621
VERSION FJ986621.1 GI:229473303
KEYWORDS .
SOURCE Influenza A virus (A/Ohio/02/2007(H1N1))
ORGANISM Influenza A virus (A/Ohio/02/2007(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Shinde,V., Bridges,C.B., Uyeki,T.M., Shu,B., Balish,A., Xu,X.,
Lindstrom,S., Gubareva,L.V., Deyde,V., Garten,R.J., Harris,M.,
Gerber,S., Vagasky,S., Smith,F., Pascoe,N., Martin,K., Dufficy,D.,
Ritger,K., Conover,C., Quinlisk,P., Klimov,A., Bresee,J.S. and
Finelli,L.
TITLE Triple-reassortant swine influenza A (H1) in humans in the United
States, 2005-2009
JOURNAL N. Engl. J. Med. 360 (25), 2616-2625 (2009)
PUBMED 19423871
REMARK Erratum:[N Engl J Med. 2009 Jul 2;361(1):102]
REFERENCE 2 (bases 1 to 1701)
AUTHORS Shinde,V., Bridges,C.B., Uyeki,T., Shu,B., Balish,A., Xu,X.,
Lindstrom,S., Gubareva,L., Garten,R.J., Deyde,D., Harris,M.,
Gerber,S., Vagoski,S., Smith,F., Pascoe,N., Martin,K., Dufficy,D.,
Ritger,K., Conover,C., Quinlisk,P., Klimov,A., Bresee,J. and
Finelli,L.
TITLE Direct Submission
JOURNAL Submitted (05-MAY-2009) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, Atlanta, 1600 Clifton Road,
N.E., Atlanta, GA 30333, USA
COMMENT ##FluData-START##
Organism Name Influenza A virus (A/Ohio/02/2007 (H1N1))
Country USA
District Ohio
Collection Date 17-Aug-2007
Host Human
Subtype H1N1
Passage History Original
Age 10
Gender F
special_notes Human infection with swine triple reassortant H1N1
##FluData-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Ohio/02/2007(H1N1))"
/mol_type="viral cRNA"
/strain="A/Ohio/02/2007"
/serotype="H1N1"
/host="Homo sapiens; age 10; gender F"
/db_xref="taxon:643704"
/segment="4"
/country="USA: Ohio"
/collection_date="17-Aug-2007"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACQ73204.1"
/db_xref="GI:229473304"
/translation="MKAILVVLLYTFTTANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVNLLENRHNGKLCKLRGVAPLHLGKCNIAGWLLGNPECESLSTASSWSYIVETSNS
DNGTCYPGDFINYEELREQLSSVSSFERFEIFPKTSSWPNHDTNRGVTAACPHAGTNS
FYRNLIWLVKKGNSYPKINKSYINNKEKEVLVLWAIHHPSTSADQQSLYQNADAYVFV
GSSRYSRKFEPEIATRPKVRDQAGRMNYYWTLVEPGDKITFEATGNLVVPRYAFALKR
NSGSGIIISDTSVHDCDTTCQTPNGAINTSLPFQNIHPVTIGECPKYVKSTKLRMATG
LRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADLKSTQNAIDGI
TNKVNSVIEKMNTQFTAVGKEFSHLERRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDDTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
ORIGIN
1 atgaaggcaa tactagtagt cctgctatat acatttacaa ccgcaaatgc cgacacatta
61 tgtataggtt atcatgcgaa caattcaact gacaccgtag acacagtact agaaaagaat
121 gtaacagtaa cacactctgt caaccttcta gaaaacaggc ataatgggaa actatgtaaa
181 ctaagagggg tagctccatt gcatttgggt aaatgtaaca ttgctggctg gctcctggga
241 aatccagagt gtgaatcact ctccacagca agctcatggt cctacattgt ggaaacatct
301 aattcagaca atgggacgtg ttacccagga gatttcatca attatgagga gctaagagag
361 cagttgagct cagtgtcatc atttgaaaga tttgagatat tccccaagac aagttcatgg
421 cccaatcatg acacgaacag aggtgtgacg gcagcatgtc ctcatgctgg gacaaacagc
481 ttctacagaa atttaatatg gctggtcaaa aaaggaaatt catacccaaa gatcaacaaa
541 tcctacatta acaataaaga gaaggaagtt ctcgtgctat gggccattca ccatccatct
601 accagtgccg accaacaaag tctctaccaa aatgcagatg cctatgtttt tgtggggtca
661 tcaagataca gcaggaagtt cgagccagaa atagcaacaa gacccaaggt gagggaccaa
721 gcagggagaa tgaactatta ctggacacta gtagagcctg gagacaagat aacattcgaa
781 gcaactggaa atctagtggt accgagatat gccttcgcat tgaaaagaaa ttctggatct
841 ggtattatca tttcagatac atcagtccac gattgtgata cgacttgtca gacacccaat
901 ggtgctataa acaccagcct cccatttcaa aatatacatc cagtcacaat tggagaatgt
961 ccaaaatatg taaaaagtac taaactgaga atggccacag gattaaggaa tatcccgtct
1021 attcaatcta gaggcctgtt tggggccatt gctggcttta ttgaaggggg ctggacagga
1081 atgatagatg gatggtacgg ttatcaccat caaaatgagc agggatcagg atatgcagcc
1141 gacctgaaga gcacacagaa tgccattgac gggatcacta acaaggtaaa ttctgttatt
1201 gaaaagatga acacacaatt cacagcagta ggtaaagagt tcagccactt ggaaagaaga
1261 atagagaatt taaataaaaa ggttgatgat ggttttctag atatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggatt accacgactc aaatgtgaaa
1381 aacttatatg aaaaagtaag aagccaacta aaaaacaatg ccaaggaaat tggaaatggc
1441 tgctttgaat tttaccacaa atgtgatgac acgtgcatgg aaagcgtcaa aaatgggact
1501 tatgattacc caaaatactc agaggaagca aaactaaaca gagaggaaat agatggggta
1561 aagttggaat caacaaggat ttaccaaatt ttggcgatct attcaacggt cgccagttca
1621 ttggtactgg tagtctccct gggggcaatc agtttctgga tgtgctctaa tgggtcgcta
1681 cagtgcagaa tatgtattta a

