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First Novel trH3N2 In New York Swine

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 2:17 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27289
Location: Pittsburgh, PA USA

gsgs wrote:

I don't think the NY swine got it from humans.

closest is A/IN/10/2011/10/22 in segments 1,4,7
but A/ME/06/2011/10/10 in 2,3,4,6,7,8
while 5 is better to IN/08 or PA/11

(4,7, match both of the first)

so there are clear signs of reassortment.

Most clear for segments 1 and 6 which are separated this way.

we won't assume it reassorts in humans ...

-----------------------

1 has C399T,G1164A,A1281G,G1422A,A1584C,G1920A (NY and IN/10)
(coded-area nucleotides, as compared to ancestor A/Sw/Ontario/33853/2005)

6 has T843C,T1020C,A1142G,T1194A (NY and ME)

------------------------------------

Code:

                                       0000000000011111111112 00000001112 000001111111111 00000000000000111 0000001111111 00000001111 00000000 0000   
                                       0112234457711224458990 35777891270 347780245556899 11233333345579223 0136990122444 26888990011 01345689 3456   
                                       4141492411267382685250 37039708600 291822500896169 79655779941356162 7107195416588 12234452949 40292067 9114   
                                       2449596707346612741061 33852362611 127843173732528 76417593866930207 2165797054526 07313410824 52428066 0643   
-codon-position------------------------    2                                 22            1    1 22 2    1     2 1  1  1   1  2   2        21  211   
---Index-------------------------------TGGACCACCTAGAGAGCAAGTT GAAGATCCGAC GCCCCAACCCAAAAC CAGTGGCCAACAGCAGC AGACTCCGACAGT CGGGTGATCAT CGAAAAAA GAGC   
   1 >Index                            ...................... ........... ............... ................. ............. ........... ........ ....   
   2 >A/Sw/Ontario/33853/2005+M(Mex)   C...A..TTCG.G......... .......TA.T .T...GGGTT....T T.A.....C.TTA.G.. ...T..A.GA... ........... .AGG.G.. ....   
   3 >A/Sw/MN/02948/2009/05/19         ---------------------- ----------- --------------- T.A.....C.TTA---- ------------- ----------- -------- ----   
   4 >A/Sw/PA/62170-1/2010/10/25       C...A.GTTCG.G.......CC ----------- .TT.TGGT...G... ----------------- GA.....A..GAA ........... -------- ..A.   
   5 >A/Sw/PA/62170-2/2010/10/25       C...A.GTTCG.G.......CC ----------- .TT.TGGT...G... ----------------- GA.....A..GAA ..A..CG.... -------- ..A.   
   6 >A/Sw/PA/62170-3/2010/10/25       C...A.GTTCG.........CC ----------- .TT.TGGT...G... ----------------- GA.....A..G.. ........... -------- ..A.   
   7 >A/Sw/PA/62170-4/2010/10/25       C...A.GTTCG.........CC ----------- .TT.TGGT...G... ----------------- GA.....A..G.. ..A..CG.... -------- ..A.   
   8 >A/Sw/Quebec/1257777/2010/11/08   ---------------------- ----------- --------------- ----------------- ------------- ----------- .AG...-- ----   
   9 >A/Sw/Quebec/1257774/2010/11/09   ---------------------- ----------- --------------- ----------------- ------------- ----------- .AG....- ----   
  10 >A/Sw/IN/A01049091/2010/11/18     ---------------------- ----------- --------------- ..............G.. ------------- T.......... -------- ----   
  11 >A/Sw/NC/A01049436/2011/01/19     ---------------------- ----------- --------------- ................. ------------- T.......... -------- ----   
  12 >A/PA/09/2011/08/20               ..AG.......A.AGAACGA.. A..AG.T..G. ...A..--------- .G...AT..G...A.AA ............. ........... .......G ....   
  13 >A/PA/11/2011/08/25               ..AG.......----------- -------..G. ...A......G.GG. .G.C.AT..G...A--- ..G..T....... .T......A.. .......G .G.T   
  14 >A/PA/10/2011/08/26               ---------------------- ----------- --------------- ------------.A--- ------------- ----------- ...----- .G.T   
  15 >A/PA/10b/2011                    ---------------------- ----------- --------------- ------------.A--- ------------- --......A.. ...----- .G.T   
  16 >A/IN/08_a/2011/07/27             .AA........A.AGAACGA.. A..AGCT..G. ...A......G.GG. .G.C.AT..G.....AA ..G.CT....... .T.A....A.. ......GG .G..   
  17 >A/IN/08_b/2011/07/27             .AA........A.AGAACGA.. A..AGCT..G. ...A......G.GG. .G.C.AT..G.....A- ..G.CT....... .T.A....A.. ......G- .G..   
  18 >A/KA/13/2009/07/27               ---------------------- ----------- --------------- ----------------- ...T..A.GA... ----------- -------- ....   
  19 >A/IN/10/2011/10/22               .....T.....A..GA.C.A.. ...AG.T..G. ..........G..G. ....A..T......G.. ............. ........... AAGGG... ....   
  20 >A/Sw/NY/A01104005/2011/09/13     .....T.....A..GA.C.A.. .GG.G.T.A.. A........TG..G. ....A..T......G.. ..G..T....... ....C..C.GA AAGGG... A...   
  21 >A/ME/06/2011/10/10               C...A.GTTCG.........CC .GG.G.TTA.T A.......T.G..GT ....A..T......G.. .A........... ....C..C.GA AAGGGG.. A...   
                                                                                                                                                      
