Rhiza Labs FluTracker Forum

JCVI released 50 full sequences at Genbank and almost all were from California. Included was one sample with D225A (as mixture with wild type) as well as two D225G and 8 D225E. Remember that the fit tamiflu resistance in Hong Kong was from a traveler from San Francisco and the HA had D225E.

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LOCUS CY054843 1724 bp cRNA linear VRL 25-JAN-2010
DEFINITION Influenza A virus (A/California/VRDL31/2009(H1N1)) segment 4,
complete sequence.
ACCESSION CY054843
VERSION CY054843.1 GI:284451639
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/California/VRDL31/2009(H1N1))
ORGANISM Influenza A virus (A/California/VRDL31/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1724)
AUTHORS Spiro,D., Halpin,R., Bera,J., Ghedin,E., Hostetler,J., Fedorova,N.,
Hine,E., Overton,L., Proudfoot,K., Kim,M., Szczypinski,B., Sitz,J.,
Katzel,D., Schnurr,D., Messenger,S., Lin,X., Wentworth,D.E.,
Bao,Y., Sanders,R., Dernovoy,D., Kiryutin,B., Lipman,D.J. and
Tatusova,T.
TITLE The NIAID Influenza Genome Sequencing Project
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1724)
CONSRTM The NIAID Influenza Genome Sequencing Consortium
TITLE Direct Submission
JOURNAL Submitted (25-JAN-2010) on behalf of JCVI/California Department of
Public Health/NCBI, National Center for Biotechnology Information,
NIH, Bethesda, MD 20894, USA
FEATURES Location/Qualifiers
source 1..1724
/organism="Influenza A virus
(A/California/VRDL31/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/California/VRDL31/2009"
/serotype="H1N1"
/host="human; gender M; age 66Y"
/db_xref="taxon:705437"
/segment="4"
/lab_host="P0 passage(s)"
/country="USA: California"
/collection_date="17-Jun-2009"
gene 14..1714
/gene="HA"
CDS 14..1714
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADB89421.1"
/db_xref="GI:284451640"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFV
GSSRYSKKFKPEIAIRPKVRXQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRVYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
sig_peptide 14..64
/gene="HA"
mat_peptide 65..1045
/gene="HA"
/product="HA1"
mat_peptide 1046..1711
/gene="HA"
/product="HA2"
ORIGIN
1 aaaagcaaca aaaatgaagg caatactagt agttctgcta tatacatttg caaccgcaaa
61 tgcagacaca ttatgtatag gttatcatgc gaacaattca acagacactg tagacacagt
121 actagaaaag aatgtaacag taacacactc tgttaacctt ctagaagaca agcataacgg
181 gaaactatgc aaactaagag gggtagcccc attgcatttg ggtaaatgta acattgctgg
241 ctggatcctg ggaaatccag agtgtgaatc actctccaca gcaagctcat ggtcctacat
301 tgtggaaaca tctagttcag acaatggaac gtgttaccca ggagatttca tcgattatga
361 ggagctaaga gagcaattga gctcagtgtc atcatttgaa aggtttgaga tattccccaa
421 gacaagttca tggcccaatc atgactcgaa caaaggtgta acggcagcat gtcctcatgc
481 tggagcaaaa agcttctaca aaaatttaat atggctagtt aaaaaaggaa attcataccc
541 aaagctcagc aaatcctaca ttaatgataa agggaaagaa gtcctcgtgc tatggggcat
601 tcaccatcca tctactagtg ctgaccaaca aagtctctat cagaatgcag atgcatatgt
661 ttttgtgggg tcatcaagat acagcaagaa gttcaagccg gaaatagcaa taagacccaa
721 agtgagggmt caagaaggga gaatgaacta ttactggaca ctagtagagc cgggagacaa
781 aataacattc gaagcaactg gaaatctagt ggtaccgaga tatgcattcg caatggaaag
841 aaatgctgga tctggtatta tcatttcaga tacaccagtc cacgattgca atacaacttg
901 tcagacaccc aagggtgcta taaacaccag cctcccattt cagaatatac atccgatcac
961 aattggaaaa tgtccaaaat atgtaaaaag cacaaaattg agactggcca caggattgag
1021 gaatgtcccg tctattcaat ctagaggcct atttggggcc attgccggtt tcattgaagg
1081 ggggtggaca gggatggtag atggatggta cggttatcac catcaaaatg agcaggggtc
1141 aggatatgca gccgacctga agagcacaca gaatgccatt gacgagatta ctaacaaagt
1201 aaattctgtt attgaaaaga tgaatacaca gttcacagca gtaggtaaag agttcaacca
1261 cctggaaaaa agaatagaga atttaaataa aaaagttgat gatggtttcc tggacatttg
1321 gacttacaat gccgaactgt tggttctatt ggaaaatgaa agaactttgg actaccacga
1381 ttcaaatgtg aagaacttat atgaaaaggt aagaagccag ttaaaaaaca atgccaagga
1441 aattggaaac ggctgctttg aattttacca caaatgcgat aacacgtgca tggaaagtgt
1501 caaaaatggg acttatgact acccaaaata ctcagaggaa gcaaaattaa acagagaaga
1561 aatagatggg gtaaagctgg aatcaacaag ggtttaccag attttggcga tctattcaac
1621 tgtcgccagt tcattggtac tggtagtctc cctgggggca atcagtttct ggatgtgctc
1681 taatgggtct ctacagtgta gaatatgtat ttaacattag gatt

