Rhiza Labs FluTracker Forum

JCVI has released a series of full sequences at Genbank. Although most were from California, three sequences were from Australia, including Australia/6/2009.

http://www.ncbi.nlm.nih.gov/nuccore/CY055075

This sequence begins with two polymorphisms that are found in Australian sequences with D225G or D225N. The third polymorphism is Y233H, which is in the Duke death cluster in North Carolina, which has D225G and D225N. The fourth polymorphism is in the China cluster in Zhejian province, which also has D225G.

Thus, the Australia HA sequence has polymorphisms which link together three distinct sub-clades with D225G and D225N, providing compelling evidence for movement of these polymorphisms by homologous recombination.

LOCUS CY055075 1734 bp cRNA linear VRL 25-JAN-2010
DEFINITION Influenza A virus (A/Australia/6/2009(H1N1)) segment 4, complete
sequence.
ACCESSION CY055075
VERSION CY055075.1 GI:284466030
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Australia/6/2009(H1N1))
ORGANISM Influenza A virus (A/Australia/6/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1734)
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., Edelman,L., Yzerman,L., 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JOURNAL Unpublished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 1734)
CONSRTM The NIAID Influenza Genome Sequencing Consortium
TITLE Direct Submission
JOURNAL Submitted (25-JAN-2010) on behalf of JCVI/Surveillance Data
Inc./NCBI, National Center for Biotechnology Information, NIH,
Bethesda, MD 20894, USA
FEATURES Location/Qualifiers
source 1..1734
/organism="Influenza A virus (A/Australia/6/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Australia/6/2009"
/serotype="H1N1"
/host="human; gender F; age 30M"
/db_xref="taxon:708523"
/segment="4"
/country="Australia: Merrylands, New South Wales"
/collection_date="18-Jul-2009"
gene 14..1714
/gene="HA"
CDS 14..1714
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADB89711.1"
/db_xref="GI:284466031"
/translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
GNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFV
GTSRYSKKFKPEIAIRPKVRDQEGRMNYHWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
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 gcaatggaac gtgttaccca ggagatttca tcgattatga
361 ggagctaaga gagcaattga gctcagtgtc atcatttgaa aggtttgaga tattccccaa
421 gacaagttca tggcccaatc atgactcgaa caaaggtgta acggcagcat gtcctcatgc
481 tggagcaaaa agcttctaca aaaatttaat atggctagtt aaaaaaggaa actcataccc
541 aaagctcagc aaatcctaca ttaatgataa agggaaagaa gtcctcgtgc tatggggcat
601 tcaccatcca tctactagtg ctgaccaaca aagtctctat cagaatgcag atgcatatgt
661 ttttgtgggg acatcaagat acagcaagaa gttcaagccg gaaatagcaa taagacccaa
721 agtgagggat caagaaggga gaatgaacta tcactggaca ctagtagagc cgggagacaa
781 aataacattc gaagcaactg gaaatctagt ggtaccgaga tatgcattcg caatggaaag
841 aaatgctgga tctggtatta tcatttcaga tacaccagtc cacgattgca atacaacttg
901 tcagacaccc aagggtgcta taaacaccag cctcccattt cagaacatac 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 aggatagaga 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 gatttaccag attttggcga tctattcaac
1621 tgtcgccagt tcattggtac tggtagtctc cctgggggca atcagtttct ggatgtgctc
1681 taatgggtct ctacagtgta gaatatgtat ttaacattag gatttcagaa gcat

A308G (codes for D89G)
Sequences with D225G/N in bold

A/SYDNEY/2503/2009
A/SYDNEY/2501/2009
A/VICTORIA/2125/2009
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 32.2 12
gb|CY055067.1| Influenza A virus (A/Australia/4/2009(H1N1)) s... 32.2 12
gb|GU332630.1| Influenza A virus (A/cat/IA/26991/2009(H1N1)) ... 32.2 12
gb|CY052005.1| Influenza A virus (A/Norway/3433/2009(H1N1)) s... 32.2 12
gb|CY049691.1| Influenza A virus (A/Singapore/GP2711/2009(H1N... 32.2 12
gb|CY047150.1| Influenza A virus (A/Catalonia/S1138/2009(H1N1... 32.2 12
gb|GU014748.1| Influenza A virus (A/Gifu-C/67/2009(H1N1)) seg... 32.2 12
gb|GQ377064.1| Influenza A virus (A/Virginia/05/2009(H1N1)) s... 32.2 12
gb|GQ232009.1| Influenza A virus (A/Kentucky/05/2009(H1N1)) s... 32.2 12

T519C

A/SYDNEY/2503/2009
A/SYDNEY/2501/2009
A/VICTORIA/2125/2009
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 32.2 12
gb|CY055067.1| Influenza A virus (A/Australia/4/2009(H1N1)) s... 32.2 12
gb|GU371256.1| Influenza A virus (A/Orenburg/IIV2974/2009(H1N... 32.2 12
gb|GU332630.1| Influenza A virus (A/cat/IA/26991/2009(H1N1)) ... 32.2 12
gb|CY052005.1| Influenza A virus (A/Norway/3433/2009(H1N1)) s... 32.2 12
gb|CY049691.1| Influenza A virus (A/Singapore/GP2711/2009(H1N... 32.2 12
gb|GU014748.1| Influenza A virus (A/Gifu-C/67/2009(H1N1)) seg... 32.2 12

T739C (codes for Y233H)

