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PostPosted: Thu Aug 04, 2011 1:19 pm 
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Commentary

http://www.recombinomics.com/News/08041 ... 011_2.html

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PostPosted: Thu Aug 04, 2011 2:01 pm 
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First 320 HA positions identical in WI, PA, MN sequences:

EPI328900 A/Minnesota/11/2010 X-203A (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI328898 A/Minnesota/11/2010 X-203 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI324857 A/swine/North Carolina/A01049436/2011 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI317003 A/swine/Indiana/A0109091/2010 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI246023 A/swine/Minnesota/02948/2009 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI314335 A/turkey/BC/1529-3/2005 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)
EPI182817 A/swine/Quebec/4001/2005 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)
EPI128344 A/Ontario/1252/2007 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)
EPI103217 A/turkey/Ontario/31232/2005 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)
EPI103199 A/swine/Ontario/33853/2005 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)
EPI103181 A/swine/Manitoba/12707/2005 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)
EPI103163 A/swine/British Columbia/28103/2005 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)
EPI103145 A/swine/Alberta/14722/2005 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)
EPI103127 A/Ontario/RV1273/2005 (A/H3N2) segment 4 (HA) 575.4 5.222608e-163 317/320 (99%)

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PostPosted: Thu Aug 04, 2011 2:04 pm 
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Next 320 positions:

EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI317003 A/swine/Indiana/A0109091/2010 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI291838 A/Minnesota/09/2010 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI328900 A/Minnesota/11/2010 X-203A (A/H3N2) segment 4 (HA) 581.0 1.122527e-164 318/320 (99%)
EPI328898 A/Minnesota/11/2010 X-203 (A/H3N2) segment 4 (HA) 581.0 1.122527e-164 318/320 (99%)
EPI324857 A/swine/North Carolina/A01049436/2011 (A/H3N2) segment 4 (HA) 581.0 1.122527e-164 318/320 (99%)
EPI246023 A/swine/Minnesota/02948/2009 (A/H3N2) segment 4 (HA) 581.0 1.122527e-164 318/320 (99%)
EPI222910 A/swine/Minnesota/7931/2007 (A/H3N2) segment 4 (HA) 542.2 5.297028e-153 311/320 (97%)
EPI246027 A/swine/Minnesota/02952/2009 (A/H3N2) segment 4 (HA) 536.6 2.464468e-151 310/320 (96%)
EPI244116 A/swine/Illinois/02940/2010 (A/H3N2) segment 4 (HA) 531.1 1.146605e-149 309/320 (96%)
EPI314335 A/turkey/BC/1529-3/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI229372 A/turkey/OH/313053/2004 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI180194 A/swine/Minnesota/24877/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI180192 A/swine/Minnesota/18815/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI103217 A/turkey/Ontario/31232/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI103199 A/swine/Ontario/33853/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI103181 A/swine/Manitoba/12707/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI103163 A/swine/British Columbia/28103/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI103145 A/swine/Alberta/14722/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI103127 A/Ontario/RV1273/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI101389 A/turkey/Ohio/313053/04 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI99786 A/swine/Ontario/Biovet1/05 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI98746 A/Turkey/Canada-Manitoba/NS-01782-2/05 (A/H3) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)
EPI98744 A/Turkey/Canada-Ontario/NS-01839-1/05 (A/H3) segment 4 (HA) 525.6 5.334635e-148 308/320 (96%)

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PostPosted: Thu Aug 04, 2011 2:07 pm 
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Posts: 28249
Location: Pittsburgh, PA USA
Next 320:

EPI328900 A/Minnesota/11/2010 X-203A (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI328898 A/Minnesota/11/2010 X-203 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI324857 A/swine/North Carolina/A01049436/2011 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI317003 A/swine/Indiana/A0109091/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI291838 A/Minnesota/09/2010 (A/H3N2) segment 4 (HA) 581.0 1.122527e-164 318/320 (99%)
EPI222910 A/swine/Minnesota/7931/2007 (A/H3N2) segment 4 (HA) 547.7 1.138522e-154 313/321 (97%)
EPI180194 A/swine/Minnesota/24877/2005 (A/H3N2) segment 4 (HA) 536.6 2.464468e-151 311/321 (96%)
EPI180128 A/swine/Illinois/34642/2005 (A/H3N2) segment 4 (HA) 536.6 2.464468e-151 311/321 (96%)
EPI289638 A/swine/Minnesota/1300/2007 (A/H3N2) segment 4 (HA) 531.1 1.146605e-149 310/321 (96%)
EPI99788 A/swine/Alberta/Biovet1/05 (A/H3N2) segment 4 (HA) 531.1 1.146605e-149 310/321 (96%)
EPI99786 A/swine/Ontario/Biovet1/05 (A/H3N2) segment 4 (HA) 531.1 1.146605e-149 310/321 (96%)
EPI180193 A/swine/Minnesota/21057/2005 (A/H3N2) segment 4 (HA) 527.4 1.483228e-148 309/321 (96%)
EPI229372 A/turkey/OH/313053/2004 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI182817 A/swine/Quebec/4001/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI168645 A/turkey/Minnesota/366767/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI166258 A/swine/Minnesota/SG-00236/2007 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 310/322 (96%)
EPI166255 A/swine/Minnesota/SG-00235/2007 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 310/322 (96%)
EPI158876 A/turkey/MN/366767/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI128344 A/Ontario/1252/2007 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI103199 A/swine/Ontario/33853/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI103181 A/swine/Manitoba/12707/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI103127 A/Ontario/RV1273/2005 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI101389 A/turkey/Ohio/313053/04 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)
EPI99784 A/swine/Quebec/Biovet1/05 (A/H3N2) segment 4 (HA) 525.6 5.334635e-148 309/321 (96%)

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PostPosted: Thu Aug 04, 2011 2:10 pm 
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Next 320

EPI328900 A/Minnesota/11/2010 X-203A (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI317003 A/swine/Indiana/A0109091/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 592.0 5.185791e-168 320/320 (100%)
EPI328898 A/Minnesota/11/2010 X-203 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI324857 A/swine/North Carolina/A01049436/2011 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 586.5 2.412714e-166 319/320 (99%)
EPI291838 A/Minnesota/09/2010 (A/H3N2) segment 4 (HA) 581.0 1.122527e-164 318/320 (99%)
EPI225758 A/swine/Minnesota/66960/2006 (A/H3N2) segment 4 (HA) 569.9 2.429843e-161 316/320 (98%)
EPI314335 A/turkey/BC/1529-3/2005 (A/H3N2) segment 4 (HA) 564.3 1.130496e-159 315/320 (98%)
EPI229372 A/turkey/OH/313053/2004 (A/H3N2) segment 4 (HA) 558.8 5.259686e-158 314/320 (98%)
EPI222674 A/swine/Oklahoma/008722/2007 (A/H3N2) segment 4 (HA) 558.8 5.259686e-158 314/320 (98%)
EPI166252 A/swine/Minnesota/SG-00234/2005 (A/H3N2) segment 4 (HA) 558.8 5.259686e-158 314/320 (98%)
EPI101389 A/turkey/Ohio/313053/04 (A/H3N2) segment 4 (HA) 558.8 5.259686e-158 314/320 (98%)
EPI324849 A/swine/Iowa/A01049254/2010 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI314667 A/swine/QC/1698-4/2009 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI314666 A/swine/QC/1698-2/2009 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI314665 A/swine/QC/1698-1/2009 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI314635 A/swine/QC/2108-2/2009 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI291813 A/Iowa/16/2009 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI230035 A/swine/Wisconsin/R7c/2001 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI228922 A/turkey/Illinois/2004 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI227574 A/turkey/NC/353568/2005 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI222910 A/swine/Minnesota/7931/2007 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI219368 A/swine/Oklahoma/001142/2009 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI219360 A/swine/Kansas/015252/2009 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI168650 A/turkey/North Carolina/353568/2005 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI103199 A/swine/Ontario/33853/2005 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI103181 A/swine/Manitoba/12707/2005 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI103145 A/swine/Alberta/14722/2005 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI103127 A/Ontario/RV1273/2005 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI25393 A/turkey/ Minnesota/764-2/03 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)
EPI25391 A/turkey/North Carolina/12344/03 (A/H3N2) segment 4 (HA) 553.3 2.447094e-156 313/320 (97%)

