Announcement

**thebes** · June 25, 2009, 09:40 AM

Re: A/Shanghai/71T/2009 acquired E627K

The CDC's view from the leaked June 19 CDC Director's daily briefing -

http://www.astho.org/pubs/19JUN20091...689c9b4cdb0ccd (slide 13)

Isolate reported in China with genetic mutation possibly representing increased adaptation to humans.

-A/Shanghai/71T/2009 sequence posted by Shanghai Public Health Clinical Center (unknown reliability)

-Change is due to mutation rather than reassortment with seasonal influenza since remainder of gene is similar to previous sequences

-No clinical data on associated case

**HenryN** · June 26, 2009, 05:13 AM

Re: A/Shanghai/71T/2009 acquired E627K

<TABLE border=0 cellSpacing=0 cellPadding=0 width="100%" align=center><TBODY><TR><TD vAlign=top><TABLE border=0 cellSpacing=0 cellPadding=0 width="100%" background=../img/frame_r11_c7.jpg align=center><TBODY><TR><TD height=33 align=middle>Shanghai isolated alpha-2 to complete the determination of influenza virus H1N1 </TD></TR><TR><TD height=20 align=middle></TD></TR></TBODY></TABLE></TD></TR><TR><TD colSpan=2 align=middle><SCRIPT>var status0_6562='';var curfontsize_6562=12;var curlineheight_6562=24;</SCRIPT><TABLE style="WORD-BREAK: break-all" border=0 cellSpacing=6 cellPadding=5 width="100%"><TBODY><TR><TD bgColor=#ffffff height=200 vAlign=top>

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记者10日从上海市公共卫生临床中心获悉，中心应急检测实验室已经成功分离出两株甲型H1N1流感病毒并完成全基因组序列测定。

10 reporters from the Shanghai Public Health Clinical Center was informed that the Center for emergency testing laboratories have successfully isolated two H1N1 Type A influenza virus and the completion of whole genome sequencing.

上海市公共卫生临床中心应急检测实验室承担国家网络实验室技术平台建设和传染病监测任务。

Shanghai Clinical Center for Public Health Emergency under the state testing laboratory network laboratory technology platform to monitor the task of building and infectious diseases.

2009年4月全球出现新型流感疫情后，应急检测实验室获卫生部批准可开展实验室检测和分离甲型H1N1流感病毒等工作。

The world in April 2009 after the emergence of new types of influenza epidemic, emergency testing laboratory approved by the Ministry of Health to carry out laboratory testing and H1N1 influenza viruses isolated alpha and so on.

自5月24日上海市首例输入性甲型H1N1流感疑似患者转送至市公卫临床中心进行医治后，中心应急检测实验室立即启动了核酸检测和病毒分离培养的工作。

Since May 24, Shanghai's first imported alpha in patients with suspected H1N1 influenza transferred to the city of clinical public health center for treatment after the emergency center immediately launched a testing laboratory of nucleic acid detection and virus isolation and culture of work.

考虑到甲型H1N1流感病毒生物学特性的不确定性，应急检测实验室同时采用细胞培养和鸡胚接种两种方法进行病毒分离。

Alpha, taking into account the biological characteristics of influenza virus H1N1 uncertainty, contingency testing laboratory using cell culture and chick embryo inoculation methods for virus isolation.

6月3日首先成功分离到5月23日自澳大利亚墨尔本回国患者标本的病毒，命名为A／Shanghai／37 T／2009（H1N1）；6月7日另一株来自5月30日从美国回国患者的甲型H1N1流感病毒分离成功，病毒命名为A／Shanghai／71T／2009（H1N1）。

June 3 to the first successful separation of May 23 from Melbourne, Australia home specimens of patients with virus, named A/Shanghai/37T/2009 (H1N1); 6 other strains on day 7 from May 30 to return from the United States alpha in patients with H1N1 influenza virus isolation success of virus named A/Shanghai/71T/2009 (H1N1).

分离到病毒，上海市公卫临床中心研究人员立即开展了全长病毒基因的PCR扩增及测序工作，并完成病毒全基因组的PCR扩增和序列测定。

Separation of the virus, the Shanghai Public Health Clinical Center, researchers conducted a total length of the virus immediately for PCR amplification and gene sequencing, and the completion of the virus genome-wide PCR amplification and sequencing.

