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PostPosted: Thu Sep 08, 2011 1:06 pm 
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Location: Pittsburgh, PA USA
niman wrote:
I have also contacted the Pennsylvania Department of Health by phone and complied with their request for e-mailed questions, which include the number of cases (suspected / confirmed) as well as unsubtypables, including relationship of fair cases to unsubtypable added by CDC for week 33, which ended August 20 and still list one case

http://www.cdc.gov/flu/weekly/weeklyarc ... regt34.htm

The response from the PA Department of Health didn't add much. They wouldn't directly address the direct question about hospitalization for the two 9F's. Instead they said one was now free of symptoms while the other was recovering (just a repeat of the "have you heard)". They didn't know of additional cases and didn't know about unsubtypables. They are closed today because of flooding. Thus, they provided no new news other than a reluctance to adress hospitalization, which I would interpret as a confirmation.

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PostPosted: Thu Sep 08, 2011 1:38 pm 
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niman wrote:
niman wrote:
The title of the thread has been changed, since the earliest isolate was from a sample collected July 27 and a second sample was from August 25, while the fair was only open from August 13-20.

If one of these patients is still recovering, she has been infected with trH3N2 for almost 6 weeks.

CDC has corrected collection date for PA/10/11 to August 26.

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PostPosted: Thu Sep 08, 2011 2:38 pm 
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niman wrote:
niman wrote:
niman wrote:
The CDC has updated to age of the Indiana case to 2, consistent with media reports. There are two isolates from this case. One is a clone from Indiana and the other is an original from University of Pittsburgh. Most or all gene segments are identical.

I just went through all gene segments. There is one difference in NA and two diiferences in MP. The other six gene segments are identical (no internet babble required).

For those who may be confused by some of the utter nonsense posted on babble boards regarding multiple cases or a link between the Indiana case and Pennsylvania, the nonsense is PURE internet babble by those who can't read entries, or those who rely on the nonsense to create more nonsense.

This case is a 2M. The CDC originally listed the age and gender as 1M. Two samples were collected, on July 24 and July 27 in Indiana. The July 24 sample was cloned 3X and sequenced by the CDC. That full sequence for all 8 gene segments was published last month and it is virtually identical to the 3 cases in PA (including M gene from H1N1). The July 27 sample was sent to the University of Pittsburgh and then to the CDC, who sequenced the original sample. Both sequences have the same name, A/Indiana/08/2011, and both sets of sequences are virtually identical.

These two sets of sequences represent 1 case (2M) who was described a week ago in the eaarly release MMWR. The story is VERY straight forward - no hidden / unreported cases, and no connection to Pennsylvania, Washington County, fairs in PA ir anywhere else, or Pittsburgh / UPMC, or any additional nonsense posted on the babble boards.

CDC has cleaned up its characterization sheets. The second sample from Indiana went from Indiana to the CDC, while one of the PA patients was tested at UPMC, which has satelites all over western PA, but has its main site in Oakland in Pittsburgh. If the sample came from Childrens Hospital, the patient was hospitlaized in Pittsburgh and/or is a possible Pittsburgh area resident.

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PostPosted: Thu Sep 08, 2011 4:13 pm 
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Three cases of influenza likely not covered by this year's flu vaccine have been found in southwestern Pennsylvania.



That doesn't mean we can expect another outbreak like the H1N1 (swine-flu) epidemic in 2009, said Howard Nadworny, M.D., chief of infectious diseases for Saint Vincent Health Center.



"We see similar isolated cases of influenza almost every year," Nadworny said. "The key is whether this strain can spread person to person. The answer is usually no."



Three children who attended the Washington County Agricultural Fair in mid-August each came down with a novel type-A influenza. One child has already recovered from the virus, while the other two are recuperating, according to the Pennsylvania Department of Health.



The strain is similar to the H3N2 flu virus, but it also has a component of the H1N1 virus commonly known as swine flu.



Though this year's vaccine covers both H3N2 and H1N1, it might not protect against this novel virus that contains components of both.



"We have seen nothing to indicate that this virus has spread from one person to another," Nadworny said. "If it can, we will start seeing more cases."



