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Go Back   FluTrackers > Genetic Tracking & Scientfic Analysis of Pandemic Influenza & Other Diseases > Genetic Analysis of Swine Influenza A/H1N1 2009

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  #1  
Old April 27th, 2009, 04:00 PM
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Default Sequences at Genbank!

http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html
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Old April 27th, 2009, 04:04 PM
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Default Re: sequences at genbank !

data in this thread:
http://www.flutrackers.com/forum/sho...d.php?t=101181
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Old April 27th, 2009, 04:06 PM
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Default Re: sequences at genbank !

Is there anything we should be worried about in those sequences gsgs.....?
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Old April 27th, 2009, 04:27 PM
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Default 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:

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Old April 27th, 2009, 04:31 PM
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Default 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)
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Old April 27th, 2009, 04:57 PM
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Default 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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Old April 27th, 2009, 06:05 PM
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Default 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)
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Old April 27th, 2009, 06:24 PM
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Default Re: sequences at genbank !

from post #4:

(deleted data)


Interesting history, eh?

GS - what exactly are you comparing - the whole sequence?

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Last edited by AlaskaDenise; April 27th, 2009 at 06:41 PM. Reason: delete misleading data
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Old April 27th, 2009, 06:29 PM
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Default Re: sequences at genbank !

Quote:
Originally Posted by vinny View Post
Is there anything we should be worried about in those sequences gsgs.....?
On the contrary, the fact that all of the California sequences have a Lysine at position 627 of the PB2 segment is fantastic news. Years of research would suggest that the California virus does not replicate well in the cooler temperatures of the upper respiratory system. Perhaps that is why we are seeing patients complain of nausea, vommiting and diarrhea. This thing replicates better in the digestive tract?

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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Old April 27th, 2009, 06:33 PM
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Default 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)
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Old April 27th, 2009, 06:34 PM
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Default Re: sequences at genbank !

Mama - would that suggest that the Mexican strain has undergone more mutation?

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Old April 27th, 2009, 06:34 PM
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Default Re: sequences at genbank !

Quote:
Originally Posted by AlaskaDenise View Post
from post #4:



Interesting history, eh?

GS - what exactly are you comparing - the whole sequence?

.
The H5N1 are not good matches. gsgs's numbers indicate the number of differences between A/california segments and the segments in the list of sequences he compared A/Calif with. The sequences only match in a segment if there are 0 differences. Hence my comment. If you look down column by column and spot the 0s and ignore the rest, you end up with with a 100% match to A/calif, and individual 100% matches to a mallard and to various swine sequences.

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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Old April 27th, 2009, 06:37 PM
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Default Re: sequences at genbank !

Thanks WetDirt - now I wish I had taken the time to learn all this sequence stuff.

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Old April 27th, 2009, 06:41 PM
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Default Re: sequences at genbank !

does this mean we can stop worrying so much........?
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Old April 27th, 2009, 06:42 PM
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Default Re: sequences at genbank !

Quote:
Originally Posted by AlaskaDenise View Post
Mama - would that suggest that the Mexican strain has undergone more mutation?

.

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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Old April 27th, 2009, 06:46 PM
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Default Re: sequences at genbank !

Quote:
Originally Posted by vinny View Post
does this mean we can stop worrying so much........?
No, it means that this is indeed a new strain and nobody is likely to have much immunity to it. And mamma's post says that it is likely to spread on surfaces better than most strains. But whether it has legs, that is, whether it can spread efficiently while maintaining its nastiness, is a different issue that we basically have to watch and wait to find out. And I'm not happy that nasal swabs might not be working as expected, which may mean a lot of cases are being missed. We know it makes a difference in birds which end you swab.
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Old April 27th, 2009, 06:46 PM
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Default Re: sequences at genbank !

Quote:
Originally Posted by Mamabird View Post
On the contrary, the fact that all of the California sequences have a Lysine at position 627 of the PB2 segment is fantastic news. Years of research would suggest that the California virus does not replicate well in the cooler temperatures of the upper respiratory system. Perhaps that is why we are seeing patients complain of nausea, vommiting and diarrhea. This thing replicates better in the digestive tract?

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?
So this discovery might suggest extra precautions by food handlers? That might also explain why areas with inadequate sanitation would spread the virus.

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Old April 27th, 2009, 06:55 PM
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Default Re: sequences at genbank !

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Originally Posted by AlaskaDenise View Post
So this discovery might suggest extra precautions by food handlers? That might also explain why areas with inadequate sanitation would spread the virus.

.
Yes, and that could also explain why the CDC has been recommending hand washing, and downplaying the usefulness of surgical masks and N95 respirators.

Previous pandemic viruses and our seasonal flu viruses have the E627K mutation from the wild state. From the posted sequences at GenBank, this virus does not. I am just thrilled with this news, but am trying to restrain myself as the H5N1 (Qinhai strain) was able to rid itself of the Lysine at 627.

We should also be pleased that the HA segment does not have multiple basic amino acids at the cleavage site. Based on existing research, this would suggest that we should not see rapid failure of multiple organs in severe human cases. All good news so far.
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Old April 27th, 2009, 06:59 PM
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Default Re: sequences at genbank !

it may be more similar in practical terms to Norovirus, which would explain why schools are being victims - except influenza will probably mutate far more - picking up polymorphisms from circulating seasonal H1N1.
Cruise ships, rest homes, etc. best beware.

What about NS1/92???

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Old April 27th, 2009, 07:02 PM
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Default Re: sequences at genbank !

