H1N1 Swine Sequences (2007)

[HenryN]

Re: H1N1 Swine Sequences (2007)

<TABLE class=resultstable cellSpacing=0 cellPadding=4 width="100%" border=0><TBODY><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=255928 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>ISDN255928 </TD><TD>A/Swine/North Carolina/00619/2005 </TD><TD>MP (7) </TD><TD>909 </TD><TD>2005 </TD><TD>H1N1 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=255936 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>ISDN255936 </TD><TD>A/Swine/North Carolina/00661/2005 </TD><TD>MP (7) </TD><TD>930 </TD><TD>2005 </TD><TD>H1 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=255941 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>ISDN255941 </TD><TD>A/Swine/North Carolina/00674/2005 </TD><TD>MP (7) </TD><TD>680 </TD><TD>2005 </TD><TD>H1 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=255947 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>ISDN255947 </TD><TD>A/Swine/North Carolina/00675/2005 </TD><TD>MP (7) </TD><TD>931 </TD><TD>2005 </TD><TD>H1 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=255953 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>ISDN255953 </TD><TD>A/Swine/North Carolina/00676/2005 </TD><TD>MP (7) </TD><TD>882 </TD><TD>2005 </TD><TD>H1 </TD></TR></TBODY></TABLE>

[HenryN]

Re: H1N1 Swine Sequences (2007)

