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PostPosted: Sat Feb 05, 2011 12:54 pm 
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niman wrote:
PB1 E618D pedigree in H3N2 isolates

EPI293963 A/Minnesota/11/2010 (A/H3N2) segment 2 (PB1) 27.0 5.96979
EPI291895 A/Wisconsin/12/2010 (A/H3N2) segment 2 (PB1) 27.0 5.64229
EPI291867 A/Pennsylvania/14/2010 (A/H3N2) segment 2 (PB1) 27.0 5.64229
EPI291840 A/Minnesota/09/2010 (A/H3N2) segment 2 (PB1) 27.0 5.64229
EPI244299 A/Kansas/13/2009 (A/H3N2) segment 2 (PB1) 27.0 5.67207

Note that the only swine H3N2 sequences with PB1 E618D have been HUMAN, signaling H2H transmission.

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PostPosted: Sat Feb 05, 2011 1:38 pm 
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http://www.cdc.gov/media/haveyouheard/2010.html

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

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PostPosted: Sat Feb 05, 2011 4:05 pm 
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Commentary

http://www.recombinomics.com/News/02051 ... ssion.html

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PostPosted: Sat Feb 05, 2011 9:43 pm 
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niman wrote:


Dr. Niman - First, thanks for the commentaries that are understandable to the layman. It sounds like it is possible that there could be a novel H3N2 circulating that has not been detected due to all the seasonal H3N2 around. Something seems strange in that there have been so many deaths in some states where pH1N1 has just shown up and hasn't been circulating long enough for it to be the cause. Plus, as has been shown in NC, most of the deaths are from Influenza B and H3N2. Am I reading too much into this?

Having a mutated pH1N1 strain along with a different novel strain circulating together could be the perfect storm.

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PostPosted: Sun Feb 06, 2011 7:24 am 
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Jim wrote:
niman wrote:


Dr. Niman - First, thanks for the commentaries that are understandable to the layman. It sounds like it is possible that there could be a novel H3N2 circulating that has not been detected due to all the seasonal H3N2 around. Something seems strange in that there have been so many deaths in some states where pH1N1 has just shown up and hasn't been circulating long enough for it to be the cause. Plus, as has been shown in NC, most of the deaths are from Influenza B and H3N2. Am I reading too much into this?

Having a mutated pH1N1 strain along with a different novel strain circulating together could be the perfect storm.

I think you may be reading too much into states like NC. Influenza B is killing somewhat more than expected, but that wouldn't be related to trH3n2. The cause of the more recent deaths in NC may in fact be H1N1 because they have been reported in the latest week and H1N1 has been on the rise for several weeks, although dominance is showing up in the most recent weeks.

trH3N2 may not yet be transmitting efficiently enough to cause jumps in fatalities. So far none of the 7 known cases have died, but the situatoon could change dramatically at any time.

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PostPosted: Sun Feb 06, 2011 7:42 am 
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HA sequences from Pennsylvania H3N2 swine collected in October, 2010 were just reelased at Genbank.