Health investigators from the state Health and Agriculture departments and the U.S. Centers for Disease Control and Prevention have not uncovered how the three children acquired the flu virus.



Most likely, they picked it up from contact with pigs or other wildlife, Nadworny said.



That doesn't mean you have to avoid farm animals or stay away from county fairs, said the state's top health official.



"We're not telling people to avoid public venues or fairs," said Eli Avila, M.D., Pennsylvania Department of Health Secretary. "But until we complete our investigation, we want to make sure the public is aware and is taking the proper precautions to protect their health."

It's good news that health officials are investigating out-of-season flu cases and publishing the results, Nadworny said.

"It increases awareness," Nadworny said. "Practitioners are more likely to do a flu test if a patient comes in with flu-like symptoms, even though we are out of season."

Flu season usually arrives in northwestern Pennsylvania between January and March, though the 2009 H1N1 outbreak occurred in the fall.

DAVID BRUCE can be reached at 870-1736 or by e-mail.

http://www.goerie.com/apps/pbcs.dll/art ... ewssitemap

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PostPosted: Fri Sep 09, 2011 4:36 am 
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niman wrote:
I have contacted the CDC regarding the release of the sequences from the Washington County Fair in Pennsylvania. Tom Skinner from media relations indicated the sequences were at GISAID and would be uploaded to Genbank (as seen in response pasted below).

I have not seen these sequences at either database. I have e-mailed GISAID, Genbank, and Becky Garten at the CDC regarding the status of the sequences.

The sequences are in the GISAID data base and GenBank is in the process of uploading them.

Tom Skinner
Senior Public Affairs Officer
Centers for Disease Control and Prevention (CDC)

Sequences released at GenBank.

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PostPosted: Fri Sep 09, 2011 4:37 am 
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Location: Pittsburgh, PA USA
LOCUS JN638733 1701 bp cRNA linear VRL 08-SEP-2011
DEFINITION Influenza A virus (A/Indiana/08/2011(H3N2)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION JN638733
VERSION JN638733.1 GI:345522854
KEYWORDS .
SOURCE Influenza A virus (A/Indiana/08/2011(H3N2))
ORGANISM Influenza A virus (A/Indiana/08/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (02-SEP-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT GenBank Accession Numbers JN638726-JN638733 represent sequences
from the 8 segments of Influenza A virus (A/Indiana/08/2011(H3N2)).

##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Indiana/08/2011
Subtype :: H3N2
Segment_name :: HA
Host_gender :: M
Host_age :: 2
Passage_history :: C1
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Indiana
Collection_day :: 27
Collection_month :: 07
Collection_year :: 2011
Isolate_note :: comment: Human infection with SOIV triple
reassortant H3N2 possessing an M gene
from H1N1pdm. ; Originating Laboratory:
Indiana State Department of Health
Laboratories, 550 W. 16th St., Suite B,
46202-5120, Indianapolis, United States
EPI_accession :: EPI333152
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Indiana/08/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Indiana/08/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 2"
/db_xref="taxon:1081253"
/segment="4"
/country="USA"
/collection_date="27-Jul-2011"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AEO00689.1"
/db_xref="GI:345522855"
/translation="MKTIIAFSCILCLIFAQKLPGSDNSMATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGGICNSPHQILDGKNCTLIDALLGDPHCDDFQNKEWDL
FVERSTAYSNCYPYYVPDYATLRSLVASSGNLEFTQESFNWTGVAQGGSSYACRRGSV
NSFFSRLNWLYNLNYKYPEQNVTMPNNDKFDKLYIWGVHHPGTDKDQTNLYVQASGRV
IVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMRSDAHIDECNSECITPNGSIPNDKPFQNVNKITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAEILVALENQ
HTIDLTDSEMSKLFERTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDIYR
NEALNNRFQIKGVQLKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICI
"
ORIGIN
1 atgaagacta tcattgcttt tagctgcatt ttatgtctga ttttcgctca aaaacttccc
61 ggaagtgaca acagcatggc aacgctgtgc ctgggacacc atgcagtgcc aaacggaaca
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctactga gctggtccag
181 agttcctcaa caggtggaat atgcaacagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggggaccct cattgtgatg acttccaaaa caaggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta cgtgccggat
361 tatgccaccc ttagatcatt agttgcctca tccggcaacc tggaatttac ccaagaaagc
421 ttcaattgga ctggagttgc tcaaggcgga tcaagctatg cctgcagaag gggatctgtt
481 aacagtttct ttagtagatt gaattggttg tataacttga attacaagta tccagagcag
541 aacgtaacta tgccaaacaa tgacaaattt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacgg acaaggacca aaccaaccta tatgtccaag catcagggag agttatagtc
661 tctaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtctagacc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acgatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa
841 agctcaataa tgagatcaga tgcacacatt gatgaatgca attctgaatg cattactcca
901 aatggaagca ttcccaatga caaacctttt caaaatgtaa acaagatcac atatggagcc
961 tgtcccagat atgttaagca aaacaccctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat attcggcgca attgcaggtt tcatagaaaa tggttgggag
1081 ggaatggtag acggttggta cggtttcagg catcagaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca agcagcaatc aaccaaatca ccgggaaact aaatagagta
1201 atcaagaaaa caaacgagaa attccatcaa atcgaaaaag aattctcaga agtagaagga
1261 agaattcagg acctagagaa atacgttgaa gacactaaaa tagatctctg gtcttacaac
1321 gctgagattc ttgttgccct ggagaaccaa catacaattg atttaaccga ctcagagatg
1381 agcaaactgt tcgaaagaac aagaaggcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttca aaatatacca caaatgtgac aatgcctgca taggatcaat cagaaatgga
1501 acttatgacc atgatatata cagaaacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctaa agtcaggata caaagattgg atcctatgga tttcctttgc catatcatgc
1621 tttttgcttt gtgttgttct gctggggttc attatgtggg cctgccaaaa aggcaacatt
1681 aggtgcaaca tttgcatttg a

