Rhiza Labs FluTracker Forum

Nonsense. Sequence data clearly supports reassortment in human.

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There are 11 US trH3N2 swine isolates from 2011 and none have the H1N1pdm09 M gene with 7 trH3N2 gene segments, while this constellation is in all 5 human trH3N2 isolates from 2011 (from three states - Indiana, Pennsylvania, and Maine).
There are also 35 US trH3N2 swine isolates from 2010 (from which 21 were collected after October 24, 2010), and none have this constellation.
Moreover, the sequences in the 2011 human trH3N2 isolates are related to the sequences in the 2010 human trH3N2 isolates.

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The above data indicate there have been sequences released from 32 swine trH3N2 isolates from samples collected within the past 12 months, and none have the constellation of gene found in 5 of 5 human trH3N2 cases infected in 2011.

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New swine flu virus sickens 3 children in Pennsylvania
Pandemic unlikely, health experts say
Saturday, October 22, 2011
By Clarke Canfield, The Associated Press
PORTLAND, Maine -- An unusual strain of swine flu has infected five young children in Maine, Pennsylvania and Indiana, health officials said Friday.

A young boy of 7 or 8 from Cumberland County, Maine became the latest case when he came down with flu symptoms in early October, not long after being exposed to pigs at an agricultural fair, the Maine Center for Disease Control and Prevention said. He and the other four children have recovered, health officials said........



Read more: http://www.post-gazette.com/pg/11295/11 ... z1bWgnj000

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Cluster of 5 HA polymorphisms that are in all 2011 human trH3N2 cases
Genbank list:
JN866186.1 Influenza A virus (A/Maine/06/2011(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 44.1 44.1 100% 0.006 100%
JN652415.1 Influenza A virus (A/swine/Indiana/A01049653/2011(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 44.1 44.1 100% 0.006 100%
JN652492.1 Influenza A virus (A/swine/Indiana/A01049745/2011(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 44.1 44.1 100% 0.006 100%
JN652491.1 Influenza A virus (A/swine/Indiana/A01049744/2011(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 44.1 44.1 100% 0.006 100%
JN655537.1 Influenza A virus (A/Pennsylvania/09/2011(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 44.1 44.1 100% 0.006 100%
JN655546.1 Influenza A virus (A/Pennsylvania/11/2011(H3N2)) segment 4 hemagglutinin (HA) gene, partial cds 44.1 44.1 100% 0.006 100%
JN655548.1 Influenza A virus (A/Pennsylvania/10/2011(H3N2)) segment 4 hemagglutinin (HA) gene, partial cds 44.1 44.1 100% 0.006 100%
JN655556.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 4 hemagglutinin (HA) gene, partial cds 44.1 44.1 100% 0.006 100%
JN638733.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 44.1 44.1 100% 0.006 100%
JN162059.1 Influenza A virus (A/swine/North Carolina/A01049436/2011(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 44.1 44.1 100% 0.006 100%
JF812289.1 Influenza A virus (A/swine/Indiana/A01049091/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 44.1 44.1 100% 0.006 100%

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GISAID list
EPI339171 A/Maine/06/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI338562 A/swine/Indiana/A01049744/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI338561 A/swine/Indiana/A01049745/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI338421 A/swine/Indiana/A01049653/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI335629 A/Indiana/08/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI335623 A/Pennsylvania/10/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI335618 A/Pennsylvania/11/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI335610 A/Pennsylvania/09/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI333152 A/Indiana/08/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI328900 A/Minnesota/11/2010 X-203A (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI328898 A/Minnesota/11/2010 X-203 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI324857 A/swine/North Carolina/A01049436/2011 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI317003 A/swine/Indiana/A0109091/2010 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 41.7 2.534079e-04 22/22 (100%)

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New swine flu strain hits Maine
By CLARKE CANFIELD / Associated Press
Posted: 10/22/2011 03:00:00 AM EDT

Saturday October 22, 2011
PORTLAND, Maine -- An unusual strain of swine flu has infected five young children in Maine, Pennsylvania and Indiana, health officials said Friday.

A young boy of 7 or 8 from Cumberland County, Maine became the latest case when he came down with flu symptoms in early October, not long after being exposed to pigs at an agricultural fair, the Maine Center for Disease Control and Prevention said. He and the other four children have recovered, health officials said....................

http://www.reformer.com/newenglandnews/ci_19169079

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Hybrid swine-origin H3N2 flu case confirmed in Maine
A child in Maine has contracted a swine-origin H3N2 influenza virus with components of the 2009 H1N1 pandemic flu strain, according to state health officials. The child became ill early this month with fever, cough, headache, sore throat, and muscle aches and after having contact with pigs, including "time spent in a closed setting at an agricultural fair," according to an alert from the Maine Center for Disease Control and Prevention (Maine CDC). The child was treated by a primary care physician, never needed hospitalization, and has recovered, according to the agency. The alert said, "The type of influenza identified in the Maine case is similar to previous, rare human infections with swine-origin H3N2 viruses, that also contain a genetic component of the pandemic H1N1 virus. This virus is genetically similar to four previous cases identified in the United States this year, three in Pennsylvania and one in Indiana, all of which had exposure to swine." The four previous cases were confirmed by the US Centers for Disease Control and Prevention in September. The Maine CDC said no further cases have been detected in the state, but an investigation is ongoing.
Oct 19 Maine CDC alert
Sep 2 and Sep 6 CIDRAP News stories on earlier cases

http://www.cidrap.umn.edu/cidrap/conten ... uscan.html

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Commentary

http://www.recombinomics.com/News/10241 ... _2011.html

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For the last 10 weeks of the 2010/2011, beginng with week 30 when the sample from first 2011 trH3N2 case was collected, most (67) of the 107 influenza A cases were not subtyped. Of those sub-typed, 30 were H3N2, 8 were H1N1, and 2 were "unable to subtype".

http://www.cdc.gov/flu/weekly/weeklyarc ... regt39.htm

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