A/North Carolina/39/2009
A/North Carolina/40/2009
A/North Carolina/41/2009
A/North Carolina/42/2009
A/North Carolina/49/2009
gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 30.2 48
gb|GU369673.1| Influenza A virus (A/Ankara/29/2009(H1N1)) seg... 30.2 48
gb|GU052197.1| Influenza A virus (A/quail/Italy/39403/1965(H1... 30.2 48
gb|GU052184.1| Influenza A virus (A/mallard/Netherlands/02/20... 30.2 48
gb|CY044171.1| Influenza A virus (A/Bethesda/SP506/2009(H1N1)... 30.2 48
gb|CY043872.1| Influenza A virus (A/mallard/Sweden/4/2005(H10... 30.2 48
gb|CY043118.1| Influenza A virus (A/Bethesda/SP508/2009(H1N1)... 30.2 48
gb|GQ325650.1| Influenza A virus (A/environment/Dongting Lake... 30.2 48
gb|GQ325642.1| Influenza A virus (A/environment/Dongting Lake... 30.2 48
gb|GQ325634.1| Influenza A virus (A/environment/Dongting Lake... 30.2 48
gb|GQ247860.1| Influenza A virus (A/ostrich/SouthAfrica/2001(... 30.2 48
gb|EU599312.1| Influenza A virus (A/teal/Egypt/912908/2005(H1... 30.2 48
gb|EU599308.1| Influenza A virus (A/teal/Egypt/912823/2005(H1... 30.2 48
gb|EU599282.1| Influenza A virus (A/shoveler/Egypt/900845/200... 30.2 48
gb|EU599276.1| Influenza A virus (A/shoveler/Egypt/900600/200... 30.2 48
gb|FJ183474.1| Influenza A virus (A/mallard/Bavaria/3/2006(H1... 30.2 48
dbj|AB450456.1| Influenza A virus (A/duck/Mongolia/149/03(H10... 30.2 48
dbj|AB450443.1| Influenza A virus (A/duck/Hokkaido/W87/2007(H... 30.2 48
gb|EU249366.1| Influenza A virus (A/shorebird/Korea/S331/2006... 30.2 48
gb|EU249364.1| Influenza A virus (A/shorebird/Korea/S285/2006... 30.2 48
dbj|AB296078.1| Influenza A virus (A/duck/Shimane/45/1997(H10... 30.2 48
dbj|AB292781.1| Influenza A virus (A/duck/Hong Kong/562/1979(... 30.2 48
dbj|AB292666.1| Influenza A virus (A/chicken/Germany/N/1949(H... 30.2 48
dbj|AB292412.1| Influenza A virus (A/duck/Hong Kong/786/1979(... 30.2 48
dbj|AB289339.1| Influenza A virus (A/swan/Shimane/1331/1981(H... 30.2 48
gb|CY014671.1| Influenza A virus (A/chicken/Germany/n/1949(H1... 30.2 48
gb|CY014644.1| Influenza A virus (A/quail/Italy/1117/1965(H10... 30.2 48
gb|CY014619.1| Influenza A virus (A/duck/Hong Kong/562/1979(H... 30.2 48
dbj|AB274041.1| Influenza A virus (A/duck/Hokkaido/18/00(H10N... 30.2 48
emb|AM087216.1| Influenza A virus (A/mallard/Iran/V15/04(H10N... 30.2 48
emb|AM087215.1| Influenza A virus (A/mallard/Iran/V40/04(H10N... 30.2 48
gb|AF311750.1| Influenza A virus (A/shorebird/Taiwan/31/99(H1... 30.2 48

T933C

gb|CY055075.1| Influenza A virus (A/Australia/6/2009(H1N1)) s... 38.2 0.19
gb|GU326329.1| Influenza A virus (A/Shandong/SWL4116/2009(H1N... 38.2 0.19
gb|CY052282.1| Influenza A virus (A/Texas/43292238/2009(H1N1)... 38.2 0.19
dbj|AB536768.1| Influenza A virus (A/Nagasaki/HA-57/2009(H1N1... 38.2 0.19
dbj|AB535748.1| Influenza A virus (A/Nagasaki/HA-63/2009(H1N1... 38.2 0.19
gb|CY051823.1| Influenza A virus (A/Texas/43242018/2009(H1N1)... 38.2 0.19
gb|GU189649.1| Influenza A virus (A/Zhejiang/DTID-ZJU03/2009(... 38.2 0.19
gb|GU112090.1| Influenza A virus (A/Zhejiang/DTID-ZJU02/2009(... 38.2 0.19
gb|GU108486.1| Influenza A virus (A/Zhejiang-Yiwu/11/2009(H1N... 38.2 0.19
gb|CY047712.1| Influenza A virus (A/Hangzhou/1/2009(H1N1)) se... 38.2 0.19
dbj|AB434336.1| Influenza A virus (A/swine/Saraburi/NIAH13021... 38.2 0.19
gb|EU296607.1| Influenza A virus (A/swine/Saraburi/NIAH13021/... 38.2 0.19
gb|AY060052.1| Influenza A virus (A/SW/MN/17138/01(H1N2)) hem... 38.2 0.19

Commentary

http://www.recombinomics.com/News/01311 ... China.html

The commentary gives more detail on the linkage and recombination. Having the same set of polymorphisms aggregated onto one sequence in Australia demonatrates how these gene pieces (polymorphisms) jump from one genetic sequence to the next and one continent to the next. Australia has markers from Australia, Asia, and North America which are key markers in sub-clades which have D225G, D225N, or both.

What is the information on whether they were fatal cases or not in these sequences?

There were at least 3 fatalities in the North Carolina cluster, so it is likely that the three sequences with D225G or D225N came from those patients. The first isolates from Zhejiang was from a severe case. She was hospitalized over a month and likely recovered, but was characterized as the first severe H1N1 case in Zhejiang Province. The status of the Australian patients is unclear. Virtually all Ukraine or Russian sequences with D225G/N were from fatal cases.