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Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

LOCUS GQ351316 1410 bp cRNA linear VRL 06-JUL-2009
DEFINITION Influenza A virus (A/Hong Kong/2369/2009(H1N1)) segment 6
neuraminidase (NA) gene, complete cds.
ACCESSION GQ351316
VERSION GQ351316.1 GI:251748197
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Hong Kong/2369/2009(H1N1))
ORGANISM Influenza A virus (A/Hong Kong/2369/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1410)
AUTHORS Tai,A.L.S., Cheng,P.K.C., Leung,T.W.C. and Lim,W.W.L.
TITLE Direct Submission
JOURNAL Submitted (05-JUL-2009) Virology Division, PHLSB, Centre for Health
Protection, 382 Nam Cheong Street, Shek Kip Mei, Kolwoon, Hong
Kong, China
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009.
FEATURES Location/Qualifiers
source 1..1410
/organism="Influenza A virus (A/Hong
Kong/2369/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Hong Kong/2369/2009"
/serotype="H1N1"
/host="Homo sapiens"
/db_xref="taxon:657077"
/segment="6"
/country="China: Hong Kong"
/collection_date="11-Jun-2009"
/note="lineage: swl"
gene 1..1410
/gene="NA"
CDS 1..1410
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="ACT10319.1"
/db_xref="GI:251748198"
/translation="MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQN
QIETCNQSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIYSK
DNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMS
CPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKS
WRNNILRTQESECACVNGSCFTVMTDGPSDGQASYKIFRIEKGKIVKSVEMNAPNYYY
EECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGS
CGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQD
IVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNS
DTVGWSWPDGAELPFTIDK"
ORIGIN
1 atgaatccaa accaaaagat aataaccatt ggttcggtct gtatgacaat tggaatggct
61 aacttaatat tacaaattgg aaacataatc tcaatatgga ttagccactc aattcaactt
121 gggaatcaaa atcagattga aacatgcaat caaagcgtca ttacttatga aaacaacact
181 tgggtaaatc agacatatgt taacatcagc aacaccaact ttgctgctgg acagtcagtg
241 gtttccgtga aattagcggg caattcctct ctctgccctg ttagtggatg ggctatatac
301 agtaaagaca acagtataag aatcggttcc aagggggatg tgtttgtcat aagggaacca
361 ttcatatcat gctccccctt ggaatgcaga accttcttct tgactcaagg ggccttgcta
421 aatgacaaac attccaatgg aaccattaaa gacaggagcc catatcgaac cctaatgagc
481 tgtcctattg gtgaagttcc ctctccatac aactcaagat ttgagtcagt cgcttggtca
541 gcaagtgctt gtcatgatgg catcaattgg ctaacaattg gaatttctgg cccagacaat
601 ggggcagtgg ctgtgttaaa gtacaacggc ataataacag acactatcaa gagttggaga
661 aacaatatat tgagaacaca agagtctgaa tgtgcatgtg taaatggttc ttgctttact
721 gtaatgaccg atggaccaag tgatggacag gcctcataca agatcttcag aatagaaaag
781 ggaaagatag tcaaatcagt cgaaatgaat gcccctaatt attactatga ggaatgctcc
841 tgttatcctg attctagtga aatcacatgt gtatgcaggg ataactggca tggctcgaat
901 cgaccgtggg tgtctttcaa ccagaatctg gaatatcaga taggatacat atgcagtggg
961 attttcggag acaatccacg ccctaatgat aagacaggca gttgtggtcc agtatcgtct
1021 aatggagcaa atggagtaaa aggattttca ttcaaatacg gcaatggtgt ttggataggg
1081 agaactaaaa gcattagttc aagaaacggt tttgagatga tttgggatcc gaacggatgg
1141 actgggacag acaataactt ctcaataaag caagatatcg taggaataaa tgagtggtca
1201 ggatatagcg ggagttttgt tcagcatcca gaactaacag ggctggattg tataagacct
1261 tgcttctggg ttgaactaat cagagggcga cccaaagaga acacaatctg gactagcggg
1321 agcagcatat ccttttgtgg tgtaaacagt gacactgtgg gttggtcttg gccagacggt
1381 gctgagttgc catttaccat tgacaagtaa
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

can't wait to hear the results.
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