<TABLE width="100%"><TBODY><TR bgColor=#e4ecf6><TD align=middle>NIGSP-SDI-00333</TD><TD align=middle>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=middle>USA</TD><TD align=middle>Conroe, TX</TD><TD align=middle>15-Feb-2007</TD><TD align=middle>Human</TD><TD align=middle>H1N1</TD><TD align=middle>Primary Specimen</TD><TD align=middle>Fershtman, MD</TD><TD align=middle>13 Y</TD><TD align=middle>M</TD><TD align=middle>455862</TD><TD align=middle></TD><TD align=middle></TD><TD align=middle>1106286053058</TD><TD align=middle>19457</TD><TD align=middle>Submitted to Genbank</TD><TD align=middle>SDI</TD><TD align=middle>SDI04</TD><TD align=middle></TD></TR><TR><TD colSpan=20><TABLE width="100%"><TBODY><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00333.HA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027163</TD><TD align=left>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00333.MP</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027164</TD><TD align=left>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00333.NA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027165</TD><TD align=left>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00333.NP</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027166</TD><TD align=left>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00333.NS</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027167</TD><TD align=left>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00333.PA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027168</TD><TD align=left>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00333.PB1</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027169</TD><TD align=left>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00333.PB2</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027170</TD><TD align=left>Influenza A virus (A/Texas/UR06-0305/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR></TBODY></TABLE>
<TABLE width="100%"><TBODY><TR bgColor=#e4ecf6><TD align=middle>NIGSP-SDI-00641</TD><TD align=middle>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=middle>USA</TD><TD align=middle>Florence, KY</TD><TD align=middle>25-Jan-2007</TD><TD align=middle>Human</TD><TD align=middle>H1N1</TD><TD align=middle>Primary Specimen</TD><TD align=middle>Janson, MD</TD><TD align=middle>6 Y</TD><TD align=middle>F</TD><TD align=middle>455901</TD><TD align=middle></TD><TD align=middle></TD><TD align=middle>1106267244536</TD><TD align=middle>19509</TD><TD align=middle>Submitted to Genbank</TD><TD align=middle>SDI</TD><TD align=middle>SDI04</TD><TD align=middle></TD></TR><TR><TD colSpan=20><TABLE width="100%"><TBODY><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00641.HA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027171</TD><TD align=left>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00641.MP</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027172</TD><TD align=left>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00641.NA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027173</TD><TD align=left>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00641.NP</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027174</TD><TD align=left>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00641.NS</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027175</TD><TD align=left>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00641.PA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027176</TD><TD align=left>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00641.PB1</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027177</TD><TD align=left>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00641.PB2</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027178</TD><TD align=left>Influenza A virus (A/Kentucky/UR06-0081/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR></TBODY></TABLE>
<TABLE width="100%"><TBODY><TR bgColor=#e4ecf6><TD align=middle>NIGSP-SDI-00723</TD><TD align=middle>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=middle>USA</TD><TD align=middle>Conroe, TX</TD><TD align=middle>06-Feb-2007</TD><TD align=middle>Human</TD><TD align=middle>H1N1</TD><TD align=middle>Primary Specimen</TD><TD align=middle>Fershtman, MD</TD><TD align=middle>6 Y</TD><TD align=middle>M</TD><TD align=middle>455911</TD><TD align=middle></TD><TD align=middle></TD><TD align=middle>1106280122496</TD><TD align=middle>19521</TD><TD align=middle>Submitted to Genbank</TD><TD align=middle>SDI</TD><TD align=middle>SDI04</TD><TD align=middle></TD></TR><TR><TD colSpan=20><TABLE width="100%"><TBODY><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00723.HA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027179</TD><TD align=left>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00723.MP</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027180</TD><TD align=left>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00723.NA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027181</TD><TD align=left>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00723.NP</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027182</TD><TD align=left>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00723.NS</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027183</TD><TD align=left>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00723.PA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027184</TD><TD align=left>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00723.PB1</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027185</TD><TD align=left>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00723.PB2</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027186</TD><TD align=left>Influenza A virus (A/Texas/UR06-0176/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR></TBODY></TABLE></TD></TR><TR bgColor=#e4ecf6><TD align=middle>NIGSP-SDI-00743</TD><TD align=middle>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=middle>USA</TD><TD align=middle>Bennington, VT</TD><TD align=middle>01-Mar-2007</TD><TD align=middle>Human</TD><TD align=middle>H1N1</TD><TD align=middle>Primary Specimen</TD><TD align=middle>Schultz, MD</TD><TD align=middle>2 Y</TD><TD align=middle>F</TD><TD align=middle>455913</TD><TD align=middle></TD><TD align=middle></TD><TD align=middle>1106280122500</TD><TD align=middle>19525</TD><TD align=middle>Submitted to Genbank</TD><TD align=middle>SDI</TD><TD align=middle>SDI04</TD><TD align=middle></TD></TR><TR><TD colSpan=20><TABLE width="100%"><TBODY><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00743.HA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027187</TD><TD align=left>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00743.MP</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027188</TD><TD align=left>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00743.NA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027189</TD><TD align=left>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00743.NP</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027190</TD><TD align=left>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00743.NS</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027191</TD><TD align=left>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00743.PA</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027192</TD><TD align=left>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00743.PB1</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027193</TD><TD align=left>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR><TR bgColor=#eeeeee><TD align=left>NIGSP-SDI-00743.PB2</TD><TD align=left>RELEASED IN GENBANK</TD><TD align=left>CY027194</TD><TD align=left>Influenza A virus (A/Vermont/UR06-0472/2007(H1N1))</TD><TD align=left>22-Oct-2007</TD></TR></TBODY></TABLE></TD></TR></TBODY></TABLE>
</TD></TR></TBODY></TABLE>
</TD></TR></TBODY></TABLE>

[HenryN]

Re: H1N1 Swine Sequences (2007)

In today's CDC conference call, there were several questions about getting new swine sequences, but as posted on this thread, a large database of swine sequences existed in 2007, and these sequences are STILL being withheld.

[mixin]

Re: H1N1 Swine Sequences (2007)

In today's CDC conference call, there were several questions about getting new swine sequences, but as posted on this thread, a large database of swine sequences existed in 2007, and these sequences are STILL being withheld.

Why aren't they being released?

[gsgs]

Re: H1N1 Swine Sequences (2007)

these were from Los Alamos database, (now closed to public) ?

