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Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

which two viruses exactly should be involved in the
1991-2002 recombination ?

Best I could find was
HA: p=0.0000000000811061249 Daejeon/258/02(H3N2) , Ningbo/198/03(H3N2)

or this:

Code: 
 1123/Daejeon/258/02(H3N2)       4782/Habana/26/05 (H3N2)
--------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------............................
..............................................................................................................
..............................................................................................................
...............................................o......................................o.......................
......o..........o.......................-..................................................................o.
.......o...o.......o..o....o....o...o...............................................ooo.........o...o.....o.o.
oo..oo.o................oo...............o.........o..o.....o.....oo....o..............o....o..o.-o......-----
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

The central region will match H3N2 isolates from 1991 like A/Seoul/45/91
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

camster said:
what is the proposed method of recombination for influenza viruses?
Click to expand...
Simple copy choice will work. Most of the recombination is between closely related sequences, so most think they are point mutations, but they are really recombination between sequences that are 99% homologous.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

I see a small indication for recombination when considering
A/Seoul/45/91 , but not so clear


Code: 
>A/Seoul/45/91(H3N2)
>A/Cheonnam/323/2002(H3N2)
--------------------------------------------------
------------------------------............................--
-.o..............o..o..o........o............o..............
........o...........o.......................................
o.......o...........o.oo............o....o........o.........
.................o.....................o....................
.....o.....o................................................
.................o.....o..........o.......ooo...............
...o......o...ooo.....o.............o.....oo................
...............oo.o.o.o.o.o........o.....oo.................
.......oo.......................................ooo........o
..o...................o........................o.......-....
............o.................o..................o..........
........................o..........................o.....o..
...o..................................o............o.......o
..........................o..............................o..
............o........o.......................o........o.....
............................................................
.-----------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------

this is a bit better:
Code: 
HA,A/Seoul/50/1991(H3N2)
HA,A/Cheonnam/323/2002(H3N2)
--------------
------------------------------------------------------------
------............................---.o..............o..o..o
........o............o......................o...........o...
....................................o.....................oo
............o.............o..........................o......
...............o.........................o.....o............
.....................................................o.....o
..........o.......oo...................o......o...ooo.....o.
............o.....oo...o...........................oo.o.o.o.
o..........o.....oo........................oo...............
........................ooo........o..o.......o...........o.
...............................-.......o....................
.........................o.o................................
..................o........o.....o.....o....................
............................................................
..o.........................................................
o....................o.................o....................
.....................................-----------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------

p=0.0002068274817671090 4 9 l: 989 cut: 600 dif: 61= 50+ 11 A/Cheonnam/323/2002(H3N2) A/Seoul/50/91(H3N2)

still not detected by my typical threshold of p=0.000001

better compare with Habana 2005,Denmark 2003,Ningbo 2003


the other parent could be this from 1996: (central region)


Code: 
se7a43.10
>A/Cheonnam/323/02(H3N2)
>A/NY/617/96(H3N2)
--------------------------------------------------------....
........................................o..o...........o....
........o..................................o................
.......................o...................o.oo............o
....o........o........o.................o...................
..o.........................o.....o.........................
..............................................o..........o..
.....o....................o.....o............o.............o
.....oo...............................oo.o.o...o..........o.
.....o.........................o............................
...........o................................................
............................................................
.............o.....o........................................
............................................................
..........................................o.................
..................................o.........................
............................................................
............................................................
................o...........................................
................o................................o..........
............o......o.................o..o...................
.....................................o......................
.o..................o.......................................
..............................o...........................o.
.............o.....................................o........
..................................o.........................
............................................................
.......o................o....o..............................
.............................--------------
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

You have to look at the recombined region
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
I see a small indication for recombination when considering
A/Seoul/45/91 , but not so clear