What would this mean for produce from the area? I remember a green onion incident a while back. (ie: rinsed in contaminated water, hard to clean)
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Old April 27th, 2009, 07:03 PM
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Default Re: sequences at genbank !

Quote:
Originally Posted by AlaskaDenise View Post
it may be more similar in practical terms to Norovirus, which would explain why schools are being victims - except influenza will probably mutate far more.
Cruise ships, rest homes, etc. best beware.

What about NS1/92???

.
Exactly correct. Perhaps also, similar to Hepatitis. Maybe more likely to get this bug off of toilet tissue in public restrooms than from someone coughing on the subway.

I haven't an opportunity to get to NS1 yet, but the other good news confirmed by CDC testing is the sensitivity to Tamiflu. The NA segment does not show the mutations that allow the virus to resist Tamiflu. However, we have seen how this can quickly change. Judicial use of this antiviral is in order.
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Old April 27th, 2009, 07:05 PM
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Default Re: sequences at genbank !

Quote:
What would this mean for produce from the area?
Good point. Time to get out that bottle of organic produce wash.

It may also explain why Canada wants health exams for Mexican workers, but any food worker should now take extra precautions.

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Old April 27th, 2009, 07:21 PM
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Default Re: sequences at genbank !

I have commented in the 'Swine flu - basic information' and in response to question that I thought it very unlikely that the the H1N1 component of the seasonal flu shot would provide any worthwhile protection against our new pandemic candidate.
As the bulk of the antigenic sites are on HA & NA and of these HA is the more important I thought this radial phylogenic tree generated by BLASTing the HA in A/California/04/2009(H1N1) might be of interst. The HA is plotted against its 100 closest relatives in the database and while you will not be able to read the text I hope you will be able to see that A/California/04/2009(H1N1) (at the top with a yellow highlight) is 'out on a limb' even among its cousins. I will try and work out how to re do this with a few of those from this screen and A/Brisbane/59/2007 (H1N1) which is the seasonal vaccine H1 component and I expect to see it as being a long way of target.

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The tree below has the vaccine selection A/Brisbane/59/2007 (H1N1) at the top, very much on its own, the next block are all very close matches and are the new sequences from CA & TX (no Mexican sequences yet but we are told they match CA/TX) and the bottom block are some of the closest matches in Genebank (4 swine & 1 avian,dates form 1999-2005, from the US and China).

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Last edited by JJackson; April 28th, 2009 at 09:44 AM. Reason: Added the second image
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Old April 27th, 2009, 07:22 PM
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Default Re: sequences at genbank !

Quote:
Originally Posted by AlaskaDenise View Post

What about NS1/92???

.
The NS segment of both the California and Texas sequence looks nothing like any H1N1 seasonal flu virus, 1918 pandemic virus, or H5N1 for that matter. Position 92 unremarkable with an aspartic acid (D) present.
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Old April 27th, 2009, 07:29 PM
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Default Re: sequences at genbank !

It really is a new strain.

Don't know if that's good or bad.

Any history at all on aspartic acid at that location?

It could be the "Typhoid Mary" of the influenza world.

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Old April 27th, 2009, 07:33 PM
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Default Re: sequences at genbank !

Dare I suggest an epigenetic change?

Recent history has been showing epigenetic changes to immune systems of other species....something like this may be the cause.

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  #27  
Old April 27th, 2009, 07:48 PM
HenryN HenryN is offline
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Default Re: sequences at genbank !

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Originally Posted by Mamabird View Post
On the contrary, the fact that all of the California sequences have a Lysine at position 627 of the PB2 segment is fantastic news. Years of research would suggest that the California virus does not replicate well in the cooler temperatures of the upper respiratory system. Perhaps that is why we are seeing patients complain of nausea, vommiting and diarrhea. This thing replicates better in the digestive tract?

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?
E627K is mammalian (not a "mutation"). Swine is mammalian.
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  #28  
Old April 27th, 2009, 07:50 PM
HenryN HenryN is offline
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Default Re: sequences at genbank !

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Originally Posted by vinny View Post
does this mean we can stop worrying so much........?
Only if you ignore 1918
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  #29  
Old April 27th, 2009, 07:52 PM
HenryN HenryN is offline
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Default Re: sequences at genbank !

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Originally Posted by Mamabird View Post
Yes, and that could also explain why the CDC has been recommending hand washing, and downplaying the usefulness of surgical masks and N95 respirators.

Previous pandemic viruses and our seasonal flu viruses have the E627K mutation from the wild state. From the posted sequences at GenBank, this virus does not. I am just thrilled with this news, but am trying to restrain myself as the H5N1 (Qinhai strain) was able to rid itself of the Lysine at 627.

We should also be pleased that the HA segment does not have multiple basic amino acids at the cleavage site. Based on existing research, this would suggest that we should not see rapid failure of multiple organs in severe human cases. All good news so far.
1918 didn't have a polybasic cleavage site.
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  #30  
Old April 27th, 2009, 07:57 PM
Mamabird Mamabird is offline
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Default Re: sequences at genbank !

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Originally Posted by AlaskaDenise View Post
It really is a new strain.

Don't know if that's good or bad.

Any history at all on aspartic acid at that location?

It could be the "Typhoid Mary" of the influenza world.

.
Pig virus with Aspartic Acid (D) at position 92 of NS1 have been found to be less virulent than with Glutamic Acid (E) at that position. However, many H5N1 viruses have Aspartic Acid, so there are likely multiple factors at play.
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