I downloaded all sequences from Los Alamos in March 2007, and maybe updated in August

[gsgs]

Re: H1N1 Swine Sequences (2007)

c:\mails\lanl

influenza A

11.Aug.2006: lanl:121 IDN HA , 6963 all HA , 29988 all , 848 H5N1-HA,
147 human H5N1-HA , 4979 all H5N1 , 553 IDN
13.Aug.2006: genbank-4893 H5N1-sequences , 3596 full , 174 genoms ,
707 HA , 503 full HA , 103 H5N1 from 2006
15.Aug.2006: genbank-4902 , 3604 full , 174 genoms, 714 Ha , 510 full ,
107 from 2006
17.Aug.2006: lanl 5003 H5N1, 150 human HA
18.Aug. genbamk 175 genoms, 715 HA, 511 full , lanl 851 H5N1-HA
23.Aug(CDC): genbank:4922, 3623 full , 716 HA , 512 full, 176 full H5N1-genoms,
175 h5n1 from 2006, 45 full
lanl: 5020 h5n1, 859 HA , 132 HA from IDN
25.Aug.:genbank 36491 fluA , lanl:855 IDN, 132 IDN-HA , 134 IDN-HA (1400MESZ),
871 IDN(14:00 MESZ) , 31285 fluA, 5036 H5N1 , 152 human H5N1-HA,1086
25.Aug.18:18 MESZ , 31292, 5043 H5N1, 1093 humasn, 153 human H5N1-HA
30.Aug.:lanl 5055 h5n1, 865 HA , 134 HA from IDN , 871 IDN , 31374 fluA
genbank:37378 fluA, 4927 H5N1, 3628 full, HA 717 H5N1,
513 full HA-H5N1, 176 genoms H5N1, 122 H5N1 from 2006, 96 full,46/30 HA

31.Aug: lanl:5072 H5N1, 4937 genbank

01.Sep.: lanl: 5426 H5N1, 1235 IDN , 190 HA IDN , 922 HA (H5N1) ,
7601 HA all fluA , 31756 all FluA
02.Sept.: genbank:5423 H5N1 , 388 IDN 06 , 214 full genomes
05.Sept. 5423 gb,5426 lanl
08.Sep.: 5456 lanl , 1258 IDN , 5461 gb, 216 genomes
13.Sep. : gb 5462 , lanl 5456
16.Sep. : lanl 5475 , gb 5462, 217 genomes
30.Sep. : lanl 5496 , gb 5535, 222 genomes
06.Oct.: genb:5648h5n1 , 230h5n1-genomes , 40075 influenzaA
lanl: 5708h5n1 , 1303IDN , 34110influenzaA
24.Oct.:lanl 6101h5n1, 1303IDN , 35245 flu-A,
genb:6179h5n1,916IDN,275 genomes,41389 flu-A
07.Nov.:genb:42123 fluA, 6827 H5N1,281 genomes,1260 H5N1-HA,746 full H5N1-HA
lanl:6761 H5N1,1303 IDN,4117 CHN,36024 fluA,1458 H5N1-HA,1077 HA from CHN,213 HA from IDN
29.Nov.:genb:42546 fluA, 6870 H5N1,284 genoms, 1271 H5N1-HA,749 full H5N1-HA
lanl:6790 H5N1,1303 IDN,4143 CHN,36411 fluA,1463 H5N1-HA,1080 HA from CHN,213 HA from IDN
07.Dec.genb:43149 fluA, 6934 H5N1,288 genomes,1284 H5N1-HA,753 full H5N1-HA
lanl:36844 fluA, 6861 H5N1,4143 CHN, 1477 H5N1-HA,1303 IDN
17.Dec.:genbank:HA:1289, full:758 genomes:398
04.Jan.07:genb:7017 H5N1,3968 full,36576 fluA,26388 full,
1326 H5N1-HA,667 full,(nucleotide),400 H5N1-genomes
lanl:38291 fluA,7904 H5N1,5053 CHN,1361 IDN,
1520 H5N1-HA,1082,HA-CHN,220 HA-IDN
protein:45483 fluA,8249 H5N1


