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PostPosted: Sat Apr 16, 2011 7:51 am 
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gsgs wrote:
> I don't follow babble boards and have no idea who Fumento is or what you are talking about.

you did in the past and Fumento was a major subject there. A future niman will refer to this
very forum as babble board, yawn.


Message boards are loaded with anonymous posters putting up utter nonsense. I just read a tiny fraction of what is posted (usually only the threads I am posting on, or "news" threads). The discussions on these boards are absurd, much like this series, where you put out bogus numbers, like 20% probability that Chihuahua is a reassortant. Your 20% is BOGUS because it has no basis. It is just a number you made up largely based on a series of misconceptions of falsehoods, which you have already mentioned.

You start with an undated chat session that claims no recent H1 sequences at GISAID, when there are sequences that contradict your nonsense on reassortment. Multiple reports cited visitors from New Mexico and Texas as introducing the Chihuahua sublade in Juarez (across the border from Las Cruces, NM). An earlier isolate, Texas/03/2010, represents the novel sub-clade and a full sequence was released some time ago and there was no reassortment. Moreover, more recent sequences at GISAID show the sub-clade throughout the US. Full sequences were relased for two, PA/02/2011 and MD/04/2011 (both collected in February) and they matched each other and the earlier sequence from Texas. Thus the real data against reassortment is overwhelming. Moreover, of the 8 Chihuahua sequences published from Mexico, 2 have D225N (from UPPER respiratory tract). I have seen or heard about unpublished sequences from Mexico, as well as multiple countries in South America that are the Chihuahua subclade, and D225N is present at a similar frequency (and the frequency in unreleased sequences from Mexico is higher than the released sequences). D225N is RARELY reported, At Genbank the number of 2010 sequences with D225N is ZERO. Earlier examples were from autopsy lung, NOT samples from the upper respiratory tract, and were collected in 2009.

Thus, the public and private DATA for D225N is OVERWHELMING, with NO evidence for reassortment.

Moreover, your bogus 20% is based on statements that are demonstrably FALSE. You claim that the pandemic H1N1 reassorted in March of 2009 based on NO data. You don't have the originating sub-clade and related sequences are in ASIA, including a VERY large series from Hong Kong, as well as sequences from Thailand. In Thailand there are 2005 swine and HUMAN H1N1 sequences with a "North American" H1 and a "European" N1, contradicting your false claim that reassortment created the pandemic H1N1 in 2009. You also claim that the related sequences in the US are "different" even though the P&I death rate in the US has been at or above the epidemic threshold for 11 weeks in a row, including this week (8.0%), when the CDC indicated the level of influenza was in sharp decline. Moreover, the P&I rate of El Paso is 16% for week 14 (latest report).

Thus, your 20% is BOGUS. There is no evidence that this is the time of year for reassortment or any examples of a human case that has pandemic H1N1 genes reassorted with swine or human flu genes anywhere.

The role of D225N is OBVIOUS to anyone paying attention, which explains the high level of severe and fatal cases because it is present at high frequency in this novel subclade. The title of the sequences from Mexico is
TITLE Detection of D222N Substitution in the Pandemic Influenza (H1N1) Virus in Chihuahua, Mexico 2011 as anyone who reads Recombinomic' commentaries and can click on a link like
http://www.ncbi.nlm.nih.gov/nuccore/CY089587
which was in the commentary on D225N in the UPPER respiratory tract
http://www.recombinomics.com/News/04141 ... Upper.html

Thus, your 20% is BOGUS, as are all of the falsehoods you have posted on the outbreak in Mexico.

Please post this utter nonsense on your babble boards like the thread started on flutrackers.com
http://www.flutrackers.com/forum/showth ... p?t=166187

with your BOGUS chat session, where someone might believe your BOGUS probablilities and posts.

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PostPosted: Sat Apr 16, 2011 1:47 pm 
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niman wrote:
Mixin wrote:
Again, Reading 101

Quote:
Gs and I had a chat recently about his concern


And the chat wasn't about GISAID (although that's what you made it about). It was about his concern about reassortment in swine.