经过序列分析比较，两病毒分别与已公布的来自美国和澳大利亚的甲型H1N1流感病毒高度同源，表明为同一类病毒。

After sequence analysis, the two viruses were published from the United States and Australia, H1N1 Type A influenza viruses highly homologous to that for the same type of virus.

继北京、广东等地后，上海市公共卫生临床中心两株甲型H1N1流感病毒的分离为今后开展诊断试剂、疫苗、分子流行病学、药物开发和传播机制等各项相关研究工作提供了基础。

Following Beijing, Guangdong and other places, the Shanghai Public Health Clinical Center, H1N1 Type A influenza virus strains isolated for the future of diagnostic reagents, vaccines, molecular epidemiology, drug development and dissemination of the relevant mechanisms to provide a foundation for research work .

上述基因组序列信息已经提交全球公共序列数据库Genebank和全球流感共享数据库（GISAID），可以供全球的科学家用于甲型H1N1流感病毒的分析和监测。

The above-mentioned genome sequence information has been submitted to Genebank sequence database of global public and global influenza shared database (GISAID), available to scientists around the world for the H1N1 Type A influenza virus analysis and monitoring.

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**HenryN** · June 26, 2009, 05:37 AM

Re: A/Shanghai/71T/2009 acquired E627K

departed NA travel log
gb|CY038017.1| Influenza A virus (A/swine/France/WVL8/1992(H1... 34.2 2.9
gb|CY037977.1| Influenza A virus (A/swine/France/WVL3/1984(H1... 34.2 2.9
gb|CY037954.1| Influenza A virus (A/swine/England/WVL16/1998(... 34.2 2.9
gb|CY037900.1| Influenza A virus (A/swine/Belgium/WVL1/1979(H... 34.2 2.9
dbj|AB450452.1| Influenza A virus (A/duck/Miyagi/47/1977(H11N... 34.2 2.9
gb|CY029577.1| Influenza A virus (A/Muscovy duck/Vietnam/4/20... 34.2 2.9
gb|EU146650.1| Influenza A virus (A/Indonesia/160H/2005(H5N1)... 34.2 2.9
gb|EU050170.1| Influenza A virus (A/quail/Shantou/22124/2005(... 34.2 2.9
gb|EU050169.1| Influenza A virus (A/guinea fowl/Shantou/20773... 34.2 2.9
gb|EU050167.1| Influenza A virus (A/chukkar/Shantou/13393/200... 34.2 2.9
gb|EU050164.1| Influenza A virus (A/chukkar/Shantou/5275/2005... 34.2 2.9
gb|EU050161.1| Influenza A virus (A/chukkar/Shantou/1530/2005... 34.2 2.9
gb|EU050160.1| Influenza A virus (A/quail/Shantou/887/2005(H6... 34.2 2.9
gb|EU050159.1| Influenza A virus (A/quail/Shantou/687/2005(H6... 34.2 2.9
gb|EU050158.1| Influenza A virus (A/pheasant/Shantou/114/2005... 34.2 2.9
gb|EU050157.1| Influenza A virus (A/pheasant/Shantou/113/2005... 34.2 2.9
gb|EU050156.1| Influenza A virus (A/chukkar/Shantou/89/2005(H... 34.2 2.9
gb|EU050155.1| Influenza A virus (A/quail/Shantou/8002/2004(H... 34.2 2.9
gb|EU050154.1| Influenza A virus (A/chukkar/Shantou/7964/2004... 34.2 2.9
gb|EU050153.1| Influenza A virus (A/guinea fowl/Shantou/7211/... 34.2 2.9
gb|EU050151.1| Influenza A virus (A/quail/Shantou/7103/2004(H... 34.2 2.9
gb|EU050150.1| Influenza A virus (A/chukkar/Shantou/6865/2004... 34.2 2.9
gb|EU050149.1| Influenza A virus (A/quail/Shantou/6806/2004(H... 34.2 2.9
gb|EU050148.1| Influenza A virus (A/quail/Shantou/6651/2004(H... 34.2 2.9
gb|EU050147.1| Influenza A virus (A/guinea fowl/Shantou/6302/... 34.2 2.9