---Index-------------------------------TGGACCACCTAGAGAGCAAGTT GAAGATCCGAC GCCCCAACCCAAAAC CAGTGGCCAACAGCAGC AGACTCCGACAGT CGGGTGATCAT CGAAAAAA GAGC   
-codon-position------------------------    2                                 22            1    1 22 2    1     2 1  1  1   1  2   2        21  211   
                                       0000000000011111111112 00000001112 000001111111111 00000000000000111 0000001111111 00000001111 00000000 0000   
                                       0112234457711224458990 35777891270 347780245556899 11233333345579223 0136990122444 26888990011 01345689 3456   
                                       4141492411267382685250 37039708600 291822500896169 79655779941356162 7107195416588 12234452949 40292067 9114   
                                       2449596707346612741061 33852362611 127843173732528 76417593866930207 2165797054526 07313410824 52428066 0643   
.
.

.
.

these are the similar sequences from genbank that I found,
difference < 0.13% in some segment
distant (nonmatching) segments are ignored
mutations that occur only once are ignored (--> ancestor Sw/Ont is mostly
"-", this does no harm since it shares none of the recent mutations
in the list)

The reassortment (including MP) is old news

http://www.recombinomics.com/News/08271 ... N1_MP.html

The 2011 human sequences evolved from the 2010 human sequences. You ignore the real data to talk about events from 2005. The human sequneces were published a YEAR ago and HA and NA are in the Nancy Cox slides as noted previously.

http://www.google.com/url?sa=t&rct=j&q= ... Q8C92QA5KQ

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gsgs

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 2:34 am

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1774
Location: germany

so much mexflu in humans, so few reassortment
but so much reassortment in swine

common ancestor in segment 1 should be ~1 year ago

ME has segment1 from the 2010-PA-swine

hmm ME,NY,IN10 are not Cancun in segment 7, so presumably from
2009

while IN08,PA10,PA11,PA09 are Cancun, also A102G(7),G324A(7)

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 2:37 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27289
Location: Pittsburgh, PA USA

gsgs wrote:

these are the similar sequences from genbank that I found,
difference < 0.13% in some segment
distant (nonmatching) segments are ignored
mutations that occur only once are ignored (--> ancestor Sw/Ont is mostly
"-", this does no harm since it shares none of the recent mutations
in the list)

You are a year late and have HUGE holes in your data. Most of the internal genes in H3N2pdm11 trace back to the Huron County Fair, were two trH1N1 were isolated (A/Ohio/01/2007 and A/Ohio/02/2007)and 2 dozen attendees had ILI. This was seen in the first set of public sequence (A/Kansas/13/2009) and confirmed with the subsequent human sequences from 2010. The 2011 sequences evolved from the 2010 sequences (HA from the dominant sequence (A/Minnesota09/2010, A/Pennsylvanai/40/2010, A/Wisconsin/12/2010, A/Minnesota/11/2010) and NA from A/Pennsylvanai/14/2010, which is closely related to the Pennsylvania swine from 2010, all of which are in the Nancy Cox slides.

You ignore the key data and talk about a few sequences that you found. You are living in a parallel universe (which doesn't have access to the most important data).

The CDC released the key sequences a YEAR ago.

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 2:40 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27289
Location: Pittsburgh, PA USA

gsgs wrote:

Please. You have no real precursors to H1N1pdm09, which had already adapted by the spring of 2009.

