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H1N2 Ohio Swine Is Other Parent For H3N2pdm11

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niman

Post subject: Re: H1N2 Ohio Swine Is Other Parent For H3N2pdm11

Posted: Thu Dec 08, 2011 2:08 pm

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27497
Location: Pittsburgh, PA USA

niman wrote:

Match Ohio in HA, NA, MP

HQ833566.1 Influenza A virus (A/swine/Ohio/FAH10-1/2010(H1N2)) segment 4 hemagglutinin (HA) gene, partial cds 3131 3131 100% 0.0 100%
CY078421.1 Influenza A virus (A/swine/South Dakota/2/2010(H1N2)) segment 4 sequence 3103 3103 99% 0.0 99%
CY078424.1 Influenza A virus (A/swine/South Dakota/3/2010(H1N2)) segment 4 sequence 3097 3097 99% 0.0 99%
JN652499.1 Influenza A virus (A/swine/Iowa/A01049846/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3092 3092 100% 0.0 99%
JN652420.1 Influenza A virus (A/swine/Iowa/A01049722/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3086 3086 100% 0.0 99%
JN652421.1 Influenza A virus (A/swine/Iowa/A01049723/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds
JN652422.1 Influenza A virus (A/swine/Iowa/A01049724/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds
JN652423.1 Influenza A virus (A/swine/Iowa/A01049728/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3086 3086 100% 0.0 99%
JN652516.1 Influenza A virus (A/swine/Indiana/A01049953/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3086 3086 100% 0.0 99%
JN652498.1 Influenza A virus (A/swine/Indiana/A01049794/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3083 3083 100% 0.0 99%
JN162060.1 Influenza A virus (A/swine/Iowa/A01049450/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds
JN652418.1 Influenza A virus (A/swine/Iowa/A01049718/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3081 3081 100% 0.0 99%
JN652503.1 Influenza A virus (A/swine/Iowa/A01049887/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3059 3059 100% 0.0 99%
JN652413.1 Influenza A virus (A/swine/Iowa/A01049646/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3053 3053 100% 0.0 99%
JN652514.1 Influenza A virus (A/swine/Iowa/A01049951/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3048 3048 100% 0.0 99%
CY081566.1 Influenza A virus (A/swine/South Dakota/4/2010(H1N2)) hemagglutinin (HA) gene, partial cds 3048 3048 99% 0.0 99%
JN652518.1 Influenza A virus (A/swine/Indiana/A01049964/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3042 3042 100% 0.0 99%
CY099367.1 Influenza A virus (A/swine/Illinois/A00907647/2011(H1N2)) hemagglutinin (HA) gene, complete cds 3037 3037 100% 0.0 99%
JN652517.1 Influenza A virus (A/swine/Minnesota/A01049956/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3031 3031 100% 0.0 99%
JF812285.1 Influenza A virus (A/swine/Iowa/A01049071/2010(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3025 3025 100% 0.0 99%
JN652502.1 Influenza A virus (A/swine/Iillinois/A01049872/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3020 3020 100% 0.0 99%
JN652501.1 Influenza A virus (A/swine/Iillinois/A01049871/2011(H1N2)) segment 4 hemagglutinin (HA) gene, complete cds 3014 3014 100% 0.0 99%

Note the ease in detection of donor sequences in swine in multiple states in collections from the fall of 2010 to the summer of 2011, with no H3N2pdm11 isolates in swine prior to the ONE example in New York in a Sept 13 collection.

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niman

Post subject: Re: H1N2 Ohio Swine Is Other Parent For H3N2pdm11

Posted: Sun Dec 18, 2011 8:24 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27497
Location: Pittsburgh, PA USA

Tandem PB1 polymorphisms A2112G and G2145A

HQ833572.1 Influenza A virus (A/swine/Ohio/FAH2-1/2008(H1N1))
HQ833564.1 Influenza A virus (A/swine/Ohio/FAH10-1/2010(H1N2))
EPI346491 A/West Virginia/06/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI346438 A/Iowa/08/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI346430 A/Iowa/07/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI346422 A/Iowa/09/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI344403 A/Indiana/08/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI344395 A/Indiana/10/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI344387 A/Indiana/10/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI342702 A/Iowa/09/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI342694 A/Iowa/08/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI342686 A/Iowa/07/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI342605 A/swine/NY/A01104005/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI340982 A/Indiana/10/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI339169 A/Maine/06/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI335627 A/Indiana/08/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI335616 A/Pennsylvania/11/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)
EPI333150 A/Indiana/08/2011 (A/H3N2) segment 2 (PB1) 63.9 2.235514e-10 34/34 (100%)