_________________
www.twitter.com/hniman

Related to:

LOCUS FJ986620 1701 bp cRNA linear VRL 08-MAY-2009
DEFINITION Influenza A virus (A/Ohio/01/2007(H1N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION FJ986620
VERSION FJ986620.1 GI:229473301
KEYWORDS .
SOURCE Influenza A virus (A/Ohio/01/2007(H1N1))
ORGANISM Influenza A virus (A/Ohio/01/2007(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Shinde,V., Bridges,C.B., Uyeki,T.M., Shu,B., Balish,A., Xu,X.,
Lindstrom,S., Gubareva,L.V., Deyde,V., Garten,R.J., Harris,M.,
Gerber,S., Vagasky,S., Smith,F., Pascoe,N., Martin,K., Dufficy,D.,
Ritger,K., Conover,C., Quinlisk,P., Klimov,A., Bresee,J.S. and
Finelli,L.
TITLE Triple-reassortant swine influenza A (H1) in humans in the United
States, 2005-2009
JOURNAL N. Engl. J. Med. 360 (25), 2616-2625 (2009)
PUBMED 19423871
REMARK Erratum:[N Engl J Med. 2009 Jul 2;361(1):102]
REFERENCE 2 (bases 1 to 1701)
AUTHORS Shinde,V., Bridges,C.B., Uyeki,T., Shu,B., Balish,A., Xu,X.,
Lindstrom,S., Gubareva,L., Garten,R.J., Deyde,D., Harris,M.,
Gerber,S., Vagoski,S., Smith,F., Pascoe,N., Martin,K., Dufficy,D.,
Ritger,K., Conover,C., Quinlisk,P., Klimov,A., Bresee,J. and
Finelli,L.
TITLE Direct Submission
JOURNAL Submitted (05-MAY-2009) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, Atlanta, 1600 Clifton Road,
N.E., Atlanta, GA 30333, USA
COMMENT ##FluData-START##
Organism Name Influenza A virus (A/Ohio/01/2007 (H1N1))
Country USA
District Ohio
Collection Date 17-Aug-2007
Host Human
Subtype H1N1
Passage History Original
Age 36
Gender M
special_notes Human infection with swine triple reassortant H1N1
##FluData-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Ohio/01/2007(H1N1))"
/mol_type="viral cRNA"
/strain="A/Ohio/01/2007"
/serotype="H1N1"
/host="Homo sapiens; age 36; gender M"
/db_xref="taxon:643703"
/segment="4"
/country="USA: Ohio"
/collection_date="17-Aug-2007"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACQ73203.1"
/db_xref="GI:229473302"
/translation="MKAILVVLLYTFTTANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVNLLENRHNGKLCKLRGVAPLHLGKCNIAGWLLGNPECESLSTASSWSYIVETSNS
DNGTCYPGDFINYEELREQLSSVSSFERFEIFPKTSSWPNHDTNRGVTAACPHAGTNS
FYRNLIWLVKKGNSYPKINKSYINNKEKEVLVLWAIHHPSTSADQQSLYQNADAYVFV
GSSRYSRKFEPEIATRPKVRDQAGRMNYYWTLVEPGDKITFEATGNLVVPRYAFALKR
NSGSGIIISDTSVHDCDTTCQTPNGAINTSLPFQNIHPVTIGECPKYVKSTKLRMATG
LRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADLKSTQNAIDGI
TNKVNSVIEKMNTQFTAVGKEFSHLERRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDDTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
ORIGIN
1 atgaaggcaa tactagtagt cctgctatat acatttacaa ccgcaaatgc cgacacatta
61 tgtataggtt atcatgcgaa caattcaact gacaccgtag acacagtact agaaaagaat
121 gtaacagtaa cacactctgt caaccttcta gaaaacaggc ataatgggaa actatgtaaa
