Rhiza Labs FluTracker Forum

CDC week 44 report updates the two cases and indicates there were differences in the sequences (indicating different sources):

Two cases of human infection with a novel influenza A virus were reported: one case by the Wisconsin Department of Health Services and one case by the Pennsylvania Department of Health. Both patients were infected with a swine origin influenza A (H3N2) virus similar to the three other swine origin influenza A (H3N2) viruses previously identified in 2009 and 2010. The Wisconsin case reported contact with pigs in the week preceding symptom onset on September 8, 2010 and required hospitalization. No contact with pigs has been identified in the Pennsylvania case in the week before symptom onset on October 24, 2010; however the case lives in an area close to pig farms. Both patients have fully recovered from their illness. The cases are not related and the viruses from these two cases have some genetic differences, indicating that they did not come from the same source.

Although both investigations are ongoing, there is no evidence of human-to-human transmission with this virus in either case. Early identification and investigation of human infections with novel influenza A viruses is critical to evaluate the extent of the outbreak and possible human-to-human transmission. Surveillance for human infections with novel influenza A viruses continues year round.

http://cdc.gov/flu/weekly/

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November 12, 2010

Reports of Human Infections with Swine Origin Influenza A (H3N2)

The November 12, 2010 FluView reports two human infections with swine origin influenza A (H3N2) viruses in the United States. Test samples from two patients submitted by Wisconsin and Pennsylvania have been confirmed at CDC as positive for swine origin triple-reassortant (tr) H3N2 influenza viruses—viruses that normally infect pigs. While human infection with swine influenza viruses is rare, it can occur. This is most likely to occur when people are in close proximity to infected pigs, such as in pig barns and livestock exhibits housing pigs at fairs. Both of the patients with confirmed trH3N2 infection reported in FluView were in the vicinity of live pigs. Dates of illness onset in the two patients are more than six weeks apart and the viruses from the two patients have some genetic differences, confirming that these two cases are not linked. Ongoing investigations in both states have not shown any evidence of community transmission of these viruses. The most likely scenario at this point is that these are two isolated cases of human infection with swine influenza viruses that, while very rare, do occur from time to time. Both patients have fully recovered from their illnesses; however, these two cases do underscore the importance of human and animal surveillance for influenza.

These two cases reported in FluView bring the total number of human infections with swine origin influenza viruses reported to CDC since 2005 to 18. Previously, three of these reports had been swine origin A (H3N2) viruses. The Pennsylvania and Wisconsin cases bring the number of reports swine origin A (H3N2) infections in humans in the United States to five. The viruses identified in Pennsylvania and Wisconsin are similar to viruses that infected a patient in Iowa in September 2009, a patient in Kansas in August 2009 and a patient in Minnesota in May 2010.

http://www.cdc.gov/media/subtopic/heard.htm#h3n2

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As you see Dr.Henry, it was imprudent to speak about a new pandemic emerging almost 100% when data wasn't enough and was not coming out of official sources.

I said to you waiting for more information before spreading alarmist news. This is a good practise in medicine and life.

Please, edit the title of this thread, it may be confusing.

-------

Now, we need to see sequences and the final results of the ongoing investigation. Also, characterization of flu A viruses in circulation previous to these cases and curret ones is warranted.

Right now, a swine H3N2 pandemic is unlikely with current data.

Thank you.

As noted, the thread was for discussion and dependent on the sequence similarity, which the CDC says shows differences. However, although there now have been 5 examples in just over a year, and none earlier, I don't think that ANY of the human H3N2 sequences have been released.

This frequency of human H3N2 cases is similar to the H1N1 frequency that preceeded the H1N1 pandemic. These two cases bring the number of examples reported in 2010 to FOUR (IA, MN, WI, PA), so a swine H3N2 pandemic may be very close and such a discussion under a thread entitled "Swine H3N2 Pandemic" is most appropriate.

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I think you are confused. I said that if the two cases were not linked AND the sequences matched, the the likelihood of a pandemic was near 100%. The "official" source did not contradict the pager alert (other than noting that the Illinois case was reported by Wisconsin, which is adjacent to Illinois).