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niman

Post subject: Re: H1N2 Ohio Swine Is Other Parent For H3N2pdm11

Posted: Sun Dec 18, 2011 8:31 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27497
Location: Pittsburgh, PA USA

A2112G G2145A Tandem at Genbank WV/06/11 not yet in the search database

JQ070790.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ070782.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ070774.1 Influenza A virus (A/Iowa/09/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ070766.1 Influenza A virus (A/Iowa/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
JQ070758.1 Influenza A virus (A/Iowa/07/2011(H3N2)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
HQ833572.1 Influenza A virus (A/swine/Ohio/FAH2-1/2008(H1N1)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
HQ833564.1 Influenza A virus (A/swine/Ohio/FAH10-1/2010(H1N2)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
JN940420.1 Influenza A virus (A/swine/NY/A01104005/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JN992755.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
JN866184.1 Influenza A virus (A/Maine/06/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JN655544.1 Influenza A virus (A/Pennsylvania/11/2011(H3N2)) segment 2 polymerase PB1 (PB1) gene, partial cds 67.9 67.9 100% 2e-09 100%
JN638731.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds
JN655554.1| Influenza A virus (A/Indiana/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds >gb|JQ070798.1| Influenza A virus (A/Indiana/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100

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niman

Post subject: Re: H1N2 Ohio Swine Is Other Parent For H3N2pdm11

Posted: Sun Dec 18, 2011 8:45 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27497
Location: Pittsburgh, PA USA

PB1 combo of T369C and T385A
HQ833572.1 Influenza A virus (A/swine/Ohio/FAH2-1/2008(H1N1)) segment 2 polymerase PB1 (PB1) gene,
HQ833564.1 Influenza A virus (A/swine/Ohio/FAH10-1/2010(H1N2))
EPI346491 A/West Virginia/06/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI346438 A/Iowa/08/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI346430 A/Iowa/07/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI346422 A/Iowa/09/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI344403 A/Indiana/08/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI344395 A/Indiana/10/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI344387 A/Indiana/10/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI342702 A/Iowa/09/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI342694 A/Iowa/08/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI342686 A/Iowa/07/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI342605 A/swine/NY/A01104005/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI340982 A/Indiana/10/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI339169 A/Maine/06/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI335627 A/Indiana/08/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI335608 A/Pennsylvania/09/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)
EPI333150 A/Indiana/08/2011 (A/H3N2) segment 2 (PB1) 32.5 1.584752e-01 17/17 (100%)

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niman

Post subject: Re: H1N2 Ohio Swine Is Other Parent For H3N2pdm11

Posted: Mon Dec 19, 2011 8:49 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27497
Location: Pittsburgh, PA USA

niman wrote:

Genbank;
JQ290186.1 Influenza A virus (A/Iowa/09/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ290174.1 Influenza A virus (A/Iowa/07/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ290170.1 Influenza A virus (A/Iowa/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ290162.1 Influenza A virus (A/West Virginia/06/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ070790.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ070782.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ070774.1 Influenza A virus (A/Iowa/09/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JQ070766.1 Influenza A virus (A/Iowa/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
JQ070758.1 Influenza A virus (A/Iowa/07/2011(H3N2)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
HQ833572.1 Influenza A virus (A/swine/Ohio/FAH2-1/2008(H1N1)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
HQ833564.1 Influenza A virus (A/swine/Ohio/FAH10-1/2010(H1N2)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
JN940420.1 Influenza A virus (A/swine/NY/A01104005/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JN992755.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 2 polymerase PB1 (PB1) gene, partial cds; and PB1-F2 protein (PB1-F2) gene, complete cds 67.9 67.9 100% 2e-09 100%
JN866184.1 Influenza A virus (A/Maine/06/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%
JN655544.1 Influenza A virus (A/Pennsylvania/11/2011(H3N2)) segment 2 polymerase PB1 (PB1) gene, partial cds 67.9 67.9 100% 2e-09 100%
JN638731.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds
JN655554.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds
JQ070798.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, complete cds 67.9 67.9 100% 2e-09 100%

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niman

Post subject: Re: H1N2 Ohio Swine Is Other Parent For H3N2pdm11

Posted: Wed Jun 06, 2012 6:11 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27497
Location: Pittsburgh, PA USA

Another Ohio H1N2 swine matching PB1, NA, MP in 2011 H3N2v discussed at thread below

viewtopic.php?f=5&t=8105

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