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HA travel log

dbj|AB535745.1| Influenza A virus (A/Nagasaki/HA-53/2009(H1N1... 32.2 12
dbj|AB535744.1| Influenza A virus (A/Nagasaki/HA-52/2009(H1N1... 32.2 12
gb|CY051799.1| Influenza A virus (A/New York/4866/2009(H1N1))... 32.2 12
dbj|AB530486.1| Influenza A virus (A/Nagasaki/HA-41/2009(H1N1... 32.2 12
gb|FJ536843.1| Influenza A virus (A/duck/Hebei/843/2005(H1N2)... 32.2 12
emb|FN386465.1| Influenza A virus (A/Anas crecca/Spain/1404/2... 32.2 12
emb|FN386464.1| Influenza A virus (A/Anas crecca/Spain/1384/2... 32.2 12
emb|FN386463.1| Influenza A virus (A/Anas plathyrhynchos/Spai... 32.2 12
gb|GQ247841.1| Influenza A virus (A/duck/Italy/1447/2005(H1N1... 32.2 12
gb|GQ280264.1| Influenza A virus (A/Nanjing/1/2009(H1N1)) seg... 32.2 12
gb|GQ229341.1| Influenza A virus (A/swine/Hong Kong/294/2009(... 32.2 12
gb|GQ232098.1| Influenza A virus (A/swine/Parma/1997(H1N1)) s... 32.2 12
gb|CY038015.1| Influenza A virus (A/swine/France/WVL8/1992(H1... 32.2 12
gb|CY037991.1| Influenza A virus (A/swine/Belgium/WVL5/1989(H... 32.2 12
gb|CY037983.1| Influenza A virus (A/swine/France/WVL4/1985(H1... 32.2 12
gb|CY037975.1| Influenza A virus (A/swine/France/WVL3/1984(H1... 32.2 12
gb|CY037967.1| Influenza A virus (A/swine/Belgium/WVL2/1983(H... 32.2 12
gb|CY037929.1| Influenza A virus (A/swine/France/WVL13/1995(H... 32.2 12
gb|CY037898.1| Influenza A virus (A/swine/Belgium/WVL1/1979(H... 32.2 12
emb|AM920728.1| Influenza A virus (A/swine/Germany/Vi5698/95(... 32.2 12
dbj|AB434336.1| Influenza A virus (A/swine/Saraburi/NIAH13021... 32.2 12
gb|FJ432778.1| Influenza A virus (A/goose/Italy/296426/2003(H... 32.2 12
gb|FJ432770.1| Influenza A virus (A/duck/Italy/281904/2006(H1... 32.2 12
gb|FJ432754.1| Influenza A virus (A/duck/Italy/69238/2007(H1N... 32.2 12
gb|CY035248.1| Influenza A virus (A/mallard duck/Minnesota/Sg... 32.2 12
gb|CY034678.1| Influenza A virus (A/mallard duck/Minnesota/Sg... 32.2 12
gb|EU296607.1| Influenza A virus (A/swine/Saraburi/NIAH13021/... 32.2 12
gb|EU139827.1| Influenza A virus (A/swine/Minnesota/37866/199... 32.2 12
gb|CY025253.1| Influenza A virus (A/swine/Italy/670/1987(H1N1... 32.2 12
gb|CY022986.1| Influenza A virus (A/swine/Italy/671/1987(H1N1... 32.2 12
dbj|AB274304.1| Influenza A virus (A/pintail/Shimane/324/98(H... 32.2 12
dbj|AB271115.1| Influenza A virus (A/swan/Hokkaido/55/1996(H1... 32.2 12
dbj|AB271113.1| Influenza A virus (A/duck/Miyagi/66/1977(H1N1... 32.2 12
gb|CY005735.1| Influenza A virus (A/duck/NZL/160/1976(H1N3)) ... 32.2 12
emb|Z30276.1| Influenza virus (H1N1) HA mRNA for hemagglutinin 32.2 12
gb|AF091317.1|AF091317 Influenza A virus (A/swine/Netherlands... 32.2 12
gb|AF091316.1|AF091316 Influenza A virus (A/swine/Belgium/1/8... 32.2 12
gb|AF091315.1|AF091315 Influenza A virus (A/swine/Italy-Virus... 32.2 12
gb|AF091314.1|AF091314 Influenza A virus (A/swine/Netherlands... 32.2 12
gb|AF091313.1|AF091313 Influenza A virus (A/duck/Bavaria/1/77... 32.2 12

_________________
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I see the collection date was back in June. Well I am surprised we do not have more than that here in California,due to the number of deaths. This is really old news that is now being released and it takes time to do that

There has been a major upsurge in 225 changes in recent sequences which were largely collected in Nov / Dec (and the one sample from 2010). The JCVI sequences generally have a serious lag because they are kept secret for 90 days after completion. Hence the sequences reelased today are generally from June-August.

