Rhiza Labs FluTracker Forum

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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www.twitter.com/hniman

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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www.twitter.com/hniman

HM570055.1 A/swine/Minnesota/03022/2010

is not mexflu = pH1N1

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no patents on genes, publish the GISAID sequences !

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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www.twitter.com/hniman

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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www.twitter.com/hniman

> 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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no patents on genes, publish the GISAID sequences !

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

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www.twitter.com/hniman

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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no patents on genes, publish the GISAID sequences !

Why are these isolates on this thread? Are any of the segments from PS73 from pH1N1? The others have a pH1N1 HA. Are any of the genes in those six isolates not pH1N1?

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www.twitter.com/hniman

It's curious that after the above denial you post A/swine/Thailand/CU-DP83/2010, which is a clear recombinant, even at the protein level. It has the two protein markers K-12E and Q297H, which were in 2009 isolates from Thailand (as well as many others including large series from Boston and Canada), but the isolate also has the S188T markers (S188T, A200T, S454N), which were also circulating in Thailand.

Thus, A/swine/Thailand/CU-DP83/2010, as picked up a series from each parental strain, which you claim is lab error or a coincidence.

You remain as lost as ever.

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www.twitter.com/hniman