gb|EU050146.1| Influenza A virus (A/chukkar/Shantou/6282/2004... 34.2 2.9
gb|EU050145.1| Influenza A virus (A/quail/Shantou/6060/2004(H... 34.2 2.9
gb|EU050144.1| Influenza A virus (A/guinea fowl/Shantou/6042/... 34.2 2.9
gb|EU050143.1| Influenza A virus (A/chukkar/Shantou/5651/2004... 34.2 2.9
gb|EU050142.1| Influenza A virus (A/quail/Shantou/5136/2004(H... 34.2 2.9
gb|EU050141.1| Influenza A virus (A/partridge/Shantou/5028/20... 34.2 2.9
gb|EU050140.1| Influenza A virus (A/partridge/Shantou/4650/20... 34.2 2.9
gb|EU050139.1| Influenza A virus (A/quail/Shantou/4606/2004(H... 34.2 2.9
gb|EU050138.1| Influenza A virus (A/chukkar/Shantou/4536/2004... 34.2 2.9
gb|EU050137.1| Influenza A virus (A/partridge/Shantou/3936/20... 34.2 2.9
gb|EU050136.1| Influenza A virus (A/chukkar/Shantou/3574/2004... 34.2 2.9
gb|EU050135.1| Influenza A virus (A/guinea fowl/Shantou/3431/... 34.2 2.9
gb|EU050134.1| Influenza A virus (A/chukkar/Shantou/3322/2004... 34.2 2.9
gb|EU050133.1| Influenza A virus (A/partridge/Shantou/3201/20... 34.2 2.9
gb|EU050132.1| Influenza A virus (A/chukkar/Shantou/3182/2004... 34.2 2.9
gb|EU050131.1| Influenza A virus (A/pheasant/Shantou/2798/200... 34.2 2.9
gb|EU050130.1| Influenza A virus (A/quail/Shantou/2766/2004(H... 34.2 2.9
gb|EU050129.1| Influenza A virus (A/partridge/Shantou/2672/20... 34.2 2.9
gb|EU050128.1| Influenza A virus (A/quail/Shantou/2614/2004(H... 34.2 2.9
gb|EU050127.1| Influenza A virus (A/chukkar/Shantou/2478/2004... 34.2 2.9
gb|EU050125.1| Influenza A virus (A/chukkar/Shantou/2113/2004... 34.2 2.9
gb|EU050122.1| Influenza A virus (A/chukkar/Shantou/1550/2004... 34.2 2.9
gb|EU050121.1| Influenza A virus (A/partridge/Shantou/1297/20... 34.2 2.9
gb|EU050120.1| Influenza A virus (A/chukkar/Shantou/1201/2004... 34.2 2.9
gb|EU050119.1| Influenza A virus (A/quail/Shantou/815/2004(H6... 34.2 2.9
gb|EU050118.1| Influenza A virus (A/chukkar/Shantou/795/2004(... 34.2 2.9
gb|EU050117.1| Influenza A virus (A/turkey/Shantou/752/2004(H... 34.2 2.9
gb|EU050116.1| Influenza A virus (A/turkey/Shantou/135/2004(H... 34.2 2.9
gb|EU050115.1| Influenza A virus (A/chukkar/Shantou/121/2004(... 34.2 2.9
gb|EU050114.1| Influenza A virus (A/partridge/Shantou/35/2004... 34.2 2.9
gb|EU050113.1| Influenza A virus (A/quail/Shantou/3/2004(H6N1... 34.2 2.9
gb|EU050112.1| Influenza A virus (A/quail/Shantou/4443/2003(H... 34.2 2.9
gb|EU050111.1| Influenza A virus (A/chukkar/Shantou/4360/2003... 34.2 2.9
gb|EU050110.1| Influenza A virus (A/chukkar/Shantou/3978/2003... 34.2 2.9
gb|EU050109.1| Influenza A virus (A/quail/Shantou/3958/2003(H... 34.2 2.9
gb|EU050108.1| Influenza A virus (A/chukkar/Shantou/3809/2003... 34.2 2.9
gb|EU050107.1| Influenza A virus (A/quail/Shantou/3692/2003(H... 34.2 2.9
gb|EU050106.1| Influenza A virus (A/quail/Shantou/3212/2003(H... 34.2 2.9
gb|EU050105.1| Influenza A virus (A/chukkar/Shantou/2888/2003... 34.2 2.9
gb|EU050104.1| Influenza A virus (A/quail/Shantou/2602/2003(H... 34.2 2.9