The cases were 6 weeks apart and the sequences don't match, so criteria for the 100% estimate was not met.

Qualifiers are included for a reason, and summary statements made which ignore the qualifiers are misleading, at best.

The failure to meet the qualifiers was NOT linked to an unreliable source, In fact the source brought this situation to light 2 days ahead of the CDC report, and the information was NOT carried by western Europe.

Detection of these cases requires sequencing, which should be increased and results should be made public.

Public sequences of isolates fromhumans infected by swine H3N2 is lacking worldwide.

_________________
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Below is a Minnesota swine sequence collected just prior to the Minnesota case in May, 2010:

LOCUS HM217202 1701 bp cRNA linear VRL 23-MAY-2010
DEFINITION Influenza A virus (A/swine/Minnesota/03008/2010(H3N2)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION HM217202
VERSION HM217202.1 GI:296238981
KEYWORDS .
SOURCE Influenza A virus (A/swine/Minnesota/03008/2010(H3N2))
ORGANISM Influenza A virus (A/swine/Minnesota/03008/2010(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Gramer,M., Juleen,K., Foss,A., Wees,C., Raymond,L., Leiferman,M.
and Otterson,T.
TITLE Direct Submission
JOURNAL Submitted (12-MAY-2010) Veterinary Diagnostic Laboratory,
University of Minnesota, 1333 Gortner Ave, St. Paul, MN 55108, USA
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus
(A/swine/Minnesota/03008/2010(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Minnesota/03008/2010"
/serotype="H3N2"
/host="swine"
/db_xref="taxon:764347"
/segment="4"
/country="USA"
/collection_date="22-Apr-2010"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADH01504.1"
/db_xref="GI:296238982"
/translation="MKTIIAFSCILCQIFAQKLPGSDNSMATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGRICSSPHQILDGKNCTLIDALLGDPHCDDFQNKKWDL
FVERSTAYSNCYPYYVPDYASLRSLVASSGTLEFTQESFNWTGVAQDGSSYACRREPD
NSFFSRLNWLYHLNYKYPALNVTMPNNDKFDKLYIWGVHHPGTDKDQTNLYVQASGRV
TVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMKSDAPIGNCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAITQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
HTIDLTDSEMNKLFERTRKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYR
DEALNNRFQIKGVQLKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICV
"
ORIGIN
1 atgaagacta tcattgcttt cagctgcatt ttatgtcaga ttttcgctca aaaacttccc
61 ggaagtgaca acagcatggc aacgctgtgc ctgggacacc atgcagtacc aaacggaacg
121 ttagtgaaaa caatcactga tgaccaaatt gaagtgacta atgctactga gctggtccag
181 agttcctcaa caggtagaat atgcagcagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag acgctctatt gggagaccct cattgtgatg atttccaaaa caagaaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta tgtgccggat
361 tatgcctccc ttagatcgct agttgcctca tccggcaccc tggaatttac ccaagaaagc
421 ttcaattgga ctggagttgc tcaagacgga tcaagctatg cttgcaggag ggaacctgat
481 aacagtttct ttagtagatt gaattggttg tatcatttga attacaaata tccagcgctg
541 aacgtaacta tgccaaacaa tgacaaattt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacgg acaaggacca aaccaaccta tatgttcaag catcagggag agttacagtt
661 tccaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtctaggcc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acaatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cgaggttact tcaaaataca aagtgggaaa
841 agctcaataa tgaagtcaga tgcacccatt ggcaactgca attctgaatg cattactcca
901 aatggaagca ttcccaatga caaacctttt caaaatgtaa acaggatcac atatggggcc
961 tgtcccagat atgttaagca aaacactctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa caagaggcat attcggcgca attgcaggtt tcatagaaaa tggttgggag
1081 gggatggttg acggttggta cggtttcagg catcaaaatt ctgaaggcac agggcaagca
1141 gcagatctta aaagcactca agcagcaatc acccaaatca ccgggaaact aaatagagta
1201 atcaagaaga cgaacgagaa attccatcag atcgaaaaag aattctcaga agtagaaggg
1261 agaattcagg acctagagaa atacgttgaa gacactaaaa tagatctctg gtcttacaac
1321 gcggagctcc ttgttgcact ggagaaccaa catacaattg atttaactga ctcagaaatg
1381 aacaaactgt tcgaaagaac aagaaagcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttta aaatatacca caaatgtgac aatgcctgca taggatcaat cagaaatgga
1501 acttatgacc ataatgtata cagagacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctga aatcaggata caaagattgg atcctatgga tttcctttgc catatcatgc
1621 tttttgcttt gtgttgttct gctggggttc attatgtggg catgccaaaa aggcaacatt
1681 aggtgcaaca tttgcgtttg a