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PostPosted: Sun Feb 06, 2011 7:47 am 
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Location: Pittsburgh, PA USA
LOCUS JF263536 1701 bp cRNA linear VRL 05-FEB-2011
DEFINITION Influenza A virus (A/swine/Pennsylvania/62170-3/2010(H3N2)) segment
4 hemagglutinin (HA) gene, complete cds.
ACCESSION JF263536
VERSION JF263536.1 GI:320542706
KEYWORDS .
SOURCE Influenza A virus (A/swine/Pennsylvania/62170-3/2010(H3N2))
ORGANISM Influenza A virus (A/swine/Pennsylvania/62170-3/2010(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS McGill,J. and Gramer,M.
TITLE Direct Submission
JOURNAL Submitted (27-JAN-2011) DVL-BPA, USDA, APHIS, NVSL, 1920 Dayton
Ave., Ames, IA 50010, USA
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus
(A/swine/Pennsylvania/62170-3/2010(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Pennsylvania/62170-3/2010"
/serotype="H3N2"
/host="swine"
/db_xref="taxon:938271"
/segment="4"
/country="USA"
/collection_date="25-Oct-2010"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADW41797.1"
/db_xref="GI:320542707"
/translation="MKTIIAFSCILCLIFAQKLPGSDNSTATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGRICNSPHQILDGKNCTLIDALLGDPHCDDFQNKEWDL
FVERSTAYSNCYPYYVPDYVSLRSLVASSGTLEFTQENFNWTGVAQDGSSYACRRKSV
NSFFSRLNWLYNLNYKYPALNVTMPNNDNFDKLYIWGVHHPGTDKDQTNLYIQASGRV
TVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMRSDAPIGNCKSECITPNGSIPNDKPFQNVNRITYGVCPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGYRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
HTIDLTDSEMNKLFERTRKQLRENAEDMGNGCFKIYHKCDNTCIGSIRNGTYDHAVYR
DEALNNRFQIKGVQLKSGYKDWILWISFAMSCFLLCVVLLGFIMWACQKGNIRCNICI
"
ORIGIN
1 atgaagacta tcattgcttt tagctgcatt ttatgtctga ttttcgctca aaaacttccc
61 gggagtgaca acagcacggc aacgctgtgc ctgggacacc atgcagtacc aaacggaacg
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctaccga gctggttcag
181 agttcctcaa caggtagaat atgcaacagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggagaccct cattgtgatg acttccaaaa caaggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta tgtgccggat
361 tatgtctccc ttaggtcact agttgcctca tccggcaccc tggaatttac ccaagaaaac
421 ttcaattgga ctggagttgc tcaagatgga tcaagctatg cttgcagaag gaaatctgtt
481 aacagtttct ttagtagatt gaattggttg tataatttga attacaaata tccagcgctg
541 aacgtaacta tgccaaacaa tgacaatttt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacag acaaagacca aaccaaccta tatattcaag catcagggag agttacagtc
661 tccaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtccagacc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acaatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa
841 agctcaataa tgaggtcaga tgcacccatt ggcaattgca aatctgaatg cattactcca
901 aatggaagca ttcccaatga caaacccttt caaaatgtaa acaggatcac atatggggtc
961 tgtcccagat atgttaagca aaacactctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat atttggcgca atcgcaggtt tcatagaaaa tggttgggag
1081 gggatggtgg acggttggta cggttacagg catcagaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca ggcagcaatc aaccaaatca ccgggaaact aaatagagta
1201 atcaagaaga caaatgaaaa attccatcag atcgaaaaag aattctcaga agtagaaggg
1261 agaattcagg atctagagaa atacgttgaa gacactaaaa tagatctctg gtcttacaac
1321 gcggagcttc ttgttgccct ggagaaccaa catacaattg atttaactga ctcagaaatg
1381 aacaaactgt tcgaaagaac aagaaagcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttca aaatatacca caaatgtgac aatacctgca taggatcaat cagaaatgga
1501 acttatgacc atgctgtata cagagacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctga agtcaggata caaagattgg atcctatgga tttcctttgc catgtcatgc
1621 tttttgcttt gtgttgttct gctggggttc attatgtggg cctgccaaaa aggcaacatt
1681 aggtgcaaca tttgcatttg a
//