gb|EU050103.1| Influenza A virus (A/quail/Shantou/1770/2003(H... 34.2 2.9
gb|EU050102.1| Influenza A virus (A/quail/Shantou/1218/2003(H... 34.2 2.9
gb|EU050101.1| Influenza A virus (A/quail/Shantou/1052/2003(H... 34.2 2.9
gb|EU050100.1| Influenza A virus (A/quail/Shantou/4680/2002(H... 34.2 2.9
gb|EU050099.1| Influenza A virus (A/quail/Shantou/1825/2002(H... 34.2 2.9
gb|EU050098.1| Influenza A virus (A/chukkar/Shantou/1712/2002... 34.2 2.9
gb|EU050097.1| Influenza A virus (A/partridge/Shantou/1403/20... 34.2 2.9
gb|EU050095.1| Influenza A virus (A/chukkar/Shantou/823/2002(... 34.2 2.9
gb|EU050093.1| Influenza A virus (A/chukkar/Shantou/467/2002(... 34.2 2.9
gb|EU050092.1| Influenza A virus (A/chukkar/Shantou/352/2002(... 34.2 2.9
gb|EU050091.1| Influenza A virus (A/quail/Shantou/5234/2001(H... 34.2 2.9
gb|EU050089.1| Influenza A virus (A/chicken/Shantou/3605/2001... 34.2 2.9
gb|EU050088.1| Influenza A virus (A/quail/Shantou/3329/2001(H... 34.2 2.9
gb|EU050087.1| Influenza A virus (A/quail/Shantou/2370/2001(H... 34.2 2.9
gb|EU050085.1| Influenza A virus (A/quail/Shantou/1811/2001(H... 34.2 2.9
gb|EU050083.1| Influenza A virus (A/quail/Shantou/1821/2000(H... 34.2 2.9
gb|EU050082.1| Influenza A virus (A/quail/Shantou/1808/2000(H... 34.2 2.9
gb|CY025255.1| Influenza A virus (A/swine/Italy/670/1987(H1N1... 34.2 2.9
gb|CY022988.1| Influenza A virus (A/swine/Italy/671/1987(H1N1... 34.2 2.9
gb|EF443160.1| Influenza A virus (A/duck/India/836/1980(H3N1)... 34.2 2.9
dbj|AB292403.1| Influenza A virus (A/duck/Hong Kong/836/1980(... 34.2 2.9
dbj|AB271114.1| Influenza A virus (A/duck/Miyagi/66/77(H1N1))... 34.2 2.9
gb|CY014237.1| Influenza A virus (A/Indonesia/CDC184/2005(H5N... 34.2 2.9
gb|DQ366340.1| Influenza A virus (A/duck/Guangxi/13/2004(H5N1... 34.2 2.9
gb|DQ366332.1| Influenza A virus (A/chicken/Guangxi/12/2004(H... 34.2 2.9
gb|DQ366324.1| Influenza A virus (A/duck/Vietnam/8/05(H5N1)) ... 34.2 2.9
gb|DQ366316.1| Influenza A virus (A/goose/Vietnam/3/05(H5N1))... 34.2 2.9
gb|DQ366308.1| Influenza A virus (A/duck/Vietnam/1/2005(H5N1)... 34.2 2.9
emb|AM183680.1| Influenza A virus (A/chicken/China/1204/04(H5... 34.2 2.9
gb|DQ493022.1| Influenza A virus (A/duck/Vietnam/40/2004(H5N1... 34.2 2.9
gb|AY207540.1| Influenza A virus (A/mallard/Stralsund/41-6/81... 34.2 2.9
gb|AY207538.1| Influenza A virus (A/softbill/South Africa/142... 34.2 2.9
gb|AY207534.1| Influenza A virus (A/duck/Miyagil/9/77(H1N1)) ... 34.2 2.9
gb|AY207527.1| Influenza A virus (A/duck/Nanchang/1944/92(H7N... 34.2 2.9
gb|CY005599.1| Influenza A virus (A/duck/Hong Kong/d73/1976(H... 34.2 2.9
gb|CY005495.1| Influenza A virus (A/duck/Nanchang/1904/1992(H... 34.2 2.9
gb|AF296752.1| Influenza A virus (A/Hong Kong/516/97(H5N1)) n... 34.2 2.9
gb|DQ349117.1| Influenza A virus (A/chicken/Hebei/718/2001(H5... 34.2 2.9
gb|CY005607.1| Influenza A virus (A/chicken/Hong Kong/17/1977... 34.2 2.9
emb|AJ412692.1| Influenza A virus (A/swine/Lot/2979/82(H1N1))... 34.2 2.9
emb|AJ427310.1| Influenza A virus (A/pheasant/Hong Kong/FY294... 34.2 2.9