NA identical to sequence below (except for H274Y)

LOCUS GQ160533 1410 bp cRNA linear VRL 15-MAY-2009
DEFINITION Influenza A virus (A/New Jersey/01/2009(H1N1)) segment 6
neuraminidase (NA) gene, complete cds.
ACCESSION GQ160533
VERSION GQ160533.1 GI:237651369
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/New Jersey/01/2009(H1N1))
ORGANISM Influenza A virus (A/New Jersey/01/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1410)
AUTHORS Shu,B., Balish,A., Garten,R., Smith,C., Emery,S., Barnes,J.,
Deyde,V., Klimov,A. and Cox,N.
TITLE Human infection with novel swine H1N1 influenza
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1410)
AUTHORS Shu,B., Balish,A., Garten,R., Smith,C., Emery,S., Barnes,J.,
Deyde,V., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (14-MAY-2009) 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 Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009. For more information, see http://www.cdc.gov/.

Some of the information does not have GenBank feature identifiers
and is being provided in the comment section.

##EpifluData-START##
Isolate A/New Jersey/01/2009
Subtype H1N1
Segment_name NA
Host_gender F
Host_age 12
Passage_history C1
Adamantane_resistance resistant
Zanamivir_resistance sensitive
Oseltamivir_resistance sensitive
Country USA
State/Province New Jersey state
Collection_month 4
Collection_year 2009
EPI_accession EPI179148
##EpifluData-END##
FEATURES Location/Qualifiers
source 1..1410
/organism="Influenza A virus (A/New Jersey/01/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/New Jersey/01/2009"
/serotype="H1N1"
/host="Homo sapiens; gender F; age 12"
/db_xref="taxon:645236"
/segment="6"
/country="USA:New Jersey state"
/collection_date="Apr-2009"
gene 1..1410
/gene="NA"
CDS 1..1410
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="ACR08567.1"
/db_xref="GI:237651370"
/translation="MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQN
QIETCNQSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIYSK
DNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMS
CPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKS
WRNNILRTQESECACVNGSCFTVMTDGPSDGQASYKIFRIEKGKIVKSVEMNAPNYHY
EECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGS
CGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQD
IVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNS
DTVGWSWPDGAELPFTIDK"
ORIGIN
1 atgaatccaa accaaaagat aataaccatt ggttcggtct gtatgacaat tggaatggct
61 aacttaatat tacaaattgg aaacataatc tcaatatgga ttagccactc aattcaactt
121 gggaatcaaa atcagattga aacatgcaat caaagcgtca ttacttatga aaacaacact
181 tgggtaaatc agacatatgt taacatcagc aacaccaact ttgctgctgg acagtcagtg
241 gtttccgtga aattagcggg caattcctct ctctgccctg ttagtggatg ggctatatac
301 agtaaagaca acagtataag aatcggttcc aagggggatg tgtttgtcat aagggaacca
361 ttcatatcat gctccccctt ggaatgcaga accttcttct tgactcaagg ggccttgcta
421 aatgacaaac attccaatgg aaccattaaa gacaggagcc catatcgaac cctaatgagc
481 tgtcctattg gtgaagttcc ctctccatac aactcaagat ttgagtcagt cgcttggtca
541 gcaagtgctt gtcatgatgg catcaattgg ctaacaattg gaatttctgg cccagacaat
601 ggggcagtgg ctgtgttaaa gtacaacggc ataataacag acactatcaa gagttggaga
661 aacaatatat tgagaacaca agagtctgaa tgtgcatgtg taaatggttc ttgctttact
721 gtaatgaccg atggaccaag tgatggacag gcctcataca agatcttcag aatagaaaag
781 ggaaagatag tcaaatcagt cgaaatgaat gcccctaatt atcactatga ggaatgctcc
841 tgttatcctg attctagtga aatcacatgt gtatgcaggg ataactggca tggctcgaat
901 cgaccgtggg tgtctttcaa ccagaatctg gaatatcaga taggatacat atgcagtggg
961 attttcggag acaatccacg ccctaatgat aagacaggca gttgtggtcc agtatcgtct
1021 aatggagcaa atggagtaaa aggattttca ttcaaatacg gcaatggtgt ttggataggg
1081 agaactaaaa gcattagttc aagaaacggt tttgagatga tttgggatcc gaacggatgg
1141 actgggacag acaataactt ctcaataaag caagatatcg taggaataaa tgagtggtca
1201 ggatatagcg ggagttttgt tcagcatcca gaactaacag ggctggattg tataagacct
1261 tgcttctggg ttgaactaat cagagggcga cccaaagaga acacaatctg gactagcggg
1321 agcagcatat ccttttgtgg tgtaaacagt gacactgtgg gttggtcttg gccagacggt
1381 gctgagttgc catttaccat tgacaagtaa
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