21.Febr.2007: genbank : 2776 flu-genomes, 2649 flu-A genomes ,
410 H5N1- genomes


3.March 2007: genbank : 410 H5N1-genomes(2.5),2676 flu-A-genome
37947(27303) flu-A-nucleotide sequences(3.7,3.5) , 7127(4044) H5N1 (1.6,1.9),
858(578) H5N1 from Indonesia,187(151) H5N1 from Africa ,
366(316) H5N1 from Europe , 1354(684) H5N1 - HA (2.1,2.5)
lanl: 40506 flu-A(5.8) ,9406 HA , 8236 H5N1(4.2) , 1606 H5N1-HA(5.7) ,
5795 CHN (14.7), 1475 IDN (8.4), 1173 CHN-HA (8.4), 257 IDN-HA (16.8)



13.Aug:4893,4979 H5N1
29.Nov:6870,6790 H5N1


07.March 2007

total,diff.,gb+la,H5N1, H3N2,H1N1,H9N2, A , B , C , PB2, PB1, PA, HA, NP, NA, M, NS,Avian,Human,Swine, A , C , G , T
---------------------------------------------------------------------------------------------------------------------------------------------------------
genb:42687,36290,38930,7164,15211,4415,2982,38273, 3654,695,4187,4193,4119,09956,4756,5685,4987,4805, 15992,24261,1727,20340073,11875374,14661487,142740 00
lanl:45343,38077,38870,8236,15680,4642,2936,40517, 4147,667,4288,4289,4231,11516,4862,6125,5112,4917, 16304,26776,1732,21507975,12586153,15480181,150927 67
38137,38930


12.April 2007: genbank : 428 H5N1-genomes,2846 flu-A-genome
40077(28982) flu-A-nucleotide sequences , 7362(4245) H5N1 ,
864(584) H5N1 from IDN ,280(244) H5N1 from Africa , 67(50) from Egypt
418(349) H5N1 from Europe , 1404(725) H5N1 - HA
lanl: 42961 flu-A ,10208 HA , 8534 H5N1 , 1693 H5N1-HA ,
5807 CHN , 1481 IDN , 92 EGY , 1174 CHN-HA , 259 IDN-HA , 48 EGY-HA

11.June 2007:genbank : 454 H5N1-genomes,2952 flu-A-genomes
42051(30237) flu-A-nucleotide sequences , 7827(4600) H5N1 ,
866(586) H5N1 from IDN , 435(378) H5N1 from Africa , 88(71) from Egypt
543(444) H5N1 from Europe , 1545(841) H5N1-HA
lanl: 44734 flu-A , 10832 HA , 8944 H5N1 , 1804 H5N1-HA ,
8083 H5N1 from CHN , 1484 IDN , 102 EGY , 1605 CHN-HA , 261 IDN-HA , 58 EGY-HA

22.June, genbank:42086, lanl:44753, 1605,261,58
29.June, genbank:43187 flu-A,7842 H5N1,454 H5N1-gnoms,546 H5N1-Eu,
441 H5N1-Af,2873 H5N1-Ch,866 H5N1-IDN,
lanl:

28.Oct.2007:genbank:492 H5N1-genomes, 3444 flu-A genomes
55587(37781) flu-A-nucleotide-sequences , 8622(5166) H5N1,
1226(835) from IDN , 483(398) from Africa , 127(83) from Egypt
638(515) from Europe , 1778(1027) H5N1-HA
lanl:54068 flu-A , 13318 HA , 9861 H5N1 , 2118 H5N1-HA ,
4184 H5N1 from CHN , 1915 IDN , 116 EGY , 770 CHN-HA , 429-HA IDN , 57 EGY-HA

1.Mar.2008: lanl closed
genbank:641 H5N1-genomes,3903 flu-A-genomes
55673 flua-A-nucleotide-sequences, 10153 H5N1,
1240 Indonesia, 644 Africa, 173 Egypt
778 Europe, 2028 H5N1-HA

03.May 2008:
689 H5N1-genomes, 3987 flu-A-genomes
58239 flu-A-nucleotide-sequences, 10590 H5N1
664 Africa,851 Europe, 2111 H5N1-HA
5211(2117) H3N2-HA,2072(1133) H1N1-HA