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www.twitter.com/hniman

Are not most deaths when infected with h1n1 due to 225G? I do not think is a huge surprise as it has been going on for months but just now being released. It is my estimation when we saw the young people here in Ca. dying suddenly it was most likely due to the mutation, just like all around the country and the world. So far we are status quo here in No. Cal. Lots of colds but nothing life life threatning here besides the storms.

I focused on the first question: “Are not most deaths when infected with h1n1 due to 225G?”
As far as I understand, the present statistics says the answer is NO.

According to a recent (Jan 22) WHO press release, only 7.1% [= 26/364] of the pH1N1 deaths are associated to the change D225G
(and 92.9% are not, thus far), in the WHO release sampling universe.

On the other hand, no less than 50 % [= 26/52] of the sequences with D225G are associated with a fatal outcome
by the data of the same press release.

Although both redactions could ressemble at a first glance, their actual definitions are quite different!

Very informative and good to know. Thank you for your explanation. All I is was getting from these forum pieces of info, was all were of fatal outcome from 225g due to H1N1. TY

The above post was edited to show that there are actually 2 California sequences with D225G, California/VRDL7/2009 and California/VRDL27/2009.

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C437T

gb|CY054811.1| Influenza A virus (A/California/VRDL27/2009(H1... 30.1 0.41
gb|CY054763.1| Influenza A virus (A/California/VRDL20/2009(H1... 30.1 0.41
gb|CY053922.1| Influenza A virus (A/Argentina/HNRG23/2009(H1N... 30.1 0.41
gb|CY053904.1| Influenza A virus (A/Argentina/HNRG15/2009(H1N... 30.1 0.41
gb|GU289665.1| Influenza A virus (A/swine/Wisconsin/R33f/2001... 30.1 0.41
gb|CY052743.1| Influenza A virus (A/Texas/45101424/2009(H1N1)... 30.1 0.41
gb|CY051807.1| Influenza A virus (A/New York/4870/2009(H1N1))... 30.1 0.41
gb|CY044212.1| Influenza A virus (A/Taiwan/T1339/2009(H1N1)) ... 30.1 0.41
gb|GQ385300.1| Influenza A virus (A/Toronto/0462/2009(H1N1)) ... 30.1 0.41
gb|CY040604.1| Influenza A virus (A/swine/North Carolina/9675... 30.1 0.41
gb|CY040590.1| Influenza A virus (A/swine/North Carolina/4162... 30.1 0.41
gb|CY040589.1| Influenza A virus (A/swine/North Carolina/3789... 30.1 0.41
gb|CY040588.1| Influenza A virus (A/swine/North Carolina/3527... 30.1 0.41
gb|CY040512.1| Influenza A virus (A/swine/Oklahoma/63607-6/20... 30.1 0.41
gb|CY040481.1| Influenza A virus (A/swine/Minnesota/63607-17/... 30.1 0.41
gb|FJ750522.1| Influenza A virus (A/ferret/Iowa/15828B/2008(H... 30.1 0.41
gb|EU798779.1| Influenza A virus (A/swine/Korea/CAS08/2005(H1... 30.1 0.41
gb|EU139832.1| Influenza A virus (A/swine/Iowa/00239/2004(H1N... 30.1 0.41
gb|EU139829.1| Influenza A virus (A/swine/North Carolina/3688... 30.1 0.41
gb|AY129156.1| Influenza A virus (A/Swine/Korea/CY02/02(H1N2)... 30.1 0.41
gb|AY060049.1| Influenza A virus (A/SW/MO/1877/01(H1N2)) hema... 30.1 0.41
gb|AY060037.1| Influenza A virus (A/SW/MN/3227/00(H1N2)) hema... 30.1 0.41
gb|AY060035.1| Influenza A virus (A/SW/MN/16356/01(H1N2)) hem... 30.1 0.41
gb|AY233393.1| Influenza A virus (A/duck/NC/91347/01(H1N2)) h... 30.1 0.41
gb|AF455679.1| Influenza A virus (A/Swine/Iowa/930/01(H1N2)) ... 30.1 0.41
gb|AF455678.1| Influenza A virus (A/Swine/Minnesota/55551/00 ... 30.1 0.41
gb|AF455676.1| Influenza A virus (A/Swine/North Carolina/9822... 30.1 0.41
gb|AY052778.1| Influenza A virus (A/Swine/Minnesota/1713/00/(... 30.1 0.41

_________________
www.twitter.com/hniman