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Sequences at Genbank!
I'm interested in expert panflu damage estimates
my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgTTags: None
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Re: sequences at genbank !
data in this thread:
I'm interested in expert panflu damage estimates
my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT
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Re: sequences at genbank !
differences to other selected genomes in promille for each of the 8 segments:
(some segments may be missing, where "0" is listed)
Code:I'm interested in expert panflu damage estimates
my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT
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Re: sequences at genbank !
Code:13: 30, 36, 45, 49, 31,499,113, 41 A/Turkey/MO/24093/99(H1N2) 153:158,136,132,255,156, 82, 43,179 A/swine/Virginia/670/1987(H1N1) 154:158,128,125,246,158, 80, 50,171 A/swine/Germany/2/1981(H1N1)=1578 155:161,145,144,259,159, 80, 60,185 A/swine/Spain/53207/2004(H1N1)
I'm interested in expert panflu damage estimates
my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT
Comment
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Re: sequences at genbank !
So it's clearly a human-swine-avian recombinant. Just like they said. And large sections of the genome have been copied faithfully for years and years. The swine part, in particular, is especially stable.
And it has happened pretty recently, as such things go.
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Re: sequences at genbank !
here the best matches in the 8 segments
this is from my last update, early 2009 (maybe only 2007 in PB1, as I just see)
columns are:
difference in promille
different nucleotides
length of matching part
enumeration
strain
0 0 2280 6904 California/04/2009-04-01/(H1N1)
Code:-------------------------------------------------------------- 304 24 787 2897 Turkey/MO/24093/99(H1N2) 306 69 2249 3703 mallard Dk/South Dakota/Sg-00127/07(H3N2) 306 69 2249 3704 mallard Dk/South Dakota/Sg-00128/07 307 69 2246 3702 pintail Dk/South Dakota/Sg-00126/07(H3N2) 307 69 2247 3701 mallard Dk/South Dakota/Sg-00125/07(H3N2) 321 50 1557 2887 Sw/Texas/4199-2/98(H3N2) 333 52 1557 2888 Sw/Minnesota/9088-2/98(H3N2) 333 52 1557 2895 Sw/Iowa/8548-1/98 342 78 2280 3760 Sw/Korea/JNS06/04(H3N2) 343 54 1573 2894 Wisconsin/10/98(H1N1) 346 79 2280 3705 Sw/Minnesota/55551/00(H1N2) ------------------------------------------------------------- 312 71 2271 5644 Wisconsin/10/98(H1N1) 340 77 2259 5652 mallard Dk/South Dakota/Sg-00125/07(H3N2) 351 80 2274 5656 Sw/Indiana/9K035/99(H1N2) 365 83 2271 5638 Sw/Nebraska/209/98(H3N2) 365 83 2271 5639 Sw/Iowa/533/99(H3N2) 365 83 2271 5640 Sw/Iowa/569/99(H3N2) 365 83 2271 5641 Sw/Minnesota/593/99(H3N2) 369 84 2271 5657 Sw/Korea/CAN04/05(H3N2) 369 84 2274 5675 Dk/NC/91347/01(H1N2) 374 43 1149 4066 Sw/Minnesota/9088-2/98(H3N2) 374 43 1149 4068 Sw/Iowa/8548-1/98 374 85 2271 5668 Sw/Illinois/100085A/01(H1N2) 374 85 2271 5670 Sw/Ohio/891/01(H1N2) 378 86 2271 5654 Sw/Iowa/930/01(H1N2) 378 86 2271 5682 Sw/Korea/CY04/07(H3N2) 378 86 2271 5683 Sw/Korea/CY05/07(H3N2) 382 44 1149 4067 Sw/Texas/4199-2/98(H3N2) 383 87 2271 5658 Sw/Korea/CAS07/05(H3N2) 383 87 2271 5659 Sw/Korea/CAS09/06(H3N2) 383 87 2271 5690 Sw/Indiana/P12439/00(H1N2) ------------------------------------------------------------------ 370 79 2130 4925 mallard duck/South Dakota/Sg-00128/2007 370 79 2131 4923 pintail duck/South