Code: 
>A/Seoul/45/91(H3N2)
>A/Cheonnam/323/2002(H3N2)
--------------------------------------------------
------------------------------............................--
-.o..............o..o..o........o............o..............
........o...........o.......................................
o.......o...........o.oo............o....o........o.........
.................o.....................o....................
.....o.....o................................................
.................o.....o..........o.......ooo...............
...o......o...ooo.....o.............o.....oo................
...............oo.o.o.o.o.o........o.....oo.................
.......oo.......................................ooo........o
..o...................o........................o.......-....
............o.................o..................o..........
........................o..........................o.....o..
...o..................................o............o.......o
..........................o..............................o..
............o........o.......................o........o.....
............................................................
.-----------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------

this is a bit better:
Code: 
HA,A/Seoul/50/1991(H3N2)
HA,A/Cheonnam/323/2002(H3N2)
--------------
------------------------------------------------------------
------............................---.o..............o..o..o
........o............o......................o...........o...
....................................o.....................oo
............o.............o..........................o......
...............o.........................o.....o............
.....................................................o.....o
..........o.......oo...................o......o...ooo.....o.
............o.....oo...o...........................oo.o.o.o.
o..........o.....oo........................oo...............
........................ooo........o..o.......o...........o.
...............................-.......o....................
.........................o.o................................
..................o........o.....o.....o....................
............................................................
..o.........................................................
o....................o.................o....................
.....................................-----------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------

p=0.0002068274817671090 4 9 l: 989 cut: 600 dif: 61= 50+ 11 A/Cheonnam/323/2002(H3N2) A/Seoul/50/91(H3N2)

still not detected by my typical threshold of p=0.000001

better compare with Habana 2005,Denmark 2003,Ningbo 2003


the other parent could be this from 1996: (central region)


Code: 
se7a43.10
>A/Cheonnam/323/02(H3N2)
>A/NY/617/96(H3N2)
--------------------------------------------------------....
........................................o..o...........o....
........o..................................o................
.......................o...................o.oo............o
....o........o........o.................o...................
..o.........................o.....o.........................
..............................................o..........o..
.....o....................o.....o............o.............o
.....oo...............................oo.o.o...o..........o.
.....o.........................o............................
...........o................................................
............................................................
.............o.....o........................................
............................................................
..........................................o.................
..................................o.........................
............................................................
............................................................
................o...........................................
................o................................o..........
............o......o.................o..o...................
.....................................o......................
.o..................o.......................................
..............................o...........................o.
.............o.....................................o........
..................................o.........................
............................................................
.......o................o....o..............................
.............................--------------
Click to expand...
The best matches for the recombined region are a series of isolates betweeen 1989 and 1991.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
I see a small indication for recombination when considering
A/Seoul/45/91 , but not so clear


Code: 
>A/Seoul/45/91(H3N2)
>A/Cheonnam/323/2002(H3N2)
--------------------------------------------------
------------------------------............................--
-.o..............o..o..o........o............o..............
........o...........o.......................................
o.......o...........o.oo............o....o........o.........
.................o.....................o....................
.....o.....o................................................
.................o.....o..........o.......ooo...............
...o......o...ooo.....o.............o.....oo................
...............oo.o.o.o.o.o........o.....oo.................
.......oo.......................................ooo........o
..o...................o........................o.......-....
............o.................o..................o..........
........................o..........................o.....o..
...o..................................o............o.......o
..........................o..............................o..
............o........o.......................o........o.....
............................................................
.-----------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------

this is a bit better:
Code: 
HA,A/Seoul/50/1991(H3N2)
HA,A/Cheonnam/323/2002(H3N2)
--------------
------------------------------------------------------------
------............................---.o..............o..o..o
........o............o......................o...........o...
....................................o.....................oo
............o.............o..........................o......
...............o.........................o.....o............
.....................................................o.....o
..........o.......oo...................o......o...ooo.....o.
............o.....oo...o...........................oo.o.o.o.
o..........o.....oo........................oo...............
........................ooo........o..o.......o...........o.
...............................-.......o....................
.........................o.o................................
..................o........o.....o.....o....................
............................................................
..o.........................................................
o....................o.................o....................
.....................................-----------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------

p=0.0002068274817671090 4 9 l: 989 cut: 600 dif: 61= 50+ 11 A/Cheonnam/323/2002(H3N2) A/Seoul/50/91(H3N2)

still not detected by my typical threshold of p=0.000001

better compare with Habana 2005,Denmark 2003,Ningbo 2003


the other parent could be this from 1996: (central region)


