Rhiza Labs FluTracker Forum

Misleading comment in latest "Have You Heard?" on latest cases in Maine and Indiana

http://www.cdc.gov/media/haveyouheard/s ... irus2.html

These reports bring the total number of confirmed cases of human infection with swine–origin influenza A viruses in the United States to 28 since 2005, with 15 of these having been infected with swine–origin influenza A (H3N2) viruses, and seven of these being the H3N2 virus with the M gene from the 2009 H1N1 virus.

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The above comments are technically correct, but EXTREMELY misleading, All trH1 cases were prior to the 2009 pandemic, while all trH3N2 cases were after the start of the pandemic (first case was in August, 2009). Similarly, all cases with H1N1pdm09 have been in 2011 (first case in July, 2011). The trH3N2 was CLEARLY adapting to humans in 2010 and was speard in humans in 2011 as the latest version, which is an evolved 2010 sequence which has acquired a H1N1pdm09 M gene (along with reassortment acquisiions of N2 and PB1).

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Sequences from the two most recent cases still cannot be accessed at Genabnk:

A/Indiana/10/2011 at http://www.ncbi.nlm.nih.gov/nuccore/JN992750

A/Maine/07/2011 at http://www.ncbi.nlm.nih.gov/nuccore/JN992747


This record has not yet been released. Please contact info@ncbi.nlm.nih.gov with the publication details if the accession has been published.

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Commentaries soon on significance of misleading dates and reports by CDC, WHO, media, and ProMED.

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Commentary

http://www.recombinomics.com/News/11131 ... Error.html

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The time from infection to illness, known as the incubation period, is about two days.
http://www.who.int/mediacentre/factsheets/fs211/en/

Other sites quote 1-4 days for the incubation period for influenza.

The first Maine case (8M, A/Maine/06/2011) was said to have visited an agricultural fair in the WEEK prior to symptoms. Since the case was from Cumberland County, the fair was almost certainly the Cumberland County fair, which was an agricultural fair that ended October 2, the week before the disease onset date of October 7 (sample collected Oct 10), but OUTSIDE of the normal incubation period of 1-4 days.

The CDC FluView had less information regarding the second case from Maine, which just had a swine exposure (the "Have You Heard?" for cases 6 & 7 cited exposure a week prior to symptoms, but referenced the week 41 FluView which descibed the FIRST Maine case and cited exposure of a week before onset). The Maine DoH just said the exposure was also an agricultural fair and since the case was in the same vicinity as the first case and the sequences of the trH3N2 from both cases in Maine are virtually identical, it is likely that the agricultural fair cited was also the Cumberland County fair. However, disease onset for the second Maine case was 2 weeks (Oct 22, sample collected Oct 24), after the first (Oct 7. sample collected Oct 10) essentially ruling out the Cumberland County fair and associated swine as a source for A/Maine/07/2011.

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Commentary

http://www.recombinomics.com/News/11131 ... _FluA.html

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LOCUS JN992747 230 bp cRNA linear VRL 14-NOV-2011
DEFINITION Influenza A virus (A/Maine/07/2011(H3N2)) segment 4 hemagglutinin
(HA) gene, partial cds.
ACCESSION JN992747
VERSION JN992747.1 GI:356598740
KEYWORDS .
SOURCE Influenza A virus (A/Maine/07/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/07/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 230)
AUTHORS Garten,R.
TITLE Direct Submission
JOURNAL Submitted (07-NOV-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/07/2011
Subtype :: H3N2
Segment_name :: HA
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 24
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human infection with SOIV triple
reassortant H3N2 possessing an M gene
from H1N1pdm.? ; Originating Laboratory:
Maine Health and Environmental Testing
Laboratory, Virology Section Department
of Human Services 221 State St, 04333,
Augusta, United States
EPI_accession :: EPI340976
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..230
/organism="Influenza A virus (A/Maine/07/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/07/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1111138"
/segment="4"
/country="USA"
/collection_date="24-Oct-2011"
gene <1..>230
/gene="HA"
CDS <1..>230
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AET21590.1"
/db_xref="GI:356598741"
/translation="SDAPIDECNSECITPNGSIPNDKPFQNVNKITYGACPRYVKQNT
LKLATGMRNVPEKQTRGIFGAIAGFIENGWEG"
ORIGIN
1 tcagatgcac ccattgatga atgcaattct gaatgcatta ctccaaatgg aagcattccc
61 aatgacaaac cttttcaaaa tgtaaacaag atcacatatg gagcctgtcc cagatatgtt
121 aagcaaaaca ccctgaaatt ggcaacagga atgcggaatg taccagagaa acaaactaga
181 ggcatattcg gcgcaattgc aggtttcata gaaaatggtt gggagggaat