181 ctaagagggg tagctccatt gcatttgggt aaatgtaaca ttgctggctg gctcctggga
241 aatccagagt gtgaatcact ctccacagca agctcatggt cctacattgt ggaaacatct
301 aattcagaca atgggacgtg ttacccagga gatttcatca attatgagga gctaagagag
361 cagttgagct cagtgtcatc atttgaaaga tttgagatat tccccaagac aagttcatgg
421 cccaatcatg acacgaacag aggtgtgacg gcagcatgtc ctcatgctgg gacaaacagc
481 ttctacagaa atttaatatg gctggtcaaa aaaggaaatt catacccaaa gatcaacaaa
541 tcctacatta acaataaaga gaaggaagtt ctcgtgctat gggccattca ccatccatct
601 accagtgccg accaacaaag tctctaccaa aatgcagatg cctatgtttt tgtggggtca
661 tcaagataca gcaggaagtt cgagccagaa atagcaacaa gacccaaggt gagggaccaa
721 gcagggagaa tgaactatta ctggacacta gtagagcctg gagacaagat aacattcgaa
781 gcaactggaa atctagtggt accgagatat gccttcgcat tgaaaagaaa ttctggatct
841 ggtattatca tttcagatac atcagtccac gattgtgata cgacttgtca gacacccaat
901 ggtgctataa acaccagcct cccatttcaa aatatacatc cagtcacaat tggagaatgt
961 ccaaaatatg taaaaagtac taaactgaga atggccacag gattaaggaa tatcccgtct
1021 attcaatcta gaggcctgtt tggggccatt gctggcttta ttgaaggggg ctggacagga
1081 atgatagatg gatggtacgg ttatcaccat caaaatgagc agggatcagg atatgcagcc
1141 gacctgaaga gcacacagaa tgccattgac gggatcacta acaaggtaaa ttctgttatt
1201 gaaaagatga acacacaatt cacagcagta ggtaaagagt tcagccactt ggaaagaaga
1261 atagagaatt taaataaaaa ggttgatgat ggttttctag atatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggatt accacgactc aaatgtgaaa
1381 aacttatatg aaaaagtaag aagccaacta aaaaacaatg ccaaggaaat tggaaatggc
1441 tgctttgaat tttaccacaa atgtgatgac acgtgcatgg aaagcgtcaa aaatgggact
1501 tatgattacc caaaatactc agaggaagca aaactaaaca gagaggaaat agatggggta
1561 aagttggaat caacaaggat ttaccaaatt ttggcgatct attcaacggt cgccagttca
1621 ttggtactgg tagtctccct gggggcaatc agtttctgga tgtgctctaa tgggtcgcta
1681 cagtgcagaa tatgtattta a

_________________
www.twitter.com/hniman

I reproduced below a table from a recent paper regarding the 1918 and 2009 pandemics, and natural human antibodies (1).

According to the table, (A/swine/Iowa/15/1930(H1N1)) also had KKEN in the respective antigenic site.

This is apparently comparable to the “normal” pH1N1 low reactor, which has the same amino acids in this particular area.

Is this strain A/swine/Iowa/03032/2010, version also a low reactor? It this the main concern regarding this isolate?


1.Jens C. Krause, Terrence M. Tumpey, Chelsey J. Huffman,Patricia A. McGraw, Melissa B. Pearce, Tshidi Tsibane, Rong Hai, Christopher F. Basler, and James E. Crowe,Jr.
Naturally Occurring Human Monoclonal Antibodies Neutralize both 1918 and 2009 Pandemic Influenza A (H1N1) Viruses_
JOURNAL OF VIROLOGY, Vol. 84, No. 6 p. 3127–3130 (Mar. 2010).

The two concerns are a duplicate G158E and acquisition of pH1N1 polymorphisms via recombination.

_________________
www.twitter.com/hniman