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PostPosted: Fri Sep 09, 2011 4:41 am 
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Posts: 27328
Location: Pittsburgh, PA USA
LOCUS JN655537 1701 bp cRNA linear VRL 08-SEP-2011
DEFINITION Influenza A virus (A/Pennsylvania/09/2011(H3N2)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION JN655537
VERSION JN655537.1 GI:345722624
KEYWORDS .
SOURCE Influenza A virus (A/Pennsylvania/09/2011(H3N2))
ORGANISM Influenza A virus (A/Pennsylvania/09/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (08-SEP-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Pennsylvania/09/2011
Subtype :: H3N2
Segment_name :: HA
Host_gender :: F
Host_age :: 2
Passage_history :: original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Pennsylvania
Collection_day :: 20
Collection_month :: 08
Collection_year :: 2011
Isolate_note :: comment: Human case of H3N2 SOIV - with
an M gene from the 2009 H1N1 Pandemic
virus. ; Originating Laboratory:
Pennsylvania Department of Health, Bureau
of Laboratories 110 Pickering Way, 19341,
Exton, United States
EPI_accession :: EPI335610
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus
(A/Pennsylvania/09/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Pennsylvania/09/2011"
/serotype="H3N2"
/host="Homo sapiens; gender F; age 2"
/db_xref="taxon:1082546"
/segment="4"
/country="USA"
/collection_date="20-Aug-2011"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AEO16287.1"
/db_xref="GI:345722625"
/translation="MKTIIAFSCILCLIFAQKLPGSDNSMATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGGICNSPHQILDGKNCTLIDALLGDPHCDDFQNKEWDL
FVERSTAYSNCYPYYVPDYATLRSLVASSGNLEFTQESFNWTGVAQGGSSYACRRGSV
NSFFSRLNWLYNLNYKYPEQNVTMPNNDKFDKLYIWGVHHPGTDKDQTNLYVQASGRV
IVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMRSDAHIDECNSECITPNGSIPNDKPFQNVNKITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAEILVALENQ
HTIDLTDSEMSKLFERTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDIYR
NEALNNRFQIKGVQLKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICI
"
ORIGIN
1 atgaagacta tcattgcttt tagctgcatt ttatgtctga ttttcgctca aaaacttccc
61 ggaagtgaca acagcatggc aacgctgtgc ctgggacacc atgcagtgcc aaacggaaca
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctactga gctggtccag
181 agttcctcaa caggtggaat atgcaacagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggggaccct cattgtgatg acttccaaaa caaggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta tgtgccggat
361 tatgccaccc ttagatcatt agttgcctca tccggcaacc tggaatttac ccaagaaagc
421 ttcaattgga ctggagttgc tcaaggcgga tcaagctatg cctgcagaag gggatctgtt
481 aacagtttct ttagtagatt gaattggttg tataacttga attacaagta tccagagcag
541 aacgtaacta tgccaaacaa tgacaaattt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacgg acaaggacca aaccaaccta tatgtccaag catcagggag agttatagtc
661 tctaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtctagacc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acgatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa
841 agctcaataa tgagatcaga tgcacacatt gatgaatgca attctgaatg cattactcca
901 aatggaagca ttcccaatga caaacctttt caaaatgtaa acaagatcac atatggagca
961 tgtcccagat atgttaagca aaacaccctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat attcggcgca attgcaggtt tcatagaaaa tggttgggag
1081 ggaatggtag acggttggta cggtttcagg catcagaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca agcagcaatc aaccaaatca ccgggaaact aaatagagta
1201 atcaagaaaa caaacgagaa attccatcaa atcgaaaaag aattctcaga agtagaagga
1261 agaattcagg acctagagaa atacgttgaa gacactaaaa tagatctctg gtcttacaac
1321 gctgagattc ttgttgccct ggagaaccaa catacaattg atttaaccga ctcagagatg
1381 agcaaaytgt tcgaaagaac aagaaggcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttca aaatatacca caaatgtgac aatgcctgca taggatcaat cagaaatgga
1501 acttatgacc atgatatata cagaaacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctaa agtcaggata caaagattgg atcctatgga tttcctttgc catatcatgc
1621 tttttgcttt gtgttgttct gctggggttc attatgtggg cctgccaaaa aggcaacatt
1681 aggtgcaaca tttgcatttg a