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PostPosted: Sun Feb 06, 2011 7:48 am 
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LOCUS JF263535 1701 bp cRNA linear VRL 05-FEB-2011
DEFINITION Influenza A virus (A/swine/Pennsylvania/62170-1/2010(H3N2)) segment
4 hemagglutinin (HA) gene, complete cds.
ACCESSION JF263535
VERSION JF263535.1 GI:320542704
KEYWORDS .
SOURCE Influenza A virus (A/swine/Pennsylvania/62170-1/2010(H3N2))
ORGANISM Influenza A virus (A/swine/Pennsylvania/62170-1/2010(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS McGill,J. and Gramer,M.
TITLE Direct Submission
JOURNAL Submitted (27-JAN-2011) DVL-BPA, USDA, APHIS, NVSL, 1920 Dayton
Ave., Ames, IA 50010, USA
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus
(A/swine/Pennsylvania/62170-1/2010(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Pennsylvania/62170-1/2010"
/serotype="H3N2"
/host="swine"
/db_xref="taxon:938269"
/segment="4"
/country="USA"
/collection_date="25-Oct-2010"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADW41796.1"
/db_xref="GI:320542705"
/translation="MKTIIAFSCILCLIFAQKLPGSDNSTATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGRICNSPHQILDGKNCTLIDALLGDPHCDDFQNKEWDL
FVERSTAYSNCYPYYVPDYVSLRSLVASSGTLEFTQENFNWTGVAQDGSSYACRRKSV
NSFFSRLNWLYNLNYKYPALNVTMPNNDNFDKLYIWGVHHPGTDKDQTNLYIQASGRV
TVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMRSDAPIGNCKSECITPNGSIPNDKPFQNVNRITYGVCPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGYRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
HTIDLTDSEMNKLFERTRKQLRENAEDMGNGCFKIYHKCDNTCIGSIRNGTYDHAVYR
DEALNNRFQIKGVQLKSGYKDWILWISFAMSCFLLCVVLLGFIMWACQKGNIRCNICI
"
ORIGIN
1 atgaagacta tcattgcttt tagctgcatt ttatgtctga ttttcgctca aaaacttccc
61 gggagtgaca acagcacggc aacgctgtgc ctgggacacc atgcagtacc aaacggaacg
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctaccga gctggttcag
181 agttcctcaa caggtagaat atgcaacagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggagaccct cattgtgatg acttccaaaa caaggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta tgtgccggat
361 tatgtctccc ttaggtcact agttgcctca tccggcaccc tggaatttac ccaagaaaac
421 ttcaattgga ctggagttgc tcaagatgga tcaagctatg cttgcagaag gaaatctgtt
481 aacagtttct ttagtagatt gaattggttg tataatttga attacaaata tccagcgctg
541 aacgtaacta tgccaaacaa tgacaatttt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacag acaaagacca aaccaaccta tatattcaag catcagggag agttacagtc
661 tccaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtccagacc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acaatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa
841 agctcaataa tgaggtcaga tgcacccatt ggcaattgca aatctgaatg cattactcca
901 aatggaagca ttcccaatga caaacccttt caaaatgtaa acaggatcac atatggggtc
961 tgtcccagat atgttaagca aaacactctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat atttggcgca atcgcaggtt tcatagaaaa tggttgggag
1081 gggatggtgg acggttggta cggttacagg catcagaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca ggcagcaatc aaccaaatca ccgggaaact aaatagagta
1201 atcaagaaga caaatgaaaa attccatcag atcgaaaaag aattctcaga agtagaaggg
1261 agaattcagg atctagagaa atacgttgaa gacactaaaa tagatctctg gtcttacaac
1321 gcggagcttc ttgttgccct ggagaaccaa catacaattg atttaactga ctcagaaatg
1381 aacaaactgt tcgaaagaac aagaaagcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttca aaatatacca caaatgtgac aatacctgca taggatcaat cagaaatgga
1501 acttatgacc atgctgtata cagagacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctga agtcaggata caaagattgg atcctatgga tttcctttgc catgtcatgc
1621 tttttgcttt gtgttgttct gctggggttc attatgtggg cctgccaaaa aggcaacatt
1681 aggtgcaaca tttgcatttg a

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PostPosted: Sun Feb 06, 2011 7:56 am 
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The two swine sequences are identical and closely related to Pennsylvania/14/2010.

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PostPosted: Sun Feb 06, 2011 8:10 am 
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Location: Pittsburgh, PA USA
A63G pedigree at GISAID

EPI291872 A/Pennsylvania/14/2010 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI291870 A/Pennsylvania/14/2010 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI291865 A/Pennsylvania/14/2010 (A/H3N2) segment 4 (HA) 27.0 5.97074

EPI249522 A/swine/Minnesota/02981/2010 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI238766 A/Fes/314//98 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI234656 A/Bangladesh/BA-1164729/2003 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI182475 A/Niedersachsen/6/2006 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI166278 A/swine/Minnesota/SG-00242/2006 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI164409 A/Thailand/CU-1103/2008 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI158052 A/Paraguay/697/2004 (A/H3) segment 4 (HA) 27.0 5.97074
EPI157455 A/Brazil/2363/2005 (A/H3) segment 4 (HA) 27.0 5.97074
EPI157429 A/Bangladesh/1164729/2003 (A/H3) segment 4 (HA) 27.0 5.97074
EPI155425 A/Canada/101/2006 (A/H3) segment 4 (HA) 27.0 5.97074
EPI146420 A/Canada/CN-RV0101-07/2006 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI146160 A/Paraguay/PY-697/2004 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI145979 A/Brazil/BR-IAL2353-0505-04099-ORIGINAL/2005 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI145744 A/FUKUSHIMA/93/2006 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI105518 A/Casa/78/98 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI105516 A/Marrakech/116/98 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI105514 A/Fes/273/98 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI105512 A/Rabat/227/98 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI105508 A/Marrakech/90/98 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI105506 A/Rabat/236/98 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI105504 A/Rabat/33/97 (A/H3N2) segment 4 (HA) 27.0 5.97074
EPI99943 A/Italy/384/2005 (A/H3N2) segment 4 (HA) 27.0 5.97074

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