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PostPosted: Thu Aug 04, 2011 2:18 pm 
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Three cases of human infection with a novel influenza A virus were reported during November and December, one each from Wisconsin, Pennsylvania, and Minnesota. Onset of the illnesses occurred in September, October, and November, respectively. All three patients were infected with swine-origin influenza A (H3N2) viruses. Two of the three cases occurred in adults, and the third occurred in a child. Two of the three patients were hospitalized; all three have fully recovered from their illness. The three cases are not related, and influenza viruses recovered from each of these cases were similar but not identical, indicating that they did not come from a common source. All three patients had either contact with swine or lived in areas close to swine farms. No evidence of human-to-human transmission of these viruses was identified in the first two cases, and investigation of the third case is ongoing.
http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5950a4.htm

The September case is WI/12/2010 and the November cases is MN/11/2010, and as seen by the prior posts the sequences were VERY closely related, and transmission was NOT eliminated by the sequence differences.

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PostPosted: Fri Aug 05, 2011 8:26 am 
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Description of MN/11/2010

December 17, 2010



Report of Human Infection with Swine Origin Influenza A (H3N2)

The December 17, 2010 FluView reported one human infection with swine origin influenza A (H3N2) virus in the state of Minnesota as part of U.S. surveillance and reporting of novel influenza A viruses. Test samples from one patient in Minnesota were confirmed at CDC as positive for swine origin triple-reassortant (tr) H3N2 influenza viruses—viruses that normally infect pigs. Although 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 at livestock exhibits housing pigs at fairs. The patient in Minnesota with confirmed trH3N2 infection had exposure to pigs prior to illness onset. There is no documented human-to-human transmission of this virus or any evidence of community transmission at this time. An investigation of this case is ongoing. Cases of human infection with swine influenza viruses underscore the importance of ongoing human and animal influenza surveillance.

This case of human infection with swine origin influenza virus (SOIV) brings the total number of human infections with swine origin influenza viruses reported to CDC since 2005 to 19. Previously, five of these reports had been swine origin A (H3N2) viruses. The most recent Minnesota case brings the number of reports swine origin A (H3N2) infections in humans in the United States to six. Human infections with swine origin H3N2 virus infections have also been reported from Pennsylvania and Wisconsin in October and November 2010, Minnesota in May 2010, Iowa in September 2009, and Kansas in August 2009.

Swine influenza (swine flu) is a respiratory disease of pigs caused by type A influenza viruses that regularly cause outbreaks of influenza in pigs. Swine flu viruses can result in high illness rates in pig herds, but generally cause few deaths in pigs. Swine influenza viruses can circulate among pigs throughout the year, but most outbreaks occur during the late fall and winter months, similar to outbreaks in humans. There are four main influenza type A virus subtypes that have been isolated in pigs: H1N1, H1N2, H3N2 and H3N1. Most flu viruses circulating in pigs are referred to as "triple-reassortant" viruses because these flu viruses contain genes from human, swine and avian influenza viruses.

It's important to note that swine influenza viruses are not transmitted to humans by food. You cannot get swine influenza from eating pork or pork products. Eating properly handled and cooked pork and pork products is safe.

In 2007 human infections with novel influenza viruses such as swine influenza became nationally notifiable. Previously, CDC has received reports of approximately one human infection with a swine influenza virus every one to two years, but in the past few years, about four cases have been reported per year.