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PostPosted: Fri Sep 09, 2011 4:45 am 
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Posts: 27328
Location: Pittsburgh, PA USA
LOCUS JN655548 401 bp cRNA linear VRL 08-SEP-2011
DEFINITION Influenza A virus (A/Pennsylvania/10/2011(H3N2)) segment 4
hemagglutinin (HA) gene, partial cds.
ACCESSION JN655548
VERSION JN655548.1 GI:345722520
KEYWORDS .
SOURCE Influenza A virus (A/Pennsylvania/10/2011(H3N2))
ORGANISM Influenza A virus (A/Pennsylvania/10/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 401)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (08-SEP-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Pennsylvania/10/2011
Subtype :: H3N2
Segment_name :: HA
Host_gender :: F
Host_age :: 9
Passage_history :: original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Pennsylvania
Collection_day :: 26
Collection_month :: 08
Collection_year :: 2011
Isolate_note :: comment: Human case of H3N2 SOIV - with
an M gene from 2009 H1N1 Pandemic virus.
; Originating Laboratory: Pennsylvania
Department of Health, Bureau of
Laboratories 110 Pickering Way, 19341,
Exton, United States
EPI_accession :: EPI335623
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..401
/organism="Influenza A virus
(A/Pennsylvania/10/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Pennsylvania/10/2011"
/serotype="H3N2"
/host="Homo sapiens; gender F; age 9"
/db_xref="taxon:1082547"
/segment="4"
/country="USA"
/collection_date="26-Aug-2011"
gene <1..>401
/gene="HA"
CDS <1..>401
/gene="HA"
/codon_start=3
/product="hemagglutinin"
/protein_id="AEO16267.1"
/db_xref="GI:345722521"
/translation="SQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLI
APRGYFKIQSGKSSIMRSDAHIDECNSECITPNGSIPNDKPFQNVNKITYGACPRYVK
QNTLKLATGMRNVPEKQTRGIFGAIAGFIEN"
ORIGIN
1 gaagccaaca aactgtaatc ccgaatatcg ggtctagacc ctgggtaagg ggtgtctcca
61 gcataataag catctattgg acgatagtaa aaccgggaga catacttttg attaacagca
121 cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa agctcaataa
181 tgagatcaga tgcacacatt gatgaatgca attctgaatg cattactcca aatggaagca
241 ttcccaatga caaacctttt caaaatgtaa acaagatcac atatggagca tgtcccagat
301 atgttaagca aaacaccctg aaattggcaa caggaatgcg gaatgtacca gagaaacaaa
361 ctagaggcat attcggcgca attgcaggtt tcatagaaaa t