Dakota/Sg-00126/2007(H3N2) 373 79 2117 4922 mallard duck/South Dakota/Sg-00125/2007(H3N2) 381 79 2073 4924 mallard duck/South Dakota/Sg-00127/2007(H3N2) 390 84 2151 2977 Swine/Nebraska/209/98 (H3N2) 390 84 2151 2978 Swine/Iowa/533/99 (H3N2) 390 84 2151 2979 Swine/Iowa/569/99 (H3N2) 390 84 2151 2980 Swine/Minnesota/593/99 (H3N2) 390 84 2151 3015 Swine/Illinois/100084/01 (H1N2) 399 86 2151 3011 Swine/Minnesota/55551/00 (H1N2) ---------------------------------------------------------------- 470 80 1700 344 Swine/Indiana/P12439/00 (H1N2) 482 82 1700 280 Swine/Indiana/9K035/99 (H1N2) 500 85 1700 504 Turkey/MO/24093/99(H1N2) 505 86 1700 2468 swine/Minnesota/1192/2001(H1N2) 511 87 1700 339 Swine/Ohio/891/01(H1N2) 517 88 1700 549 SW/MN/23124-T/01(H1N2) 517 88 1700 2115 swine/Guangxi/17/2005(H1N2) 529 90 1700 550 SW/MN/23124-S/01(H1N2) 529 90 1700 552 SW/MN/16419/01(H1N2) 535 91 1700 345 Swine/Illinois/100085A/01 (H1N2) 542 56 1032 296 Wisconsin/10/98 (H1N1) ------------------------------------------------------------------ 250 13 520 6925 Sw/Oklahoma/18717/99(H3N2) 251 13 516 6921 Sw/Colorado/23619/99(H3N2) 262 14 533 6922 Sw/Wisconsin/14094/99(H3N2) 262 14 533 6924 Sw/Illinois/21587/99(H3N2) 263 14 531 6923 Sw/Oklahoma/18089/99(H3N2) 312 16 512 6926 Sw/NorthCarolina/16497/99(H3N2) 316 31 980 6927 Turkey/MO/24093/99(H1N2) 329 48 1457 6963 Sw/Iowa/533/99(H3N2) 336 49 1457 6961 Sw/Indiana/P12439/00(H1N2) 336 49 1457 6969 Sw/Korea/CY04/07(H3N2) 336 49 1457 6970 Sw/Korea/CY05/07(H3N2) 337 33 979 6928 Sw/Texas/4199-2/98(H3N2) 337 33 979 6929 Sw/Iowa/8548-1/98 339 19 560 6972 SW/NC/45319/99(H1N2) 339 19 560 6973 SW/NC/17366/01(H1N2) 339 19 560 6974 SW/CO/17871/01(H1N2) 343 50 1457 6971 Sw/Korea/CY09/07(H3N2) ------------------------------------------------------------------ 589 83 1409 1741 Sw/England/195852/92(H1N1) 652 92 1409 1742 Sw/Germany/Vi5698/95(H1N1) 712 98 1376 1746 Sw/Belgium/74/85(H1N1) 751 101 1344 1773 Sw/Ille et Vilaine/1455/99(H1N1) 753 105 1394 1772 Sw/Cotes d'Armor/1488/99(H1N1) 754 106 1404 1749 Italy/1424-4/95(H1N1) 765 108 1410 1737 Sw/Belgium/1/83(H1N1) 777 104 1338 1777 Sw/Italy/1492/97(H1N1) 786 103 1310 1778 Sw/Italy/1513-8/98(H1N1) 787 111 1410 1739 turkey/France/87075/87(H1N1) 787 111 1410 1788 Sw/Italy/53949/04(H1N1) 787 111 1410 1789 Sw/Italy/65296/04(H1N1) 794 112 1410 1738 Sw/Finistere/3616/84(H1N1) 795 102 1282 1750 Sw/Italy/1424-3/95(H1N1) 801 113 1410 1736 Sw/Lot/2979/82(H1N1) 801 113 1410 1790 Sw/Spain/53207/04(H1N1) 801 113 1410 1791 Sw/Italy/247578/04(H1N1) 801 113 1410 1793 Sw/Spain/51915/03(H1N1) 812 106 1305 1774 Cotes d'Armor/1121/00(H1N1) 815 115 1410 1794 Sw/Virginia/671/1987(H1N1) -------------------------------------------------------------------- 230 22 955 2735 Sw/HK/5190/99(H3N2) 230 22 955 2736 Sw/HK/5200/99(H3N2) 230 22 955 2737 Sw/HK/5212/99(H3N2) 261 25 955 2739 Sw/HK/1197/02(H3N2) 261 25 955 2740 Sw/HK/1144/02(H3N2) 272 26 955 2738 Sw/HK/9745/01(H3N2) 272 26 955 2743 HK/1774/99(H3N2) 293 28 955 2741 Sw/HK/7982/00(H3N2) 314 30 955 2742 Sw/HK/9296/01(H3N2) 345 33 955 2721 Sw/Leipzig/145/92(H3N2) 366 35 955 2726 Sw/Cotes d'Armor/1482/99(H1N1) 397 38 955 2722 wild boar/Germany/WS169/06(H3N2) 397 38 955 2727 Sw/Italy/1521/98(H1N2) ------------------------------------------------------------ 346 29 838 6427 Sw/Texas/4199-2/98(H3N2) 346 29 838 6428 Sw/Minnesota/9088-2/98(H3N2) 357 30 838 6429 Sw/Iowa/8548-1/98 381 32 838 6444 Sw/Indiana/9K035/99(H1N2) 395 33 835 6436 Sw/North Carolina/98225/01(H1N2) 395 33 835 6437 Sw/Minnesota/55551/00(H1N2) 395 33 835 6445 SW/MN/3327/00(H1N2) 395 33 835 6453 SW/IN/14810-T/01(H1N2) 395 33 835 6454 SW/IN/14810-S/01(H1N2) 395 33 835 6455 Sw/Korea/CAS09/06(H3N2) 407 34 835 6456 Sw/Korea/CAN04/05(H3N2) 407 34 835 6457 Sw/Korea/CAS07/05(H3N2) 407 34 835 6467 Sw/Korea/CAS08/05(H1N1) 407 34 835 6506 Sw/Iowa/930/01(H1N2) 417 35 838 6430 Sw/Nebraska/209/98(H3N2) 417 35 838 6438 Turkey/MO/24093/99(H1N2) 417 35 838 6483 turkey/OH/313053/04(H3N2)