hawkeye said:
can't wait to hear the results.
Click to expand...
Hopes and dreams of reassorters dashed. It is swine NA, and exactly matches NJ isolate and only one difference (besides H274Y) with larger series.
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Is it tamiflu resistant Dr niman....?,thanks.
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Travel log of polymorphism shared with NJ (and OK) in pandemic H1N1.

gb|GQ338380.1| Influenza A virus (A/Oklahoma/03/2009(H1N1)) s... 30.2 45
gb|CY041452.1| Influenza A virus (A/California/UR06-0439/2007... 30.2 45
gb|GQ160533.1| Influenza A virus (A/New Jersey/01/2009(H1N1))... 30.2 45
gb|CY032399.1| Influenza A virus (A/equine/Sao Paulo/1/1969(H... 30.2 45
gb|CY032295.1| Influenza A virus (A/equine/Sao Paulo/6/1963(H... 30.2 45
gb|EU409969.1| Influenza A virus (A/swine/Ohio/K1207/06(H1N1)... 30.2 45
gb|EU516136.1| Influenza A virus (A/New Mexico/05/2007(H1N1))... 30.2 45
gb|EU516135.1| Influenza A virus (A/Alaska/01/2007(H1N1)) seg... 30.2 45
gb|EU429796.1| Influenza A virus (A/chicken/Germany/N/1949(H1... 30.2 45
gb|CY028774.1| Influenza A virus (A/Virginia/UR06-0361/2007(H... 30.2 45
gb|CY028461.1| Influenza A virus (A/California/UR06-0442/2007... 30.2 45
gb|CY028421.1| Influenza A virus (A/Illinois/UR06-0215/2007(H... 30.2 45
gb|CY028405.1| Influenza A virus (A/Ohio/UR06-0429/2007(H1N1)... 30.2 45
gb|EU158122.1| Influenza A virus (A/mallard/Italy/250/02(H7N1... 30.2 45
gb|CY028149.1| Influenza A virus (A/Kentucky/UR06-0182/2007(H... 30.2 45
gb|CY028141.1| Influenza A virus (A/Kansas/UR06-0191/2007(H1N... 30.2 45
gb|CY028069.1| Influenza A virus (A/Illinois/UR06-0093/2007(H... 30.2 45
gb|CY027941.1| Influenza A virus (A/Virginia/UR06-0295/2007(H... 30.2 45
gb|CY027845.1| Influenza A virus (A/California/UR06-0125/2007... 30.2 45
gb|CY027821.1| Influenza A virus (A/Illinois/UR06-0074/2007(H... 30.2 45
gb|CY027765.1| Influenza A virus (A/Ohio/UR06-0112/2007(H1N1)... 30.2 45
gb|CY027709.1| Influenza A virus (A/Virginia/UR06-0549/2007(H... 30.2 45
gb|CY027701.1| Influenza A virus (A/Illinois/UR06-0131/2007(H... 30.2 45
gb|CY027677.1| Influenza A virus (A/Kentucky/UR06-0449/2007(H... 30.2 45
gb|CY027373.1| Influenza A virus (A/Kentucky/UR06-0424/2007(H... 30.2 45
gb|CY027485.1| Influenza A virus (A/Illinois/UR06-0115/2007(H... 30.2 45
gb|CY027469.1| Influenza A virus (A/Ohio/UR06-0394/2007(H1N1)... 30.2 45
gb|CY027437.1| Influenza A virus (A/Illinois/UR06-0094/2007(H... 30.2 45
gb|CY027421.1| Influenza A virus (A/Tennessee/UR06-0262/2007(... 30.2 45
gb|CY027397.1| Influenza A virus (A/Illinois/UR06-0136/2007(H... 30.2 45
gb|CY027357.1| Influenza A virus (A/California/UR06-0564/2007... 30.2 45
gb|CY027277.1| Influenza A virus (A/Illinois/UR06-0116/2007(H... 30.2 45
gb|CY027245.1| Influenza A virus (A/Tennessee/UR06-0124/2007(... 30.2 45
gb|CY027237.1| Influenza A virus (A/Virginia/UR06-0117/2007(H... 30.2 45
gb|CY027229.1| Influenza A virus (A/Colorado/UR06-0499/2007(H... 30.2 45
gb|CY027213.1| Influenza A virus (A/California/UR06-0585/2007... 30.2 45
gb|CY027149.1| Influenza A virus (A/North Carolina/UR06-0011/... 30.2 45
gb|CY027141.1| Influenza A virus (A/Ohio/UR06-0177/2007(H1N1)... 30.2 45
gb|CY027093.1| Influenza A virus (A/Illinois/UR06-0137/2007(H... 30.2 45
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