The chat gave a 20% chance that there was reassortment in Chihuahua, which was THOROUGHLY discounted by the sequences released Wednesday at GISAID (which were predicted by uunpublished data with D225N, which had NO reassortment. The argument is about GISAID because that is where the PUBLIC DATA is, no speculation or bogus odds required.

K149N at GISAID
EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI266546 A/Boston/115/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
EPI218962 A/Wisconsin/629-D02206/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.19077
K149N at Genbank
CY089605.1 Influenza A virus (A/Mexico/InDRE2222/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089593.1 Influenza A virus (A/Mexico/InDRE2200/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089590.1 Influenza A virus (A/Mexico/InDRE2197/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089587.1 Influenza A virus (A/Mexico/InDRE2195/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089583.1 Influenza A virus (A/Mexico/InDRE2192/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089391.1 Influenza A virus (A/Mexico/InDRE1947/2011(H1N1)) hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY089389.1 Influenza A virus (A/Mexico/InDRE1946/2011(H1N1)) hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY089387.1 Influenza A virus (A/Mexico/InDRE1945/2011(H1N1)) hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY064500.1 Influenza A virus (A/Boston/115/2009(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
CY050420.1 Influenza A virus (A/Wisconsin/629-D02206/2009(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
As seen by the above PA/02/2011 and MD/04/2011 are very close to each other and the 8 sequences from Chihuahua. Full sequences from the two US isolates have been released, and there is no reassortment.

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PostPosted: Sat Apr 16, 2011 1:48 pm 
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T462A at GISAID
EPI310133 A/Utah/08/2011
EPI310130 A/Texas/07/2011
EPI310103 A/Pennsylvania/02/2011
EPI310093 A/Oregon/03/2011
EPI309970 A/Maryland/04/2011
EPI269540 A/swine/Minnesota/03022/2010

T462A at Genbank
CY089605.1 A/Mexico/InDRE2222/2011
CY089593.1 A/Mexico/InDRE2200/2011
CY089590.1 A/Mexico/InDRE2197/2011
CY089587.1 A/Mexico/InDRE2195/2011
CY089583.1 A/Mexico/InDRE2192/2011
CY089391.1 A/Mexico/InDRE1947/2011
CY089389.1 A/Mexico/InDRE1946/2011
CY089387.1 A/Mexico/InDRE1945/2011
HM570055.1 A/swine/Minnesota/03022/2010

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PostPosted: Sat Apr 16, 2011 1:55 pm 
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Here is a quick explanation of the prior two posts for those not familiar with pedigrees. The posts show all sequences at Genbank with the two conscutive markers as well as all sequences at GISAID.

All eight of the sequences from Mexico (Chihuahua) have both markers. Similarly, 5 recent (2011) isolates from the US also have both markers (UT/08, TX/07, PA/02, OR/03. MD/04) demonstrating that the sub-clade has spread across the US, and this spread is recent because all isolates with both markers (in the US and Mexico) are from 2011.

Moreover, full sequences for two of the sequences have been published and each segment matches each other as well as an earlier sequence, TX/03/10, indicating no reassortment.

Moreover, MD/04/2011 has H274Y and therefore is Tamiflu resistant.

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PostPosted: Sun Apr 17, 2011 2:28 am 
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HM570055.1 A/swine/Minnesota/03022/2010

is not mexflu = pH1N1

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PostPosted: Sun Apr 17, 2011 4:02 am 
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gsgs wrote:
HM570055.1 A/swine/Minnesota/03022/2010

is not mexflu = pH1N1

Reality check. New polymorphisms on pandemic H1N1 frequently trace back to swine, and when new polymorphism enter a gene pool by definition they don't trace back to the gene pool. The polymorphim pedigrees have ALL sequences at Genbank or GISAID that have the poylmorphism and a minimum degree of identifty adjacent to that polymorphism. Most pedigrees go back to swine sequences that are not pandemic H1N1.