Code: 
se7a43.10
>A/Cheonnam/323/02(H3N2)
>A/NY/617/96(H3N2)
--------------------------------------------------------....
........................................o..o...........o....
........o..................................o................
.......................o...................o.oo............o
....o........o........o.................o...................
..o.........................o.....o.........................
..............................................o..........o..
.....o....................o.....o............o.............o
.....oo...............................oo.o.o...o..........o.
.....o.........................o............................
...........o................................................
............................................................
.............o.....o........................................
............................................................
..........................................o.................
..................................o.........................
............................................................
............................................................
................o...........................................
................o................................o..........
............o......o.................o..o...................
.....................................o......................
.o..................o.......................................
..............................o...........................o.
.............o.....................................o........
..................................o.........................
............................................................
.......o................o....o..............................
.............................--------------
Click to expand...
All six of the recombinants have a similar recombined region, but it is not exactly the same in each. The database has giant holes, so the recombination could have been somewhat earlier, and then changed further. Although the swine sequences were exact, the recombined regions were in PB2 and PA and these genes do not chnage as rapidly as HA. Thefore, exact matches with sequences that have been floating around for 10 years are not going to be as obvious as the recombination in the internal genes.

The key point is there is no reason for the six 2002 HA to have 1991 sequences in the center unless there was recombination, and recombination in the lab is unlikely because the 2002 sequence fell into two seperate groups (and the lab would have to have had 1991 sequneces floating around and all contaminants would have to had happened in the identical region).

Korea is a disaster zone as far as recombination is concerned, and the sequences fly out in many directions (the precursors for the Qinghai strain came from Korea).
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

but why is there no HA similar to one of these
Korean maybe-recombinants isolated worlwide ever ?
If those were real recombinants then at least
they didn't spread and the 2003/4-Fujian-semipandemic
was not affected/initiated by that recombination.

The Habana/26/05 sequence looks also suspect to me.
Different mutation rates in HA1 and HA2 may explain some
of the other irregularities.

I found no other clear,obvious recombination candidates in human
H3N2-HA1. (4600 sequences examined)


Code: 
se7a43hk.nam, 4623 sequences, nucleotide positions 300-900 of HA only
p=0.0000000030709767637  4369/Habana/26/2005 (H3N2)                  3754/Wisconsin/68e/2005(H3)
p=0.0000000201891826443   976/Daejeon/258/2002(H3N2)                  965/Denmark/18-2/03(H3N2)
p=0.0000000418979466040   978/Incheon/260/2002(H3N2)                 3261/Finland/319/2003 (H3N2)
p=0.0000000867885326359   981/Kyongbuk/320/2002(H3N2)                 943/Wyoming/3/03(H3N2)
p=0.0000016188996383076   759/Kwangju/1/97(H3N2)                     3545/Oslo/871/99(H3N2)
p=0.0000021358936936049   755/Kangwon/11/99(H3N2)                     699/Madrid/SO2523/99(H3N2)
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

You are assuming one event. In a BLAST of the recombined region, all top hits are 1999-2001 human H3N2.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
but why is there no HA similar to one of these
Korean maybe-recombinants isolated worlwide ever ?
If those were real recombinants then at least
they didn't spread and the 2003/4-Fujian-semipandemic
was not affected/initiated by that recombination.

The Habana/26/05 sequence looks also suspect to me.
Different mutation rates in HA1 and HA2 may explain some
of the other irregularities.