emb|AJ410566.1| Influenza A virus genomic RNA for neuraminida... 34.2 2.9
emb|AJ410565.1| Influenza A virus genomic RNA for neuraminida... 34.2 2.9
emb|AJ410561.1| Influenza A virus genomic RNA for neuraminida... 34.2 2.9
emb|AJ410559.1| Influenza A virus genomic RNA for neuraminida... 34.2 2.9
emb|AJ410558.1| Influenza A virus genomic RNA for neuraminida... 34.2 2.9
emb|AJ410557.1| Influenza A virus genomic RNA for neuraminida... 34.2 2.9
gb|AF250481.1|AF250481 Influenza A virus (A/Teal/Hong Kong/W3... 34.2 2.9
gb|AF084275.1|AF084275 Influenza A virus (A/HongKong/486/97(H... 34.2 2.9
gb|AF084274.1|AF084274 Influenza A virus (A/HongKong/485/97(H... 34.2 2.9
gb|AF084273.1|AF084273 Influenza A virus (A/HongKong/483/97(H... 34.2 2.9
gb|AF084272.1|AF084272 Influenza A virus (A/HongKong/482/97(H... 34.2 2.9
gb|AF084271.1|AF084271 Influenza A virus (A/HongKong/481/97(H... 34.2 2.9
gb|AF046089.1| Influenza A virus (A/Hong Kong/156/97(H5N1)) n... 34.2 2.9
gb|AF046081.1| Influenza A virus (A/Chicken/Hong Kong/220/97 ... 34.2 2.9
emb|AJ416629.1| Influenza A virus (A/African starling/England... 34.2 2.9
gb|AF098554.1|AF098554 Influenza A virus (A/Goose/Hong Kong/w... 34.2 2.9
gb|AF098553.1|AF098553 Influenza A virus (A/Duck/Hong Kong/y2... 34.2 2.9
gb|AF098552.1|AF098552 Influenza A virus (A/Duck/Hong Kong/p4... 34.2 2.9
gb|AF098550.1|AF098550 Influenza A virus (A/Chicken/Hong Kong... 34.2 2.9
gb|AF098549.1|AF098549 Influenza A virus (A/Chicken/Hong Kong... 34.2 2.9
gb|AF098548.1|AF098548 Influenza A virus (A/Chicken/Hong Kong... 34.2 2.9
gb|AF098547.1|AF098547 Influenza A virus (A/Chicken/Hong Kong... 34.2 2.9
gb|AF102670.1| Influenza A virus (A/Hong Kong/542/97(H5N1)) n... 34.2 2.9
gb|AF102669.1| Influenza A virus (A/Hong Kong/514/97(H5N1)) n... 34.2 2.9
gb|AF102668.1| Influenza A virus (A/Hong Kong/483/1997(H5N1))... 34.2 2.9
gb|AF102667.1| Influenza A virus (A/Hong Kong/532/1997(H5N1))... 34.2 2.9
gb|AF102666.1| Influenza A virus (A/Hong Kong/503/97(H5N1)) n... 34.2 2.9
gb|AF102665.1| Influenza A virus (A/Hong Kong/491/97(H5N1)) n... 34.2 2.9
gb|AF102664.1| Influenza A virus (A/Hong Kong/485/97(H5N1)) n... 34.2 2.9
gb|AF102663.1| Influenza A virus (A/Hong Kong/481/97(H5N1)) n... 34.2 2.9
gb|AF102662.1| Influenza A virus (A/Hong Kong/538/97(H5N1)) n... 34.2 2.9
gb|AF102661.1| Influenza A virus (A/HongKong/97/98(H5N1)) neu... 34.2 2.9
gb|AF102660.1| Influenza A virus (A/Hong Kong/516/97(H5N1)) n... 34.2 2.9
gb|AF102659.1| Influenza A virus (A/Hong Kong/507/97(H5N1)) n... 34.2 2.9
gb|AF102658.1| Influenza A virus (A/Hong Kong/486/97(H5N1)) n... 34.2 2.9
gb|AF102657.1| Influenza A virus (A/Hong Kong/488/97(H5N1)) n... 34.2 2.9
gb|AF102656.1| Influenza A virus (A/Hong Kong/482/97(H5N1)) n... 34.2 2.9
gb|AF057292.1|AF057292 Influenza A virus (A/chicken/Hong Kong... 34.2 2.9
gb|AF028708.1|AF028708 Influenza A virus (A/HongKong/156/97(H... 34.2 2.9
gb|AF036357.1| Influenza A virus (A/HongKong/156/97(H5N1)) ne... 34.2 2.9