The recent example of the two rare tandem polymorphisms was used to sow that in the entire Genbank database there were only eight matches and all eight were 2011 isolates from Chihuahua. At GISAID there were only five sequences that matched and all five were 2011 isoaltes from the United States, including Texas/07/2011 supporting the epidemiological data showing that the H1N1 in Chihuahua was in travelers to Mexico from TEXAS (and New Mexico).
In addition, two of the five had full sequences (A/Pennsylvani/02/2011 and A/Maryland/04/2011) and the full sequence matched each other and were closely related to the eight gene segments of A/Texas/03/2010, which is a early precursor to the Chihuahua sub-clade indicating NO resassortment.

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PostPosted: Sun Apr 17, 2011 5:24 am 
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gsgs wrote:
HM570055.1 A/swine/Minnesota/03022/2010

is not mexflu = pH1N1

Here is the pedigree for the sequences from T462A and A489C (K149N) at Genbank and GISAID, which is pretty easy to interpret

CY089605.1 Influenza A virus (A/Mexico/InDRE2222/2011(H1N1)) hemagglutinin (HA) gene, partial cds 56.0 56.0 100% 4e-08 100%
CY089593.1 Influenza A virus (A/Mexico/InDRE2200/2011(H1N1)) hemagglutinin (HA) gene, partial cds 56.0 56.0 100% 4e-08 100%
CY089590.1 Influenza A virus (A/Mexico/InDRE2197/2011(H1N1)) hemagglutinin (HA) gene, partial cds 56.0 56.0 100% 4e-08 100%
CY089587.1 Influenza A virus (A/Mexico/InDRE2195/2011(H1N1)) hemagglutinin (HA) gene, partial cds 56.0 56.0 100% 4e-08 100%
CY089583.1 Influenza A virus (A/Mexico/InDRE2192/2011(H1N1)) hemagglutinin (HA) gene, partial cds 56.0 56.0 100% 4e-08 100%
CY089391.1 Influenza A virus (A/Mexico/InDRE1947/2011(H1N1)) hemagglutinin (HA) gene, complete cds 56.0 56.0 100% 4e-08 100%
CY089389.1 Influenza A virus (A/Mexico/InDRE1946/2011(H1N1)) hemagglutinin (HA) gene, complete cds 56.0 56.0 100% 4e-08 100%
CY089387.1 Influenza A virus (A/Mexico/InDRE1945/2011(H1N1)) hemagglutinin (HA) gene, complete cds 56.0 56.0 100% 4e-08 100%
EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000

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PostPosted: Sun Apr 17, 2011 5:46 am 
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> Most pedigrees go back to swine sequences that are not pandemic H1N1.

are you really saying here that mutations from triple-reassortment strains
"jump" to mexflu through recombination or whatever ?

Nobody AFAIK thinks this. It all seems to go back clearly to that
one mexflu-creation virus which then mutated.
(my "mexflu/index")

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PostPosted: Sun Apr 17, 2011 6:01 am 
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gsgs wrote:
> Most pedigrees go back to swine sequences that are not pandemic H1N1.

are you really saying here that mutations from triple-reassortment strains
"jump" to mexflu through recombination or whatever ?

Nobody AFAIK thinks this. It all seems to go back clearly to that
one mexflu-creation virus which then mutated.
(my "mexflu/index")

Yada yada. You remain as lost as ever. Your "coincidences" became old YEARS ago.

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PostPosted: Tue Apr 19, 2011 5:47 am 
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today:

A/swine/Thailand/CU-DP83/2010(H1N1)
A/swine/Thailand/CU-PL63/2010(H1N1)
A/swine/Thailand/CU-PL65/2010(H1N1)
A/swine/Thailand/CU-PS73/2010(H1N1
A/swine/Thailand/CU-RP1/2010(H1N1
A/swine/Thailand/CU-RP3/2010(H1N1))
A/swine/Thailand/CU-SA433/2010(H1N1


PS73 got segment
1,2,6,7 from European swine H1N1 1978
3 from triple-reassortant swine H3N2, 1998
4,8 from classical swine H1N1 , 1931
5 missing

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