_________________
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Below is a sequence from Kansas swine deposited just after the Kansas case in August 2009:

LOCUS CY045559 1762 bp cRNA linear VRL 02-SEP-2009
DEFINITION Influenza A virus (A/swine/Kansas/015252/2009(H3N2)) segment 4
sequence.
ACCESSION CY045559
VERSION CY045559.1 GI:257127203
KEYWORDS .
SOURCE Influenza A virus (A/swine/Kansas/015252/2009(H3N2))
ORGANISM Influenza A virus (A/swine/Kansas/015252/2009(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1762)
AUTHORS Evseenko,V., Boon,A., Webby,R., Daniels,C.S. and Gramer,M.
TITLE Unpublished
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1762)
AUTHORS Evseenko,V., Boon,A., Webby,R., Daniels,C.S. and Gramer,M.
TITLE Direct Submission
JOURNAL Submitted (02-SEP-2009) Infectious Diseases, St. Jude Children's
Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee
38105, USA
FEATURES Location/Qualifiers
source 1..1762
/organism="Influenza A virus
(A/swine/Kansas/015252/2009(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Kansas/015252/2009(H3N2)"
/serotype="H3N2"
/host="swine"
/db_xref="taxon:670137"
/segment="4"
/country="USA"
/collection_date="2009"
misc_feature 1..1762
/db_xref="IRD:CEIRS-SJC001-173310.4"
gene 30..1730
/gene="HA"
CDS 30..1730
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACV42084.1"
/db_xref="GI:257127204"
/translation="MKTIIAFSYILCLIFAQKLPGSDNGMATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGRICNSPHQILDGKNCTLIDALLGDPHCDDFQNKEWDL
FVERSTAYSSCYPYYVPDYASLRSLVASSGTLKFTQKSFNWTGVAQNGASYACKRESV
NSFFSKLNWLHNLDYKYPALNVTMPNNDEFDKLYIWGVHHPGTDKDQTNLYVQASGRV
TVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMRSDAPIGNCNSECITPNGSISNDKPFQNVNRITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKVDLWSYNAELLVALENQ
HTIDLTDSEMNKLFERTRKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYR
DEALNNRFQIKGVQLKSGYKDWILWISFATSCFLLCVVLLGFIMWACQKGNIRCNICI
"
sig_peptide 30..77
/gene="HA"
mat_peptide 78..1064
/gene="HA"
/product="HA1"
mat_peptide 1065..1727
/gene="HA"
/product="HA2"
ORIGIN