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PostPosted: Fri Sep 09, 2011 4:47 am 
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Posts: 27328
Location: Pittsburgh, PA USA
LOCUS JN655546 1081 bp cRNA linear VRL 08-SEP-2011
DEFINITION Influenza A virus (A/Pennsylvania/11/2011(H3N2)) segment 4
hemagglutinin (HA) gene, partial cds.
ACCESSION JN655546
VERSION JN655546.1 GI:345722576
KEYWORDS .
SOURCE Influenza A virus (A/Pennsylvania/11/2011(H3N2))
ORGANISM Influenza A virus (A/Pennsylvania/11/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1081)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (08-SEP-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT GenBank Accession Numbers JN655540-JN655547 represent sequences
from the 8 segments of Influenza A virus
(A/Pennsylvania/11/2011(H3N2)).

##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Pennsylvania/11/2011
Subtype :: H3N2
Segment_name :: HA
Host_gender :: F
Host_age :: 9
Passage_history :: original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Pennsylvania
Collection_day :: 25
Collection_month :: 08
Collection_year :: 2011
Isolate_note :: comment: Human case of H3N2 SOIV - with
an M gene from 2009 H1N1 Pandemic virus.
; Originating Laboratory: University of
Pittsburgh Medical Center Microbiology
Lab, Lothrop St, Pittsburgh, United
States
EPI_accession :: EPI335618
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..1081
/organism="Influenza A virus
(A/Pennsylvania/11/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Pennsylvania/11/2011"
/serotype="H3N2"
/host="Homo sapiens; gender F; age 9"
/db_xref="taxon:1082548"
/segment="4"
/country="USA"
/collection_date="25-Aug-2011"
gene 1..>1081
/gene="HA"
CDS 1..>1081
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AEO16278.1"
/db_xref="GI:345722577"
/translation="MKTIIAFSCILCLIFAQKLPGSDNSMATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGGICNSPHQILDGKNCTLIDALLGDPHCDDFQNKEWDL
FVERSTAYSNCYPYYVPDYATLRSLVASSGNLEFTQESFNWTGVAQGGSSYACRRGSV
NSFFSRLNWLYNLNYKYPEQNVTMPNNDKFDKLYIWGVHHPGTDKDQTNLYVQASGRV
IVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMRSDAHIDECNSECITPNGSIPNDKPFQNVNKITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWE"
ORIGIN
1 atgaagacta tcattgcttt tagctgcatt ttatgtctga ttttcgctca aaaacttccc
61 ggaagtgaca acagcatggc aacgctgtgc ctgggacacc atgcagtgcc aaacggaaca
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctactga gctggtccag
181 agttcctcaa caggtggaat atgcaacagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggggaccct cattgtgatg acttccaaaa caaggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta cgtgccggat
361 tatgccaccc ttagatcatt agttgcctca tccggcaacc tggaatttac ccaagaaagc
421 ttcaattgga ctggagttgc tcaaggcgga tcaagctatg cctgcagaag gggatctgtt
481 aacagtttct ttagtagatt gaattggttg tataacttga attacaagta tccagagcag
541 aacgtaacta tgccaaacaa tgacaaattt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacgg acaaggacca aaccaaccta tatgtccaag catcagggag agttatagtc
661 tctaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtctagacc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acgatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa
841 agctcaataa tgagatcaga tgcacacatt gatgaatgca attctgaatg cattactcca
901 aatggaagca ttcccaatga caaacctttt caaaatgtaa acaagatcac atatggagca
961 tgtcccagat atgttaagca aaacaccctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat attcggcgca attgcaggtt tcatagaaaa tggttgggag
1081 g

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PostPosted: Fri Sep 09, 2011 6:14 am 
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