Rhiza Labs FluTracker Forum

Today is the one year anniversary of the H1N1 pandemic in the US. On March 30 the first sample from a child (9F) in southern California was collected and on April 1 the sample from a second child (10M) was collected. Sequences from these two samples (California/5/2009 and California/4/2009) were virtually identical and were swine H1N1 even though neither child was linked to swine or each other. Therefore, it was clear that a pandemic involving a jump of swine H1N1 to humans had begun.

The subsequent sequencing of samples from cases in Mexico left no doubt that the virus had already spread far and wide in North America, and within days additional cases throughout the US were lab confirmed.

In the year that followed the striking similarities between 2009 H1N1 and 1918 H1N1 accumulated, and these similarities invalidated the influenza surveillance program. The H1N1 primarily attcked those under 65 and quickly moved to the lung, creating a long series of false negatives from samples collected from the upper respiratory tract. In addition to false negatives by the rapid test as well as PCR tests, sequences from the upper respiratory tract differed from the lower respiratory tract.

As a result, a fantasy was created by extremely biased sampling and testing to create gross under-representations of infections and deaths.

The much cited 36,000 deaths for seasonal flu is not based on lab confirmation, but is linked to P&I data, which shows significant similarities between the number of pandemic deaths and seasonal flu deaths, even though 90% of the seasonal deaths are over 65, and 90% of pandemic deaths are under 65.

Thus, the CDC extrapolation of 2,000 lab confirmed H1N1 deaths to 12,000 true deaths is still a gross under-representation of the true number of deaths, which is why this week's P&I death rate is above the epidemic threshold, even though no state is reporting widespread H1N1 and only 3 southeastern states are reporting regional levels. The number of samples tested is at an all time low because the current surveillance is geared toward seasonal flu and an older population.

In short the weekly reports on lab confirmed cases have created a fantasy, which has little to do with the number of H1N1 infections and deaths in the US.

_________________
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LOCUS FJ966952 1701 bp cRNA linear VRL 17-AUG-2009
DEFINITION Influenza A virus (A/California/05/2009(H1N1)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION FJ966952
VERSION FJ966952.1 GI:227831758
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/California/05/2009(H1N1))
ORGANISM Influenza A virus (A/California/05/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Dawood,F.S., Jain,S., Finelli,L., Shaw,M.W., Lindstrom,S.,
Garten,R.J., Gubareva,L.V., Xu,X., Bridges,C.B. and Uyeki,T.M.
CONSRTM Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team
TITLE Emergence of a novel swine-origin influenza A (H1N1) virus in
humans
JOURNAL N. Engl. J. Med. 360 (25), 2605-2615 (2009)
PUBMED 19423869
REMARK Erratum:[N Engl J Med. 2009 Jul 2;361(1):102]
REFERENCE 2 (bases 1 to 1701)
AUTHORS Garten,R.J., Davis,C.T., Russell,C.A., Shu,B., Lindstrom,S.,
Balish,A., Sessions,W.M., Xu,X., Skepner,E., Deyde,V.,
Okomo-Adhiambo,M., Gubareva,L., Barnes,J., Smith,C.B., Emery,S.L.,
Hillman,M.J., Rivailler,P., Smagala,J., de Graaf,M., Burke,D.F.,
Fouchier,R.A., Pappas,C., Alpuche-Aranda,C.M., Lopez-Gatell,H.,
Olivera,H., Lopez,I., Myers,C.A., Faix,D., Blair,P.J., Yu,C.,
Keene,K.M., Dotson,P.D. Jr., Boxrud,D., Sambol,A.R., Abid,S.H., St
George,K., Bannerman,T., Moore,A.L., Stringer,D.J., Blevins,P.,
Demmler-Harrison,G.J., Ginsberg,M., Kriner,P., Waterman,S.,
Smole,S., Guevara,H.F., Belongia,E.A., Clark,P.A., Beatrice,S.T.,
Donis,R., Katz,J., Finelli,L., Bridges,C.B., Shaw,M.,
Jernigan,D.B., Uyeki,T.M., Smith,D.J., Klimov,A.I. and Cox,N.J.
TITLE Antigenic and genetic characteristics of swine-origin 2009 A(H1N1)
influenza viruses circulating in humans
JOURNAL Science 325 (5937), 197-201 (2009)
PUBMED 19465683
REFERENCE 3 (bases 1 to 1701)
AUTHORS Shu,B., Balish,A., Garten,R., Smith,C., Emery,S., Barnes,J.,
Deyde,V., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (27-APR-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 Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009. For more information, see http://www.cdc.gov/

Some of the information does not have GenBank feature identifiers
and is being provided in the comment section.

