Rhiza Labs FluTracker Forum

Markers run across all 8 gene segments, no reassortment required. The vast majority of Chihuahua sequences are in the US at GISAID with rapid evolution in 2010 and 2011.

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www.twitter.com/hniman

It looks like that to you because you haven't looked at the sequences. Full sequences are at GISAID (TX/03/2010, PA/02/2011, MD/04/2011) and more are deposited but not released. All clearly show that all 8 gene segments are closely related to each other.

You live in a parallel universe, no reality required.

The Air Force has only published HA sequences, including those in Germany.

You continue to post utter nonsense. The Chihuahua story is all about D225N (along with EXTENSIVE recombination and emerging H274Y).

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www.twitter.com/hniman

You are more lost than ever. The Air Force posted a phylogenetic tree with the Ecuador sequences, which had K149N (they use H1 numbering and list it as K146N). There are 12 HA sequences from Mexico and 8 more from the US with K149N, as well as the silent upstream T462A. Below is the pedigree with the tamdem changes (T462A and A489C). Thus, the eight US sequences from 2011 are VERY closely related to the 12 Chihuahua HA sequences, also from 2011 (and both polymorphisms are in the 4 Ecuador sequences, including the sequence with D225N). Full sequences from two of the US sequences (PA/02/2011 and MD/04/2011) are PUBLISHED and have the SAME constellation of gene segments as TEXAS/03/201, isolated in June 2010 (and two of the 2011 sequences from the CDC are from TEXAS).

This is also conirmed by unreleased sequneces (which also have D225N).

Your claim of reassortment AFTER the sequences are published is like your claim that the 2009 pandemic wasn't a pandemic AFTER WHO had raised the phase from 3 to 4 to 5 to 6.

Now it is two years later and you continue to clutter the boards with UTTER nonsense.

Reality pedigree with GISAID accession numbers showing the 20 PUBLIC chihuahua sequences, including the two with published FULL sequences:

EPI316818 A/Mexico/InDRE2415/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI316816 A/Mexico/InDRE2413/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI316811 A/Mexico/InDRE2408/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI316809 A/Mexico/InDRE2407/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI316451 A/Texas/08/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI316424 A/Pennsylvania/04/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI316387 A/New Jersey/05/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI315913 A/Mexico/InDRE2222/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315901 A/Mexico/InDRE2200/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315898 A/Mexico/InDRE2197/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315895 A/Mexico/InDRE2195/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315891 A/Mexico/InDRE2192/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315840 A/Mexico/InDRE1947/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315838 A/Mexico/InDRE1946/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315836 A/Mexico/InDRE1945/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
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

The Air Force is slide 11

http://www.fda.gov/downloads/AdvisoryCo ... 246395.pdf

It clearly shows K146N (K149N in H3 Numbering) on the branch leading to the four Ecuador sequences and only Ecuador sequences. Thus, there are now 24 public HA sequences with K149N (and adjacent T462A), which are the 4 from Ecuador, 8 from US, and 12 from Mexico. Full sequences from two of the eight in the US are published and have NO reassortment - they match the A/TEXAS/03/2010 sequence collected almost a year ago (June 2010).

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www.twitter.com/hniman

For those confused about the reassortment talk and links, a review is in order. WHO issued a pandemic alert for countries in North and South America, citing increased activity in Ecuador, Mexico, and Venezuela. The locatons and timing exactly match the appearance of the Chihuahua sub-clade with D225N.

The Air Force presentation cited a late season burst of vaccination failures, which included a phylogenetic tree showing two US cases. Both were earlier versions of the Chihhuahau sub-clade. The tree also had four Ecuador sequences from Dec 2010 or Jan 2011, which also had D225N, as well as the rare marker, K149N. This marker is also in all 8 isolates from Chihuahua, Mexico, as well as 8 isolates from the United States. Full sequences for two of the US isolates were released, which matched a Texas sequences from June, 2010, indicating this emerging sub-clade was acquiring additional changes, including K149N and D225N, but had the same constellation of genes which were present a year ago, indicating no ressortment.

In spite of the PUBLICATION of these sequences showing no reassortment, as well as sequences showing D225N in Ecuador and Mexico, GSGS continues to post nonsense about his fanatsy, which has already been demonstrated to be FALSE.

This behavior is similar to postings of a year ago claiming that the 2009 pandemic would not be designated as a pandemic, even after WHO increased the phase from 3 to 4 to 5 to 6.

These nonsensical posts denying reality were annoying then and are annoying now.

WHO has issued an alert due to the emergence and spread of a novel sub-clade with D225N, which has NOTHING to do with reassortment, as demonstrated by complete PUBLISHED sequences of this sub-clade in Texas (in June 2010) followed by Pennsylvania and New Jersey (in February 2011), which match HA sequences in Ecuador, Mexico, and multiple locations in the US (as well as anecdotal reports on sequences in Venezuela).

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www.twitter.com/hniman

No "big" reassortment with non-mexflu segments, but
likely (IMO) inter-mex reassortment.

it can best be seen by comparing segments 2 and 4
CA,Mex,2009 had the Chi-mutations in segment 2 but not 4
GER/AF2207,Jan.2010 had the Chi mutations in segment 4


CA,Mx-City,2009/10 markers: (also A/Taipei/1472T/2009/10/21)

G110C(1),A1381G(1),A1674G(1)
T1760G(2),C1955T(2),T2241C(2)
T1305C(3)
C1434T(5)
G724A(8)


Gisaid should publish the whole segments so we can see !
No full genomes of chi at genbank.
CDC,WHO,Euroflu should comment

Usually I'd say American strains will die, only Asian strains survive summer.
But reassorted viruses often bear the potential to dominate

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no patents on genes, publish the GISAID sequences !

What you say about your parallel universe doesn't mean much.

In the real world GISAID published the full sequence from Texas/03/2010 in Sept 2010. The CDC delayed release of 2011 H1N1 sequence, but a full set, including PA/02/2011 and NJ/04/2011 were released in April demonstrating NO reassortment in Chihuahua. All 8 gene segments of the 2011 isolates match the 2010 isolate, which is not ambiguous, no imaginary sequences required.

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www.twitter.com/hniman

what was "published" is still not available for us here.
The new HA appears out of nothing and has no
mutations from Mx-City,CA 2009 which appears to be the precursor

While the (almost) full set of HA-mutations did already exist in Jan.2010

Some of the experts will hopefully comment.




A/Germany/AF2207/2010/01/19,1-1200,A142G,G536A,G607A,C681T,A957G,G1080A

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no patents on genes, publish the GISAID sequences !

The GISAID sequences can be accessed by any serious reserchers (no internet babbling required).
The new HA doesn't not appear out of nothing. Its markers were co-circulating and acquired by recombination, no random mutation or reassortment nonsense required.

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www.twitter.com/hniman

> acquired by recombination

you are in your universe, but everyone else lives parallel

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no patents on genes, publish the GISAID sequences !