I found no other clear,obvious recombination candidates in human
H3N2-HA1. (4600 sequences examined)


Code: 
se7a43hk.nam, 4623 sequences, nucleotide positions 300-900 of HA only
p=0.0000000030709767637  4369/Habana/26/2005 (H3N2)                  3754/Wisconsin/68e/2005(H3)
p=0.0000000201891826443   976/Daejeon/258/2002(H3N2)                  965/Denmark/18-2/03(H3N2)
p=0.0000000418979466040   978/Incheon/260/2002(H3N2)                 3261/Finland/319/2003 (H3N2)
p=0.0000000867885326359   981/Kyongbuk/320/2002(H3N2)                 943/Wyoming/3/03(H3N2)
p=0.0000016188996383076   759/Kwangju/1/97(H3N2)                     3545/Oslo/871/99(H3N2)
p=0.0000021358936936049   755/Kangwon/11/99(H3N2)                     699/Madrid/SO2523/99(H3N2)
Click to expand...
Many sequences dead end and sequences from Korea are not very extensive. The public sequences are VERY biased and only approximate what is circulating.

You are mixing a single recombination event, with importance of that particular event. G743A in H5N1 NA is silent, but now it is all over Europe, not because it is obviously important, but because it was at the right place at the right time.

Once recombination is acknowledge, the slope gets very slippery very quickly.

Recombination is the name of the game, and most examples are short surviving regions.

Influenza knows what it is doing, even if the bioinformatics analysis doesn't (no press reelases, peer reviewed papers, or message boards required).
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

when you remove the Habana and the Korea/02 sequences from the database
then no recombination can be found in human HA1 of H3.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
when you remove the Habana and the Korea/02 sequences from the database
then no recombination can be found in human HA1 of H3.
Click to expand...
Recombination involves the exchange of genetic information, not bioinformatics psuedo definitions applied to a VERY biased database.

In N2 from human H3N2, odds were a billion to one that there was recombnation (240 examples of statistically significant homologous recombination in a VERY biased database).

The story is in the sequence, and recombination remains the name of the game.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

I wouldn't rely too much on that p-value.
They would have commented something, if they thought
recombination in NA were likely.

Presumably they also assume that the mutation-probability is
equal for all positions, but ~80% of mutations are at 3rd positions,
that should reduce the p-value a lot.


But I assume we agree that recombination is much more frequent in
birds or swine than in humans.
Except there are lots of lab-errors...

They really should test H5N1 or H9N2.

The decisive hypothetical H5N1-panflu-recombination could well happen in
birds and then transmit to humans, it needn't happen in humans.
However we have no example that recombination was responsable for an influenza
epidemic so far. The 1918-?-recombination is being much disputed.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
when you remove the Habana and the Korea/02 sequences from the database
then no recombination can be found in human HA1 of H3.
Click to expand...

Here is the line on homologous recombination in N2 from human H3N2

NA 1365 (1059) 1475 754 1.2 × 10-10 240 0 No

1059 unique sequences with 1475 BP were examined, and 240 statistically significant positives (for homologous recombination) were found with a p value of 1.2X10 to the -10 (odds were more than a billion to one that the results were not due to chance).
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
when you remove the Habana and the Korea/02 sequences from the database
then no recombination can be found in human HA1 of H3.
Click to expand...
Here's are some clues:

When 240 examples of homologous recombination are found in N2 and zero are found in H3, there is internal inconsistancy. Moreover, the 240 is a LOW estimate, because the database was VERY limited and the analysis required the presence of both parents in the VERY limited database.

Most of the time when one assay is positive and another is negative, the positive is correct.

Similarly, most scientists don't publish negative data because there are MANY reasons for negative data that have nothing to do with the hypothesis that is being tested.

A billion to one is well into the "statistically significant" category.

However, real data doesn't require statistics. It is OBVIOUS.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
I wouldn't rely too much on that p-value.
They would have commented something, if they thought
recombination in NA were likely.
Click to expand...
From the abstract (which summarize the main points) of the paper:

Using an exhaustive search and a nonparametric<SUP> </SUP>test for mosaic structure, we identified 315 sequences (
sim.gif
2%)<SUP> </SUP>in five different RNA segments that, after a multiple comparisons<SUP> </SUP>correction, had statistically significant mosaic signals compatible<SUP> </SUP>with homologous recombination.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
. The 1918-?-recombination is being much disputed.
Click to expand...
By the groups that can't find recombination.