1 agcaaaagca ggggatattt ctattaacca tgaagactat cattgctttt agctacattt
61 tatgtctgat tttcgctcaa aaacttcccg gaagtgacaa cggcatggca acgctgtgcc
121 tgggacacca tgcagtaccg aacggaacgt tagtgaaaac aattacggat gaccaaattg
181 aagtgactaa tgctactgag ctggttcaga gttcctcaac aggaagaata tgcaacagtc
241 ctcaccaaat tcttgatggg aaaaattgca cactgataga tgctctattg ggagaccctc
301 attgtgatga cttccaaaac aaggaatggg acctttttgt tgaacgaagc acagcctaca
361 gcagctgtta cccttattat gtgccggatt atgcctccct taggtcacta gttgcctcat
421 ccggcaccct gaaatttacc caaaaaagct tcaattggac tggagttgct caaaatggag
481 caagctatgc ttgcaaaagg gaatctgtta acagtttctt tagtaaattg aactggttgc
541 ataatttgga ttacaaatat ccagcgctga acgtaactat gcccaacaat gacgaatttg
601 acaaattgta catttggggg gtccaccacc cgggtacgga caaggaccaa accaacctat
661 atgttcaagc atcagggaga gttacagtct ccaccaaaag aagccaacaa actgtaatcc
721 cgaatatcgg gtctagaccc tgggtaaggg gtgtctccag cataataagc atctattgga
781 caatagtaaa accgggagac atacttttga ttaacagcac agggaatcta attgcccctc
841 ggggttattt caaaatacaa agtgggaaaa gctcaataat gaggtcagat gcacccattg
901 gcaactgcaa ttctgagtgc attactccaa atggaagcat ttccaatgac aaaccttttc
961 aaaatgtaaa caggatcaca tatggggcct gtcccaggta tgttaagcaa aacactctga
1021 aattggcaac agggatgcgg aatgtaccag agaaacaaac tagaggcata ttcggcgcaa
1081 tcgcaggttt catagaaaat ggttgggagg ggatggtgga cggttggtac ggtttcaggc
1141 atcagaattc tgaaggcaca ggacaagcag cagatcttaa aagcactcaa gcagcaatca
1201 accaaatcac cgggaaacta aatagggtaa tcaagaaaac gaacgagaaa ttccatcaaa
1261 tcgaaaaaga attctcagaa gtagaaggga gaattcagga cctagagaaa tacgttgaag
1321 acactaaagt agatctctgg tcttacaatg cggagcttct tgttgctctg gagaaccaac
1381 atacaattga tttaactgac tcagaaatga acaaactgtt cgaaagaaca agaaagcaac
1441 tgcgggaaaa tgctgaggac atgggcaatg gttgcttcaa aatataccac aagtgtgata
1501 atgcttgcat agggtcaatc agaaatggaa cttatgacca tgatgtatac agagacgagg
1561 cattaaacaa tcggttccag atcaaaggtg ttcagctgaa gtcaggatac aaagattgga
1621 tcctatggat ttcctttgcc acatcatgct ttttgctttg tgttgttctg ctggggttca
1681 ttatgtgggc ctgccaaaag ggcaacataa gatgcaacat ttgcatttga gtgcattaat
1741 taaaaacacc cttgtttcta ct

