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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Mon Nov 29, 2010 9:56 am 
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EPI291835 A/Minnesota/09/2010 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI291812 A/Iowa/16/2009 (A/H3N2) segment 7 (MP) 27.0 5.67241

EPI272364 A/swine/SD/1/2010 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI244303 A/Kansas/13/2009 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI179349 A/swine/NC/00573/2005 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI179341 A/swine/IL/00685/2005 (A/H1N1) segment 7 (MP) 27.0 5.67241

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Mon Nov 29, 2010 9:59 am 
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Posts: 27277
Location: Pittsburgh, PA USA
EPI291882 A/Texas/14/2008 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI291843 A/Minnesota/10/2009 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI291835 A/Minnesota/09/2010 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI291812 A/Iowa/16/2009 (A/H3N2) segment 7 (MP) 27.0 5.67241

EPI273589 A/swine/Nakhon Pathom/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI272372 A/swine/Chonburi/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI272364 A/swine/SD/1/2010 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI271843 A/swine/Chachoengsao/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI255757 A/swine/MN/23506/2009 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI251021 A/Hafang/6/1995 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI244303 A/Kansas/13/2009 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI235255 A/swine/Chachoengsao/2003 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI174550 A/swine/Herzlake/IDT5337/06 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI174549 A/swine/Herzlake/IDT5336/06 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI174548 A/swine/Herzlake/IDT5335/06 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI174544 A/swine/Stadtlohn/IDT3853/05 (A/H1N2) segment 7 (MP) 27.0 5.67241
EPI174540 A/swine/Merzen/IDT4114/05 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI174534 A/swine/Egglham/IDT5250/05 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI174532 A/swine/Bad Griesbach/IDT4191/05 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI174527 A/swine/Lohne/IDT3357/04 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI173006 A/swine/Ratchaburi/NIAH59/2004 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI172998 A/swine/Nakhon pathom/NIAH586-1/2005 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI172966 A/swine/Ratchaburi/NIAH550/2003 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI172007 A/chicken/MA/11801/1986 (A/H5N2) segment 7 (MP) 27.0 5.67241
EPI158500 A/chicken/NY/21665-73/1998 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI99269 A/swine/Schwerin/103/89 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI77693 A/swine/Iowa/1/1986 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI68755 A/swine/Wisconsin/663/1980 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI64013 A/swine/Wisconsin/629/1980 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62825 A/swine/Wisconsin/8/1980 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62806 A/swine/Wisconsin/661/1980 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62787 A/swine/Wisconsin/641/1980 (A/H1N1) segment 7 (MP) 27.0 5.67241

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Mon Nov 29, 2010 10:05 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 27277
Location: Pittsburgh, PA USA
EPI291835 A/Minnesota/09/2010 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI287429 A/swine/Guangdong/968/2006 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI287428 A/swine/Guangdong/811/2006 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI287427 A/swine/Guangdong/423/2006 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI287426 A/swine/Guangdong/223/2006 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI287425 A/swine/Guangdong/211/2006 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI274497 A/swine/Toyama/1/1978 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI274489 A/swine/Shizuoka/1/1978 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI273944 A/swine/Okinawa/2/2005 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI272828 A/swine/Kanagawa/1/1978 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI272364 A/swine/SD/1/2010 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI272193 A/chicken/Shandong/WL/2009 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI272191 A/chicken/Shandong/PD/2009 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI244303 A/Kansas/13/2009 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI243542 A/feces/Hunan/3-91/2007 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI243534 A/feces/Hunan/2-28/2007 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI243526 A/environment/Hunan/5-38/2007 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI243518 A/environment/Hunan/2-84/2007 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI243510 A/environment/Hunan/1-81/2007 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI243502 A/environment/Hunan/1-70/2007 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI243494 A/environment/Hunan/1-23/2007 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI243486 A/environment/Hunan/1-18/2007 (A/H9N2) segment 7 (MP) 27.0 5.67241
EPI242641 A/swine/Wisconsin/1/1968 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI242605 A/swine/Hong Kong/1/1974 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI241026 A/New Jersey/11/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI240824 A/swine/Nebraska/1968 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI240822 A/swine/Italy/v.45/1979 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI236413 A/swine/Guangdong/113/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI236405 A/swine/Guangdong/111/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI236397 A/swine/Guangdong/110/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI236389 A/swine/Guangdong/107/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI236381 A/swine/Guangdong/106/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI231014 A/duck/Korea/276-7/2008 (A/H6N2) segment 7 (MP) 27.0 5.67241
EPI226613 A/swine/Guangdong/102/2002 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI222037 A/environment/Hunan/5-32/2007 (A/H5N1) segment 7 (MP) 27.0 5.67241
EPI179366 A/New Jersey/8/1976 (A/H1N1 seasonal) segment 7 (MP) 27.0 5.67241
EPI173038 A/swine/Ehime/1/1980 (A/H1N2) segment 7 (MP) 27.0 5.67241
EPI173030 A/swine/Niigata/1/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI173022 A/swine/Hokkaido/2/81 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI171237 A/swine/Tennessee/107/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI171134 A/swine/Wisconsin/30954/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI156234 A/swine/Tennessee/109/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI155007 A/swine/Kyoto/3/1979 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI153835 A/swine/Wisconsin/1/61 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI130174 A/swine/Tennessee/24/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI130135 A/swine/Wisconsin/1/61 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI130040 A/swine/Hong Kong/126/1982 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI100034 A/swine/Alberta/56626/03 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI100016 A/swine/Ontario/57561/03 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI76855 A/swine/Tennessee/7/1978 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI76285 A/swine/Wisconsin/30747/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI76266 A/swine/Tennessee/3/1978 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI74177 A/swine/Tennessee/118/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI72259 A/swine/Tennessee/112/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI72240 A/swine/Tennessee/106/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI72221 A/swine/Tennessee/105/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI72183 A/swine/Tennessee/10/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI72088 A/swine/Tennessee/23/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI71803 A/swine/Wisconsin/2/1966 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI71784 A/swine/Wisconsin/1/1967 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI71765 A/swine/Wisconsin/1/1957 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI71423 A/Wisconsin/301/1976 (A/H1N1 seasonal) segment 7 (MP) 27.0 5.67241
EPI69255 A/swine/Tennessee/37/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI68904 A/swine/Tennessee/48/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI68774 A/swine/Arizona/148/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI68632 A/swine/Tennessee/61/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI68611 A/swine/Minnesota/24/1975 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI63920 A/swine/Iowa/1/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62768 A/swine/Wisconsin/2/1970 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62712 A/swine/Wisconsin/1/1971 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62674 A/swine/Tennessee/1/1975 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62617 A/swine/Nebraska/123/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62579 A/swine/Minnesota/27/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62560 A/swine/Kentucky/1/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62541 A/swine/Illinois/1/1975 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62392 A/swine/Tennessee/62/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62373 A/swine/Tennessee/10/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62031 A/swine/Tennessee/31/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI62012 A/swine/Tennessee/21/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI61993 A/swine/Tennessee/19/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI61974 A/swine/Iowa/4/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI61898 A/swine/Iowa/1/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI61880 A/swine/Tennessee/19/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI61861 A/swine/Tennessee/17/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI61842 A/swine/Tennessee/15/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI61823 A/swine/Tennessee/7/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI61804 A/swine/Tennessee/3/1976 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI31059 A/swine/Tennessee/25/1977 (A/H1N1) segment 7 (MP) 27.0 5.67241