As far as H3N2pdm11 is concerned, you don't have the 2010 human sequences, when the trH3N2 was adapting to humans (and of course there are many different MP versions in humans and all US trH3N2 cases are AFTER the start of the 2009 pandemic).

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gsgs

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 2:55 am

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1774
Location: germany

the other sequences were sorted out as too distant,
not a candidate precursor of Sw/NY

but I'll check again

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no patents on genes, publish the GISAID sequences !

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 3:02 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27289
Location: Pittsburgh, PA USA

gsgs wrote:

the other sequences were sorted out as too distant,
not a candidate precursor of Sw/NY

but I'll check again

You have huge holes in your data. For PB2 the ME sequence is close to the 2010 human sequences. The other H3N2pdm12 isolates including the NY swine are further evolved, but the same lineage. In addition to the PA swine, the PB2 from A/swine/Minnesota/A01047613/2010 is also close to the 2010 human PB2 sequences.

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 3:30 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27289
Location: Pittsburgh, PA USA

gsgs wrote:

the other sequences were sorted out as too distant,
not a candidate precursor of Sw/NY

but I'll check again

I'll give you the sequences for the PB2 branch so you can see what you are missing. You probably can find the swine sequences, and eventually you will get the three human Iowa sequences. Not all of the swine sequneces are H3N2, which might be why you don't see them.

There are more precursors, but here is part of the branch closest to the H3N2pdm11 sequences:

First is A/Illinois/09/2007 with related A/swine/Ohio/2026/2008

A second outside branch has A/swine/South Dakota/152B/2009

Next is A/swine/Minnesota/02782/2009

Then comes the branch where the human sequences are clustered.

One cluster has A/Minnesota/09/2010 followed by a tighter cluster with A/swine/Minnesota/A1047613/2010, A/Pennsylvania/40/2010, A/Wisconsin/12/11/2010 (these human sequences show the same clustering as seen in Nancy Cox's HA tree).

A related branch has the four Pennsylvania swine, A/Pennsylvania/14/2010, and A/Maine/06/2011.

The third and more evolved branch has A/Indiana/10/2011, A/swine/NY, A/Iowa/07/2011, A/Iowa/08/2011 on one branch and A/Indiana/08/2011, A/Pennsylvania/09/2011 on the other branch.

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gsgs

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 3:39 am

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1774
Location: germany

I had not yet included the H1 ones

OK, I found an old file for the Ohio/2007
last updated 2010/10/28, we must have had a thread ... I don't remember

they are similar in segments 1,2,3,8
again reassortment --> likely evolves in swine, not humans

differences
Sw/NY11 - Ohio07 ~ 1.4%
Sw/NY11 - Ont05 ~ 2.1%
Sw/NY/11 - Tr98 ~ 3.5%

so Ohio is indeed close to the ancestor from 2007 in 1,2,3,8
just from the mutationcounts, I didn't check the single mutations yet

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gsgs

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 3:41 am

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1774
Location: germany

whats the Nanxy Cox slide ?

why don't you make a file with all the relevant sequences
in computer-readable form, so others can check it ?

A/Ohio/01/2007
A/Ohio/02/2007
A/Kansas/13/2009
A/Minnesota09/2010
A/Pennsylvanai/40/2010
A/Wisconsin/12/2010
A/Minnesota/11/2010
A/Pennsylvanai/14/2010
A/swine/Minnesota/A01047613/2010
A/Illinois/09/2007
A/swine/Ohio/2026/2008
A/swine/South Dakota/152B/2009
A/swine/Minnesota/02782/2009
A/Minnesota/09/2010
A/swine/Minnesota/A1047613/2010
A/Pennsylvania/40/2010
A/Wisconsin/12/11/2010
A/Pennsylvania/14/2010
A/Maine/06/2011.
A/Indiana/10/2011
A/swine/NY
A/Iowa/07/2011
A/Iowa/08/2011
A/Indiana/08/2011
A/Pennsylvania/09/2011

_________________
no patents on genes, publish the GISAID sequences !

Last edited by gsgs on Fri Dec 02, 2011 3:46 am, edited 1 time in total.

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 3:44 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27289
Location: Pittsburgh, PA USA

gsgs wrote:

whats the Nanxy Cox slide ?

why don't you make a file with all the relevant sequences
in computer-readable form, so others can check it ?

In Nancy Cox's presentation she has H3N2 slides for H3 and N2, which has the relevant human sequences

http://www.google.com/url?sa=t&rct=j&q= ... Q8C92QA5KQ

HA tree is slide 7, NA tree is slide 8.

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