_________________
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Most recent full swine HA sequence from Illinois (none from Wisconsin)

LOCUS HM778115 1649 bp cRNA linear VRL 22-AUG-2010
DEFINITION Influenza A virus (A/swine/Illinois/03040/2010(H3N2)) segment 4
hemagglutinin (HA) gene, partial cds.
ACCESSION HM778115
VERSION HM778115.1 GI:303305451
KEYWORDS .
SOURCE Influenza A virus (A/swine/Illinois/03040/2010(H3N2))
ORGANISM Influenza A virus (A/swine/Illinois/03040/2010(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1649)
AUTHORS Gramer,M., Juleen,K., Foss,A., Wees,C., Raymond,L., Leiferman,M.
and Otterson,T.
TITLE Direct Submission
JOURNAL Submitted (20-JUL-2010) Veterinary Diagnostic Laboratory,
University of Minnesota, 1333 Gortner Ave, St. Paul, MN 55108, USA
FEATURES Location/Qualifiers
source 1..1649
/organism="Influenza A virus
(A/swine/Illinois/03040/2010(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Illinois/03040/2010"
/serotype="H3N2"
/host="swine"
/db_xref="taxon:866598"
/segment="4"
/country="USA"
/collection_date="18-Jun-2010"
gene 1..>1649
/gene="HA"
CDS 1..>1649
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADM13519.1"
/db_xref="GI:303305452"
/translation="MKTIIAFSYISCLIFAQKLPGSDNSMATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGRICNSPHQILDGKNCTLIDALLGDPHCDDFQNKGWDL
FVERSTAYSNCYPYYVPDYTSLRSLVASSGTLEFTQESFNWTGVAQDGSSYACKRKSV
NSFFSRLNWLHSLNYKYPALNVTMPNNDKFDKLYIWGVHHPGTDKDQTNLYVQASGGV
TVSTKRNQQTVIPNIGSRPWVRGVSSIISIHWTIVKPGDILLINSTGNIIAPRGYFKI
QSEKSSIMRSDAPIGNCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIEKWLGRDGGRLVRFRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
HTIDLTDSEMNKLFERTRKQLRENAEDMGNGCLKIYHKCDNACIESIRNGTYDHDVYR
DEALNNRFQIKGVQLKSGYKDWILWISFATSCFLLCVVLLG"
ORIGIN
1 atgaagacta tcattgcttt tagctacatt tcatgtctga ttttcgccca aaaacttccc
61 ggaagtgaca acagcatggc aacgctatgc ctgggacacc atgcagtacc aaacggaacg
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctactga gctggttcag
181 agttcctcaa caggtagaat atgcaacagt cctcatcaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggagaccct cattgtgatg acttccaaaa caagggatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgct acccttatta tgtgccggat
361 tatacctccc ttaggtcact agttgcctca tctggcaccc tggaattcac ccaagaaagc
421 ttcaattgga ctggagttgc tcaagatgga tcaagctatg cttgcaaaag gaaatctgtt
481 aacagtttct ttagtagatt aaattggttg catagtttga attacaaata tccagcgctg
541 aacgtaacta tgccaaacaa tgacaaattt gacaaattgt acatttgggg ggttcaccac
601 ccaggtacgg acaaggacca aaccaaccta tatgttcaag catcaggggg agttacagtc
661 tccaccaaaa gaaaccaaca aactgtaatc ccgaatatcg gatctagacc ctgggtaagg
721 ggtgtctcca gcataataag catccattgg acaatagtaa aaccgggaga catacttttg
781 attaacagca cagggaacat aatcgcccct cggggttact tcaaaataca aagtgagaaa
841 agctcaataa tgagatcaga tgcacccatc ggcaactgca attctgaatg cattactcca
901 aatggaagca ttcccaatga caaacctttt caaaatgtaa acaggatcac gtatggggcc
961 tgccccagat atgttaagca aaacactctg aaattggcaa cagggatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat attcggcgca atcgcaggtt tcatagaaaa atggttggga
1081 agggatggtg gacggttggt acggttcagg catcaaaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca ggcagcaatc aaccaaatca ccgggaaact aaatagagta
1201 atcaagaaaa caaacgagaa attccatcag atcgaaaaag aattctcaga agtagaaggg
1261 agaattcagg acctagagaa atacgttgaa gatactaaaa tagatctctg gtcttacaat
1321 gcggagcttc ttgttgccct agagaaccaa catacaattg atttaactga ctcagaaatg
1381 aacaaactgt tcgaaagaac aaggaagcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttaa aaatatacca caaatgtgac aatgcctgca tagaatcaat cagaaatgga
1501 acttatgatc atgatgtata cagagacgag gcattaaaca atcgattcca gatcaaaggt
1561 gttcagctga agtcaggata caaagattgg atcctatgga tttcctttgc cacatcatgc
1621 tttttgcttt gtgttgttct gctgggttt

_________________
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Question, noting the categories below, Why would the Page Alert go out in the first place if this swineH3N2 was not of concerne in it transmitting, and in the second place, WHY send this out to Europe, etc...if it is not a H2H transmission event? If an ALERT warrants immediate attention, and conveys the highest level of importance...again, then WHY send out an alert for something that does not transmit H2H?


WHO Page Aert:Categories of Health Alert Messages:

Health Alert
Conveys the highest level of importance; warrants immediate action or attention.

Health Advisory
Provides important information for a specific incident or situation; may not require immediate action.

Health Update
Provides updated information regarding an incident or situation; unlikely to require immediate action.

I have found the sequences from the patient (22M) from Kansas, A/Kansas/13/2009. Full sequences of all 8 gene segments are at GISAID. The were submitted by the CDC in February.

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