##EpifluData-START##
Isolate A/California/05/2009
Subtype H1N1
Segment_name HA
Host_gender F
Host_age 9
Passage_history C1
Adamantane_resistance resistant
Zanamivir_resistance sensitive
Oseltamivir_resistance sensitive
Country USA
State/Province California state
Collection_day 30
Collection_month 3
Collection_year 2009
EPI_accession EPI176493
##EpifluData-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/California/05/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/California/05/2009"
/serotype="H1N1"
/host="Homo sapiens; gender F; age 9"
/db_xref="taxon:641807"
/segment="4"
/country="USA: California state"
/collection_date="30-Mar-2009"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACP41926.1"
/db_xref="GI:227831759"
/translation="MKAILVVMLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFV
GSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
ORIGIN
1 atgaaggcaa tactagtagt tatgctatat 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 atctagtggt accgagatat gcattcgcaa tggaaagaaa tgctggatct
841 ggtattatca tttcagatac accagtccac gattgcaata caacttgtca gacacccaag
901 ggtgctataa acaccagcct cccatttcag 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 agttgatgat ggtttcctgg acatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggact accacgattc aaatgtgaag
1381 aacttatatg aaaaggtaag aagccagcta 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

_________________
www.twitter.com/hniman

LOCUS FJ966082 1701 bp cRNA linear VRL 01-JUN-2009
DEFINITION Influenza A virus (A/California/04/2009(H1N1)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION FJ966082
VERSION FJ966082.1 GI:227809829
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/California/04/2009(H1N1))
ORGANISM Influenza A virus (A/California/04/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
CONSRTM Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team
TITLE Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in
Humans
JOURNAL N. Engl. J. Med. (2009) In press
PUBMED 19423869
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 1701)
AUTHORS Garten,R.J., Davis,C.T., Russell,C.A., Shu,B., Lindstrom,S.,
Balish,A., Sessions,W.M., Xu,X., Skepner,E., Deyde,V.,
Okomo-Adhiambo,M., Gubareva,L., Barnes,J., Smith,C.B., Emery,S.L.,
Hillman,M.J., Rivailler,P., Smagala,J., de Graaf,M., Burke,D.F.,
Fouchier,R.A., Pappas,C., Alpuche-Aranda,C.M., Lopez-Gatell,H.,
Olivera,H., Lopez,I., Myers,C.A., Faix,D., Blair,P.J., Yu,C.,
Keene,K.M., Dotson,P.D. Jr., Boxrud,D., Sambol,A.R., Abid,S.H., St
George,K., Bannerman,T., Moore,A.L., Stringer,D.J., Blevins,P.,
Demmler-Harrison,G.J., Ginsberg,M., Kriner,P., Waterman,S.,
Smole,S., Guevara,H.F., Belongia,E.A., Clark,P.A., Beatrice,S.T.,
Donis,R., Katz,J., Finelli,L., Bridges,C.B., Shaw,M.,
Jernigan,D.B., Uyeki,T.M., Smith,D.J., Klimov,A.I. and Cox,N.J.
TITLE Antigenic and genetic characteristics of swine-origin 2009 A(H1N1)
influenza viruses circulating in humans
JOURNAL Science 325 (5937), 197-201 (2009)
PUBMED 19465683
REFERENCE 3 (bases 1 to 1701)
AUTHORS Shu,B., Balish,A., Garten,R., Smith,C., Emery,S., Barnes,J.,
Deyde,V., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (27-APR-2009) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta,
GA 30333, USA
COMMENT GenBank Accession Numbers FJ966079-FJ966086 represent sequences
from the 8 segments of Influenza A virus
(A/California/04/2009(H1N1)).

Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009. For more information, see http://www.cdc.gov/.

Some of the information does not have GenBank feature identifiers
and is being provided in the comment section.

##FluData-START##
Isolate A/California/04/2009
Subtype H1N1
Host_gender M
Host_age 10
Passage_history CX
Adamantane_resistance resistant
Zanamivir_resistance sensitive
Oseltamivir_resistance sensitive
Country USA
State/Province California
Collection_day 1
Collection_month 4
Collection_year 2009
EPI_isolate GISAID EPI_ISL_29573
EPI_accession EPI176470
##FluData-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/California/04/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/California/04/2009"
/serotype="H1N1"
/host="Homo sapiens: gender M; age 10"
/db_xref="taxon:641501"
/segment="4"
/country="USA: California"
/collection_date="01-Apr-2009"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACP41105.1"
/db_xref="GI:227809830"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFV
GSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
LRNIPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
sig_peptide 1..51
/gene="HA"
mat_peptide 52..1032
/gene="HA"
/product="HA1"
mat_peptide 1033..1698
/gene="HA"
/product="HA2"
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 ggaaacacct
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 aatgcagata catatgtttt tgtggggtca
661 tcaagataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gagggatcaa
721 gaagggagaa tgaactatta ctggacacta gtagagccgg gagacaaaat aacattcgaa
781 gcaactggaa atctagtggt accgagatat gcattcgcaa tggaaagaaa tgctggatct
841 ggtattatca tttcagatac accagtccac gattgcaata caacttgtca aacacccaag
901 ggtgctataa acaccagcct cccatttcag aatatacatc cgatcacaat tggaaaatgt
961 ccaaaatatg taaaaagcac aaaattgaga ctggccacag gattgaggaa tatcccgtct
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 agttgatgat ggtttcctgg acatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggact accacgattc aaatgtgaag
1381 aacttatatg aaaaggtaag aagccagcta 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

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Commentary

http://www.recombinomics.com/News/04021 ... S_1st.html

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