HAs:
01.01.2008:2103,192,5108,145,2203,383,470,14,902
03.05.2008:2447,192,6123,147,2431,383,501,14,920,3 7,70,24,20,4,8,12

2.6.2008,genomes:
total:4241, A:4034, B:207, C:0
A/human:2450, H1N1:716,H3N2:1572,H2N2:29,H1N2:23,H5N1:107,H9N2:1 ,H7N7:1,H7N3:1
A/avian:1323, H:37,34,70,64,638,140,144,6,106,19,35,13,8,0,3
decades<1940:0,40s:1,50s:3,60s:8,70s:84,80s:155,90 s:169,00s:903

21.July 2008,genomes:
total:4474, A:4265, B:208, C:0
A/human:2503,
A/avian:1461, decades:<1940:0,40s:1,50s:3,60s:8,70s:87,80s:165,9 0s:186,00s:1009
H5N1:590 , N.Am:529

16.Aug.2008:
human H3N2,HA,1990-2008: all/full
22,45,85,186,125,147,181,165,222,305,291,115,596,9 49,846,830,665,443,574
4,0,3,56,60,54,55,59,85,168,190,82,228,331,278,227 ,92,223,73
swine H3N2,HA,1990-2008:
1,1,5,5,5,2,7,7,10,20,7,13,10,8,7,18,9,2,0
1,0,1,0,0,0,1,2,2,5,1,5,4,7,4,13,5,0,0
human H3N2,HA,1990-2008,Asia:
11,13,23,31,39,35,44,66,67,66,37,38,217,202,313,35 4,387,22,65
0,0,3,2,4,2,0,30,33,46,30,29,36,35,38,33,23,3,0

flugenome.org, 18.August,2008:
4132 genomes, 289 genotypes
1578:A,D,B,3A,A,2A,B,1A
686:A,A,B,1B,A,1A,B,1A
591:K,G,D,5J,F,1J,F,1E

03.Sep.2008:
H1N1,HA,2008:289 H3N2,HA,2008:662 H1N1,NA,2008:79 H3N2,NA,2008:72

02.Dec.2008 , genbank nucleotide-sequences:
76263 flu, = 69583+5625+722 (ABC)
17255 flu-A HA : 7704+2609+2390+991 (H3N2,H1N1,H5N1,H9N2)
H5N1 China: 2+9+56+0+8+50+236+323+471+563+1258+800+16+8 (1995-2008)
H5N1 Hongkong: 269+8+32+79+284+182+96+24+8+136+176+48 (1997-2008)
H5N1 Indonesia: 56+169+308+614+96+0 (2003-2008)
H5N1 Europe:45+261+508+150+11 (<2005,2005-2008)
H5N1 Africa:9+544+302+14 (<2006,2006-2008)
H5N1 Thailand:752+401+86+53+75 (2004-2008)
H5N1 Vietnam:7+108+637+536+12+506+0 (<2003,2003-2008)

genomes:4094=3867+226+1(ABC) ; 2593+1190+153+76+62 (human,avian,swine,environment,equine)
1566+873+355+111+268+85+150+109 (H3N2,H1N1,H5N1,H9N2,H7,H2,H6,H3N8)

flugenome.org : 4394 genomes, 298 genotypes
5559+5382+5421+15753+5473+8535+7358+6842 for segments 1-8
368 genomes for China 228 of these are H5N1 from 5 genotypes


04.Feb.2009 :
fluA : 71752=7004+6978+6891+17793+7247+9891+8481+7460
HA: 3145+233+8742+245+2812+444+798+28+1061+94+81+38+36 +5+9+17
NA: 3912+4928+242+38+72+212+111+283
fluB: 5649=335+333+336+2456+354+1010+362+463
fluC: 722=90+88+88+138+87+108+123
genomes : 3997+226+1 , 1585(H3N2)+887(H1N1)+382(H5N1)+114(H9N2)+64(H6N1)+ 40(H7N1)

flugenome.org,05.Feb.2009

flugenome, 25.02.2009
63724=5710+5694+5723+16831+5833+9041+7696+7196
=945+0+27651+27193+6673+780
=25986+3+43+13+8+687+805+17+3+32992+4+11+13+2+3+7+ 16+12+8+2774+52+260+5
79403 sequences from release 170.0, gbflu5
classification by flugenome.org