If it is YHY rather than YYY what is conferring the resistance?
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

niman said:
Hopes and dreams of reassorters dashed. It is swine NA, and exactly matches NJ isolate and only one difference (besides H274Y) with larger series.
Click to expand...

Hmmm. Is it a recombinant? If it's a recombinant, what did it recombine with in order to acquire H274Y? If there aren't any flanking polymorphisms that are derived from a different strain, how can you tell the difference between recombination and de novo mutation?
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Did anyone in her family, or any traveling HK acquaintances, have a lingering seasonal H1N1 from HK - thereby setting the stage for a dual infection?

.
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

pjie2 said:
Hmmm. Is it a recombinant? If it's a recombinant, what did it recombine with in order to acquire H274Y? If there aren't any flanking polymorphisms that are derived from a different strain, how can you tell the difference between recombination and de novo mutation?
Click to expand...
Coincidences get very old very fast. The recombination leads to exchanges of SNPs, as described in the Nature Precedings paper. The donor sequence would be seasonal H1N1, which matches on the 3' side (like A/Indiana/1/2008).
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

Thanks. Sorry did not read closely enough just looked at the sequences. You were just giving Jersey Girl as a close pre change relative.
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

pjie2 said:
Hmmm. Is it a recombinant? If it's a recombinant, what did it recombine with in order to acquire H274Y? If there aren't any flanking polymorphisms that are derived from a different strain, how can you tell the difference between recombination and de novo mutation?
Click to expand...
Here is the H274Y travel log (sequences that can donate H274Y)

gb|EU567011.1| Influenza A virus (A/Indiana/01/2008(H1N1)) se... 36.2 0.73
gb|DQ493078.1| Influenza A virus (A/Vietnam/CL2009/2005(H5N1)... 36.2 0.73
gb|DQ250165.1| Influenza A virus (A/Vietnam/CL2009/2005(H5N1)... 36.2 0.73
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

JJackson said:
Thanks. Sorry did not read closely enough just looked at the sequences. You were just giving Jersey Girl as a close pre change relative.
Click to expand...
Identical pre-change in NA (also has one of the three HA polymorphisms).
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

AlaskaDenise said:
Did anyone in her family, or any traveling HK acquaintances, have a lingering seasonal H1N1 from HK - thereby setting the stage for a dual infection?

.
Click to expand...
There is no evidence that the recombination happened in San Francisco. Pandemic H1N1 with H274Y is FIT and circulating below the radar (in MILD cases).
 
Re: Tamiflu Resistant Pandemic H1N1 Sequence Released (Hong Kong)

pjie2 said:
Hmmm. Is it a recombinant? If it's a recombinant, what did it recombine with in order to acquire H274Y? If there aren't any flanking polymorphisms that are derived from a different strain, how can you tell the difference between recombination and de novo mutation?
Click to expand...
The donor sequence was described last year (before the pandemic H1N1 was known)

<a rel="nofollow" href="http://www.recombinomics.com/News/09030801/H274Y_Spread.html">Commentary</a>

.
 
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