These trH3N2 viruses are different from the 2009 H1N1 virus that has been circulating in the United States since late April 2009. They are also different from human seasonal influenza A (H3N2) viruses that typically circulate among people during the flu season. Swine trH3N2 viruses commonly circulate in pigs in North America, but human infections are rarely detected. These viruses are different from the swine classical H1N1 or swine trH1N1 influenza viruses that also circulate in pigs in North America because they have H3N2 surface antigens. TrH3N2 viruses first were detected in North American swine herds in the late 1990s. The H3 and N2 genes originated from human seasonal H3N2 influenza viruses that circulated globally among humans in the late 1990s. However, currently circulating swine H3 and N2 genes are now notably different from human influenza virus H3 and N2 genes.

Although the vast majority of instances of human infection with animal influenza viruses do not result in human-to-human transmission, each case should be fully investigated to be sure that such viruses are not spreading among humans and to limit further exposure of humans to infected animals if infected animals are identified. Surveillance for both seasonal and novel influenza viruses is conducted by CDC and its state and local health partners year round.

For more information about swine influenza, visit http://www.cdc.gov/flu/swineflu/

Weekly U.S. surveillance updates are published in FluView and posted at http://www.cdc.gov/flu/weekly/fluactivitysurv.htm

http://www.cdc.gov/media/haveyouheard/2010.html#1217

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PostPosted: Fri Aug 05, 2011 1:32 pm 
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For those confused by abble circulating on babble boards

http://www.flutrackers.com/forum/showpo ... ostcount=3

trH3N2 designates H3N2 triple reassortants (tr). In the US, classical H1N1 infected swine were infected by a seasonal H3N2 in the early 90's, leading to swine H3N2 with a human H3, N2, and PB1 (there is no swine H3 or N2). Swine infected with this double reassortant (3 human and 5 swine flu genes) were infected with avian influenza which led to the replacement of swine PA and PB2 with avian PA and PB2. These were called triple reassortants because of three human flu genes (H3, N2, PB1), two avian flu genes (PB2 and PA), and three swine genes (NP, MP, NS). There have been multiple swaps of the HA and NA genes, including pandmeic H1N1, which has swapped out the human H3 and N2 for swine H1 and N1.

The polymerase complex with avian PB2 and PA, as well as human PB1, has been VERY stable, so all swine H3N2 is trH3N2 since the polymerase complex has human and avian flu genes, while the H3 and N2 are human, and the remaining genes are swine.

Thus, there is little doubt that the novel influenza being reported is swine H3N2 which is trH3N2 (or pandemic H3N2).

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PostPosted: Fri Aug 05, 2011 1:54 pm 
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CDC isn't talking about the latest trH3N2 acknowldeged..
http://www.cdc.gov/flu/weekly/

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PostPosted: Sat Aug 06, 2011 8:20 am 
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niman wrote:
CDC isn't talking about the latest trH3N2 acknowldeged..
http://www.cdc.gov/flu/weekly/

Five cases of human infection with a novel influenza A virus were reported during the 2010--11 influenza season from three states. All five cases were infected with swine-origin influenza A (H3N2) viruses. Two cases occurred in September (Pennsylvania and Wisconsin), one case in October (Pennsylvania), and two cases in November (Minnesota). Two of the five cases occurred in adults, and three occurred in children. Two of the five cases were hospitalized; all five have recovered fully from their illness. The two cases in Pennsylvania were not related. The cases in Wisconsin and Pennsylvania had direct contact with swine or lived in areas close to swine farms. The two cases from Minnesota occurred in a father (index case) and child. The father had a nasopharyngeal swab positive for swine-origin influenza A (H3N2) virus and had direct swine exposure 6 days before illness onset. The child, whose infection with influenza A (H3N2) virus was confirmed several weeks later by serologic testing, did not have direct swine exposure, and most likely acquired infection from close contact with her father. Other persons in the same household also had ILI during the same period, but serologic results were either negative or inconclusive.

http://www.cdc.gov/mmwr/preview/mmwrhtm ... mm6021a5_w

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