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Mon Nov 29, 2010 10:10 am 
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Posts: 27277
Location: Pittsburgh, PA USA
EPI291835 A/Minnesota/09/2010 (A/H3N2) segment 7 (MP) 27.0 5.67241
EPI272364 A/swine/SD/1/2010 (A/H1N1) segment 7 (MP) 27.0 5.67241
EPI244479 A/swine/Taichung/200-8/2002 (A/H1N1) segment 7 (MP) 27.0 5.67241

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Wed Dec 01, 2010 7:28 pm 
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Location: Pittsburgh, PA USA
Linkage analysis

http://www.recombinomics.com/News/12011 ... _Link.html

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Fri Dec 17, 2010 2:11 pm 
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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/subtopic/heard.htm#1217

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Fri Dec 17, 2010 2:50 pm 
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Although there have been 19 triple reassortants reported in the US, the most recent six have all been trH3N2, including three in the last three months (Wisconsin, Pennsylvania, Minnesota). Two of the four in 2010 have been in Minnesota. The sequence data on the first three shows that they are more closely related to each other than swine, signaling human to human transmission.

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Fri Dec 17, 2010 6:17 pm 
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Commentary

http://www.recombinomics.com/News/12171 ... demic.html

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Fri Dec 17, 2010 9:31 pm 
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What do we know about human-to-human spread of swine flu?
In September 1988, a previously healthy 32-year-old pregnant woman was hospitalized for pneumonia and died 8 days later. A swine H1N1 flu virus was detected. Four days before getting sick, the patient visited a county fair swine exhibition where there was widespread influenza-like illness among the swine.

In follow-up studies, 76% of swine exhibitors tested had antibody evidence of swine flu infection but no serious illnesses were detected among this group. Additional studies suggest that one to three health care personnel who had contact with the patient developed mild influenza-like illnesses with antibody evidence of swine flu infection.

http://www.cdc.gov/flu/swineflu/keyfacts_humans.htm

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 Post subject: Re: Swine H3N2 Pandemic
PostPosted: Sat Dec 18, 2010 9:35 am 
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niman wrote:
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.

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.

http://www.cdc.gov/media/subtopic/heard.htm#1217

The above comments on the cases in Pennsylvania and Wisconsin have an odd inconsistancy with the earllier pager alert and CDC update, which gave Sept 8 as the disease onset data for the Wisconsin case and Oct 24 as the date for Pennsylvania (and the 6 week gap was noted in the earlier report).

The current report (copied above) is more consistant with the collection dates for the public sequences, which have Pennsylvania/14 collected at the end of October, but Wisconsin/12 from the beginning of November (almost 2 months after the disease onset date cited earlier). Wisconsin/12 is from a 10 month old male, while the pager alert cited a 7 month old child.

There was a similar inconsistancy with the original case in Kansas. The press release from Kansas descibed a child, but Kansas/13 was said to be from a 22 year old male.

It is unclear if these inconsistancies reflect additional cases or are entry errors or delays in isolating the Wisconsin virus.

However, the collection date of the end of October for PA, and beginning of November for WI may be very close in time to the Minnesota case, which is said to be from November.

Thus, the number of cases or clustering in time may be different than published reports (and of course additional November and December cases may not yet have been made public).

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