**HenryN** · June 26, 2009, 09:11 AM

Re: A/Shanghai/71T/2009 acquired E627K

Both Genbank and GISAID now have two versions of PB2, the original, with E627K and clone 2 which has reverted back to the wild type. GISAID used to also have clone 1, which also had E627K, but it has been replaced with clone 2.

**Toaster2** · June 26, 2009, 09:33 AM

Re: A/Shanghai/71T/2009 acquired E627K

I just found it out too: see the comment posted in the original sequence:

COMMENT [WARNING] On Jun 24, 2009 this sequence was replaced by
gi:241914528. GenBank Accession Numbers GQ253497-GQ253504 represent sequences from the 8 segments of Influenza A virus (A/Shanghai/71T/2009(H1N1)).

GI:241914528 still has E at 627, so no E627K has occurred in Shanghai (explaining why it was not seen in any sequences afterward).

**gsgs** · June 26, 2009, 10:07 AM

Re: A/Shanghai/71T/2009 acquired E627K

Code:

                                           00112222222 1 00 00111 000000111 00000000111 0000 00000  
                                           34280011122 1 06 67024 127888112 35666779222 4679 23457  
                                           04873300644 6 43 51080 195015444 18999453258 9027 96842  
                                           31192818349 1 00 86128 781436368 68789270163 2033 17979  
-codon-position----------------------------   11112  2   1  12211  11  1    1 12 11  22    1  1 1   
---Index-----------------------------------GAAGGGGGGGC G GT TAGGC CGGAAGGAG GTTGTATGTGG GGGG AAAGG  
  1 >A/Shanghai/71T-orig./2009/05/31       ...AAAAAA.. A .. A.... .A.GTAAGA AC......CAA AA.. .G...  
 12 >A/Shanghai/71T-corr./2009/05/31       .......AA.. A .. A.... .A....A.A A.......C.. AA.. .G...  
  2 >A/Shanghai/1/2009/05/23               .GG.....R.. A A. A..AT .A....A.A A....G..... AA.. GGGAA  
  3 >A/Shanghai/37T/2009/05/24             AGG.....A.. A A. A..AT TA....A.A A.GTGGAT... AAA. GG..A  
  6 >A/Shanghai/60T/2009/05/28             .GG.....A.. A A. ----- .A....A.A ----------- AA.. GG..A  
  5 >A/******/Cancun-NY/Index/2009-04-15   ........A.. . .. A...T .A....A.A A....G..... AA.. .G...  
  7 >A/Bayern/63/2009//                    ........ATA A .. A..AT .A....A.A A....G..... AA.C .G...  
  8 >A/Ohio/07/2009/04/24                  ........A.. A .. A.A-- .AA...A.A A....G..... AA.. .G...  
  9 >A/NY/3007/2009/04/27                  ........A.. A .. A..AT .A....A.A A....G..... AA.. .G...  
 10 >A/Georgia/01/2009/04/27               ........A.. A -- AG.AT .A....A.A A....G..... AA.. .G...  
 11 >A/Canada-ON/RV1526/2009//             ........A.. A .C W..AT .A....A.A A....G..... AA.. .G...  
  4 >A/******/index/2009-02-01             ........... . .. ..... ......... ........... .... .....