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LOCUS JN992750 1701 bp cRNA linear VRL 14-NOV-2011
DEFINITION Influenza A virus (A/Indiana/10/2011(H3N2)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION JN992750
VERSION JN992750.1 GI:356598746
KEYWORDS .
SOURCE Influenza A virus (A/Indiana/10/2011(H3N2))
ORGANISM Influenza A virus (A/Indiana/10/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Garten,R.
TITLE Direct Submission
JOURNAL Submitted (07-NOV-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Indiana/10/2011
Subtype :: H3N2
Segment_name :: HA
Host_gender :: M
Host_age :: 59
Passage_history :: X1
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Indiana
Collection_day :: 22
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human infection with SOIV triple
reassortant H3N2 possessing an M gene
from H1N1pdm.? ; Originating Laboratory:
Indiana State Departmnet of Health
Laboratories, 550 W. 16th St., Suite B,
46202-5120, Indianapolis, United States
EPI_accession :: EPI340984
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Indiana/10/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Indiana/10/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 59"
/db_xref="taxon:1111139"
/segment="4"
/country="USA"
/collection_date="22-Oct-2011"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AET21593.1"
/db_xref="GI:356598747"
/translation="MKTIIAFSCILCLIFAQKLPGSDNSMATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGRICNSPHQILDGKNCTLIDALLGDPHCDDLQNKEWDL
FVERSTAYSNCYPYYVPDYATLRSLVASSGNLEFTQESFNWTGVAQDGSSYACRRGSV
NSFFSRLNWLYNLNYKYPEQNVTMPNNDKFDKLYIWGVHHPGTDKDQTNLYVQASGRV
IVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMRSDAHIDECNSECITPNGSIPNDKPFQNVNKITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
HTIDLTDSEMSKLFERTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDIYR
NEALNNRFQIKGVQLKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICI
"
ORIGIN
1 atgaagacta tcattgcttt tagctgcatt ttatgtctga ttttcgctca aaaacttccc
61 ggaagtgaca acagcatggc aacgctgtgc ctgggacacc atgcagtgcc aaacggaaca
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctactga gctggtccag
181 agttcctcaa caggcagaat atgcaacagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggggaccct cattgtgatg acctccaaaa caaggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta tgtgccagat
361 tatgccaccc ttaggtcact agttgcctca tctggcaacc tggaatttac ccaagaaagc
421 ttcaattgga ctggagttgc tcaagacgga tcaagctatg cctgcagaag gggatctgtt
481 aacagtttct ttagtagatt gaattggttg tataacttga attacaagta tccagagcag
541 aacgtaacta tgccaaacaa tgacaaattt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacgg acaaggacca aaccaatcta tatgtccaag catcagggag agttatagtc
661 tctaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtctagacc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acgatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa
841 agctcaataa tgagatcaga tgcacacatt gatgaatgca attctgaatg cattactcca
901 aatggaagca ttcccaatga caaacctttt caaaatgtaa acaagatcac atatggagcc
961 tgtcccagat atgttaagca aaacaccctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat attcggcgca attgcaggtt tcatagaaaa tggttgggag
1081 ggaatggtag acggttggta cggtttcagg catcagaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca agcagcaatc aaccaaatca ccgggaaact aaatagagta
1201 atcaagaaaa cgaacgagaa attccatcaa atcgaaaaag aattctcaga agtagaaggg
1261 agaattcagg acctagagaa atacgttgaa gacaccaaaa tagatctctg gtcttacaac
1321 gctgagcttc ttgttgccct ggagaaccaa catacaattg atttaaccga ctcagagatg
1381 agcaaactgt tcgaaagaac aagaaggcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttca aaatatacca caaatgtgac aatgcctgca taggatcaat cagaaatgga
1501 acttatgacc atgatatata cagaaacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctaa agtcaggata caaagattgg atcctatgga tttcctttgc catatcatgc
1621 tttttgcttt gtgttgttct gctggggttc attatgtggg cctgccaaaa aggcaacatt
1681 aggtgcaaca tttgcatttg a

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Commentary

http://www.recombinomics.com/News/11141 ... 6_NOT.html

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