79403=(222)+7467+7442+7365+20897+7739+11226+9056+7 989


79403
,,222
1:7467=5681+1786
2:7442=5665+1777
3:7365=5696+1669
4:20897=16435+4462
5:7739=5809+1930
6:11226=8980+2246
7:9056=7665+1391
8:7989=7159+830

1:5681=2570+108+1322+1+3+33+311+6+11+17+1298+1
2:5665=861+7+3+1834+73+1182+1625+2+78
3:5696=33+2507+118+1315+1191+10+73+369+50+5+25
4:16435=2793+224+8364+208+2636+413+670+18+883+80+7 6+27+24+4+8+7
5:5809=2934+4+84+18+21+1799+9+940
6:8980=3502+4569+227+31+58+154+98+266+75
7:7665=243+3417+26+9+1265+2693+12
8:7159=6382+777

41:2793=239+2398+82+72+2
42:224=114+9+2+13+7+12+3+59+5
43:8364=7957+71+68+90+1+177
44:208=171+7+26+4
45:2636=24+76+125+1+8+35+27+49+7+2271+13
46:413=43+253+10+3+11+7+86
47:670=236+6+15+17+8+388
48:18=18
49:883=2+192+564+6+20+39+33+3+7+17
410:80=62+1+3+4+9+1
411:76=11+7+58
412:27=25+2
413:24=6+14+4
414:4=3+1
415:8=8
416:7=3+1+3

61:3502=1332+132+2+8+171+43+122+81+36+1562+10+3
62:4569=3321+498+27+167+124+7+423+1+1
63:227=109+101+8+5+2+2
64:31=23+5+3
65:58=1+6+7+44
66:154=104+15+28+4+3
67:98=2+3+4+21+9+41+18
68:266=145+80+41
69:75=66+9

81:6382=2993+4+28+809+2540+7+1
82:777=181+581+9+4+2

[gsgs]

Re: H1N1 Swine Sequences (2007)

I have 458 swine H1N1 sequences from lanl, which I could send,
but apparantly those from this thread are not included

do you have them ? Can you upload or send ?

[Skatman]

Re: H1N1 Swine Sequences (2007)

Could these have been released as a result of CIDRAP's study?

http://www.cidrap.umn.edu/cidrap/content/influenza/swineflu/news/may2209genetics.html

Genetic study: Novel H1N1 likely originated in pigs

Lisa Schnirring * Staff Writer

May 22, 2009 (CIDRAP News) ? Officials from the US Centers for Disease Control and Prevention (CDC) today unveiled the first comprehensive analysis of the novel H1N1 influenza virus, shedding some light on its source, which appears to be pigs in an area where surveillance gaps exist.

The study of the antigenic and genetic characteristics of the new flu virus appeared today in an early online edition of Science. Nearly 60 researchers from across the globe assisted with the study. They analyzed full and partial genomes of 76 novel H1N1 samples, 17 from Mexico and 59 from 12 US states.

Nancy Cox, MD, director of the CDC's influenza division, told reporters at a CDC media briefing today, "With any new pathogen, it's important to understand the origin to stop reemergence."

Tracing the new flu's ancestors
Each of the eight genetic components of the new virus most closely resembles influenza viruses found in pigs, which suggests novel H1N1 likely originated in pigs, she said, adding that researchers can't tell if humans contracted the virus directly from swine or if an intermediary host played a role.

"The study reinforces that swine are an important reservoir," she said. "The result shows the global need for more systematic surveillance in pigs."

Based on the current data, researchers don't have a hypothesis on what an intermediary host could have been for the new virus. "What we can say is that the closest gene progenitors were circulating in swine," Cox said.