removed are:

4 mutations in PB2
4 mutations in NP
3 mutations in NA

11 mutations removed in total. (I wonder, how many mutations can be "removed" from
the Alberta-pig )

we still have the mutation at 703 in PB2, which is close to the critical one at 701
we still have T658A(4) but not C1408T(4) which is unusual and unique.
we still have G316A(6) but not A742G(6) which could suggest reassortment.
But with just one such position the evidence for reassortment is thin

still amazing, how that mutation could arise with those 6 others in the lab

**HenryN** · June 26, 2009, 10:21 AM

Re: A/Shanghai/71T/2009 acquired E627K

Originally posted by gsgs View Post

Code:

 
                                           00112222222 1 00 00111 000000111 00000000111 0000 00000  
                                           34280011122 1 06 67024 127888112 35666779222 4679 23457  
                                           04873300644 6 43 51080 195015444 18999453258 9027 96842  
                                           31192818349 1 00 86128 781436368 68789270163 2033 17979  
-codon-position----------------------------   11112  2   1  12211  11  1    1 12 11  22    1  1 1   
---Index-----------------------------------GAAGGGGGGGC G GT TAGGC CGGAAGGAG GTTGTATGTGG GGGG AAAGG  
  1 >A/Shanghai/71T-orig./2009/05/31       ...AAAAAA.. A .. A.... .A.GTAAGA AC......CAA AA.. .G...  
 12 >A/Shanghai/71T-corr./2009/05/31       .......AA.. A .. A.... .A....A.A A.......C.. AA.. .G...  
  2 >A/Shanghai/1/2009/05/23               .GG.....R.. A A. A..AT .A....A.A A....G..... AA.. GGGAA  
  3 >A/Shanghai/37T/2009/05/24             AGG.....A.. A A. A..AT TA....A.A A.GTGGAT... AAA. GG..A  
  6 >A/Shanghai/60T/2009/05/28             .GG.....A.. A A. ----- .A....A.A ----------- AA.. GG..A  
  5 >A/******/Cancun-NY/Index/2009-04-15   ........A.. . .. A...T .A....A.A A....G..... AA.. .G...  
  7 >A/Bayern/63/2009//                    ........ATA A .. A..AT .A....A.A A....G..... AA.C .G...  
  8 >A/Ohio/07/2009/04/24                  ........A.. A .. A.A-- .AA...A.A A....G..... AA.. .G...  
  9 >A/NY/3007/2009/04/27                  ........A.. A .. A..AT .A....A.A A....G..... AA.. .G...  
 10 >A/Georgia/01/2009/04/27               ........A.. A -- AG.AT .A....A.A A....G..... AA.. .G...  
 11 >A/Canada-ON/RV1526/2009//             ........A.. A .C W..AT .A....A.A A....G..... AA.. .G...  
  4 >A/******/index/2009-02-01             ........... . .. ..... ......... ........... .... .....

removed are:

4 mutations in PB2
4 mutations in NP
3 mutations in NA

11 mutations removed in total. (I wonder, how many mutations can be "removed" from
the Alberta-pig )

we still have the mutation at 703 in PB2, which is close to the critical one at 701
we still have T658A(4) but not C1408T(4) which is unusual and unique.
we still have G316A(6) but not A742G(6) which could suggest reassortment.
But with just one such position the evidence for reassortment is thin

still amazing, how that mutation could arise with those 6 others in the lab

The SECOND cloned sequence is not necessarily a "corrected" sequence. At GISAID the original sequence remains.

In fact the lab has generated E627K in two (original and C1) of the three sequences (only C2 has E627) deposited at GISAID (although C1 has now been removed).

Announcement

A/Shanghai/71T/2009 acquired E627K

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