1918 was obvious recombination between swine and human H1N1.

Although these groups know that 1918 had nothing to do with reassortment, they still have major issues with recombination. The relationship between WSN/33 (human H1N1 from 1933) and swine/Iowa/15/31 (swine H1N1 from 1931) and the 1918 pandemic strain is the same accross all 8 gene segments. This is NOT an accident or coincidence

http://www.recombinomics.com/presentations.html

1918 Pandemic Evolution Via Recombination Between Human and Swine H1N1
Niman HL
Recombinomics, Inc., Pittsburgh, Pennsylvania, USA

Although complete sequences of all eight gene segments of the 1918 pandemic strain of H1N1 have been published, the origin and evolution of the strain remain unclear. 10 polymorphisms in the four internal genes distinguished the 1918 strain from avian isolates, but pandemic polymorphisms match both human and swine H1N1 sequences. Similarly, phylogenetic analysis indicates the pandemic strain is most closely related to human and swine H1N1 from the early 1930’s. Recent H1N1 and H1N2 sequences from swine in Canada demonstrate absolute fidelity with extended regions of PA and PB2 from 1977 swine isolates from 1977, as well as regions of PA identity with a swine isolate from 1931. These identities strongly suggested that the swine evolution was via recombination and support use of polymorphism tracing to determine parental strains.

Although human and swine sequences from isolates collected prior to the 1918 pandemic are not available, full sequences have been generated on human and swine H1N1 isolates from the 1930’s. Representative human, A/WSN/33, or swine, A/swine/Iowa/15/30 or A/swine/Iowa/1976/31, contain over 90% of the polymorphisms in six of the eight gene segments of A/Brevig Mission/1/1918 or A/South Carolina/1/18. The matches in the remaining two genes, NA and NP, are 84% and 86%, respectively. In six of the eight genes, the percentage of human polymorphisms are higher than the swine polymorphisms, PB2(51/40), PB1(55/40), PA(52/39), HA(53/49), MP(52/40), NS(55/41) while the swine polymorphisms are greater in the remaining two gene segments, NP(42/47) and NA(34/51). Moreover, although the matching regions alternate, the regions are defined by clustered polymorphisms. These acquisition patterns provide additional support for generation of the pandemic strain via recombination between human and swine H1N1.

The differences between the 1918 pandemic strain containing polymorphisms that are found in two mammalian sources, swine and human, and a pandemic strain such as avian H5N1 which has acquired the ability to efficiently transmit in a mammalian host, will be discussed.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

niman said:
From the abstract (which summarize the main points) of the paper:

Using an exhaustive search and a nonparametric<SUP> </SUP>test for mosaic structure, we identified 315 sequences (
sim.gif
2%)<SUP> </SUP>in five different RNA segments that, after a multiple comparisons<SUP> </SUP>correction, had statistically significant mosaic signals compatible<SUP> </SUP>with homologous recombination.
Click to expand...

..and the headline summarizes the abstract.
Even if there were strong evidence for short recombinations (<100),
there should also be some more longer ones.
This is unusual, that I can't find them in human sequences.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

> In six of the eight genes, the percentage of human polymorphisms
> are higher than the swine polymorphisms, PB2(51/40), PB1(55/40),
> PA(52/39), HA(53/49), MP(52/40), NS(55/41) while the
> swine polymorphisms are greater in the remaining two gene
> segments, NP(42/47) and NA(34/51).

can you explain, how you define "human polymorphism" and
"swine polymorphism" ? How I can verify the numbers ?
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
..and the headline summarizes the abstract.
Even if there were strong evidence for short recombinations (<100),
there should also be some more longer ones.
This is unusual, that I can't find them in human sequences.
Click to expand...
Please.
 
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