The researchers reported that several scenarios exist for how and where the reassortment event happened that produced the novel H1N1 virus. However, they wrote that divergence from previously sequenced strains, suggested by long branch lengths on the new virus's phylogenetic tree, indicates lack of surveillance for a number of years in the original novel flu host.

The high degree of genetic uniformity among the viral samples analyzed so far suggests that cross-species introduction to humans was a single event or multiple events involving very similar viruses, the group reported.

Researchers still haven't identified what factors are giving the new virus the ability to replicate and transmit in humans but have yet to find the adaptation or transmissibility markers seen in other viruses such as the 1918 H1N1 virus or H5N1.

Antigenic profile
During the analysis of the novel H1N1 samples, the research group also characterized the antigenic properties. Cox said they found that the viruses were very homogenous, showing much less variability, or drift, than seasonal influenza viruses. "That makes our job in coming up with a reference vaccine virus much easier," she said.

Cox said that influenza viruses in swine have been shown to mutate at a slower rate, perhaps because the animals don't live very long and don't have many subsequent infections. However, she warned that now that the virus is circulating in humans, the virus might start mutating similarly to seasonal influenza viruses.

A call for more swine surveillance
Anne Schuchat, MD, interim deputy director of CDC's science and public health program, said the findings of the study underscore the need for animal and human health experts to communicate more closely and conduct joint investigations.

Cox said animal health officials in the United States conduct some swine surveillance, but in other parts of the world the activity is much more limited. "That's where we see the greatest gaps," she said.

Marie Gramer, DVM, PhD, a swine flu expert at the University of Minnesota, told CIDRAP News that formal surveillance for swine influenza isn't conducted due to a lack of coordinated funding and effort.

Gramer pointed to some tensions between human and animal health communities that some veterinary experts believe have been fanned by steady messaging from the CDC and World Health Organization that pigs and poultry are the source of all pandemics, an impression she says has hurt the animal agriculture industry.

She said it isn't realistic to expect the animal agriculture industry, reeling from the financial effects of influenza suspicions, to fund and research surveillance for all of its animal health issues.

"Influenza viruses are shared between people and animals," Gramer said. "Surveillance should be done jointly, not separately."

Garten RJ, Davis CT, Russell CA, et al. Antigenic and genetic characteristics of swine-origin 2009 A (H1N1) influenza viruses circulating in humans. Science 2009 May 22; early online publication

[HenryN]

Re: H1N1 Swine Sequences (2007)

Why aren't they being released?

Hoarding for publication.

[HenryN]

Re: H1N1 Swine Sequences (2007)

these were from Los Alamos database, (now closed to public) ?

I downloaded all sequences from Los Alamos in March 2007, and maybe updated in August

These sequences were only available when posted above (late 2007) for a few weeks.

[HenryN]

Re: H1N1 Swine Sequences (2007)

Could these have been released as a result of CIDRAP's study?

http://www.cidrap.umn.edu/cidrap/content/influenza/swineflu/news/may2209genetics.html

Marie Gramer, DVM, PhD, a swine flu expert at the University of Minnesota, told CIDRAP News that formal surveillance for swine influenza isn't conducted due to a lack of coordinated funding and effort.

Gramer pointed to some tensions between human and animal health communities that some veterinary experts believe have been fanned by steady messaging from the CDC and World Health Organization that pigs and poultry are the source of all pandemics, an impression she says has hurt the animal agriculture industry.

She said it isn't realistic to expect the animal agriculture industry, reeling from the financial effects of influenza suspicions, to fund and research surveillance for all of its animal health issues.

"Influenza viruses are shared between people and animals," Gramer said. "Surveillance should be done jointly, not separately."

Garten RJ, Davis CT, Russell CA, et al. Antigenic and genetic characteristics of swine-origin 2009 A (H1N1) influenza viruses circulating in humans. Science 2009 May 22; early online publication

No, the swine sequences (thousands) are being withheld by the veterinary groups. They are in a private database. The sequences I linked in 2007 were generated at the University of Minnesota.