I'm interested in expert panflu damage estimates
my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT
Comment
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Re: sequences at genbank !
from post #4:
(deleted data)
Interesting history, eh?
GS - what exactly are you comparing - the whole sequence?
."The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation
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Re: sequences at genbank !
Originally posted by vinny View PostIs there anything we should be worried about in those sequences gsgs.....?
Suggests perhaps that the virus is more transmittable through touch and contaminated surfaces than coughs and sneezes. Might also suggest that the best way to detect the virus in a suspect patient is through anal swabs rather than nasal swabs. Virus loads in the intestines probably greater than the respiratory tract.
Now, what about the other sequences, particullary Mexico, where we have a large number of deaths. Is the E627K mutation present?
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Re: sequences at genbank !
well, this is similar to American swine e.g.
A/swine/OH/511445/2007(H1N1)
in segments 123458
67 are European swine , but also A/swine/Virginia/670/1987(H1N1)I'm interested in expert panflu damage estimates
my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT
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Re: sequences at genbank !
Mama - would that suggest that the Mexican strain has undergone more mutation?
."The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation
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Re: sequences at genbank !
Originally posted by AlaskaDenise View Postfrom post #4:
Interesting history, eh?
GS - what exactly are you comparing - the whole sequence?
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My comment about the recency of the recombination is based on the lack of tiny changes in the sequences gsgs chose to compare with. If the new strain was old, then there would likely be several near matches with just 1 or 2 differences. But for the most part, either the whole segment is the same, zero differences, or completely different. This suggests that the new strain is, errrm, new.
Oh, and pigs don't fly, but mallards do, and it's the intercontinental shorebird and anseriform traffic that could be moving the european swine sequences around.
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Re: sequences at genbank !
Thanks WetDirt - now I wish I had taken the time to learn all this sequence stuff.
."The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation
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Re: sequences at genbank !
Originally posted by AlaskaDenise View PostMama - would that suggest that the Mexican strain has undergone more mutation?
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Perhaps. It may also mean that California is just one amino acid mutation away from having a serious pandemic threat. Not a good time to get complacent.
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