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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

gsgs said:
here are some more pictures :
http://www.setbb.com/fluwiki2/viewtopic.php?p=842&mforum=fluwiki2

the clearest recombination-signal is from the Denmark/2003 sequence.
My program usually only considers one breakpoint so these
are not so easily found then.
Also, it lists only the best candidate (Habana) for one virus
(Daejeon) and then omits other candidates (1992).
The p-value for the 1992 sequences is not so small.

Also, when you remove the "c" , which are non-synonymous and
can be explained by immunity-avoiding, then the picture is less clear.



Code: 
outer/?       middle/1992
    \             |
      \           |
        \        /
          \    /                  
          / \/___recombination
        /    | 
      /   Daejeon/2002
    /
Denmark/2003


or



Code: 
middle?       
  \           
    \   Daejeon/2002
      \    /
        \/____recombination
         |
         |
   Denmark/2003


or even 2 recombinations, one before Daejeon/2002 and one after Daejeon/2002 ?
Click to expand...
I'm not sure why you think this is relevant, since the Korean sequences clearly have two breakpoints, which is why the beginning and end of the gene look like contempory H3N2, and only the middle third looks like the isolates from a decade earlier.

The sequences represent reality. Your pictures support your hypothesis, which is not supported by the data, which probably produces considerable confusion for those trying to understand recombination.

If you post a comparison of the Daejeon/2002 with an H3N2 from 2002, the recombination in the middle third will be obvious.

The paper with the recombination examples described the vast majority (over 300) as short stretches, which would involve two cross overs. Two cross-overs are also involved in the vast majority of single nucleotide polymorphism switches when closely related seqeunces recombine.

The examples in the sequence database are clear. Your model of one cross over has no experimental (or conceptual) support.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

Here is a quick summary of the 2002 Korean HA H3N2 recombinants. Three of the six have 1991 sequences in the center third of the gene (the other 3 also have 1991 in the center, but have contemporary sequences in teh center of the 1991 sequences). Thus, instead of being 2002-2002-2002 they are 2002-1991-2002.

I put up some blast results using the middle third of the gene to show that a search of all of genbank returned H3N2 human sequences from the late 80's to early 90's. I then posted some examples of sequences that just had two tandem changes, and showed that once again those combnations were quite restricted, although some combinations were in H3N2 swine and in some instances were re-emerging in 2006 in Iran (and the Iran re-emergence was somewhat limited becauise those sequences only have about 230 base pairs - they are likely recombinants, but only a small piece of the sequence has been released).

In any event, the Korean isolates are OBVIOUS recombinants, generated when the 2002 sequence was used as a template to copy the first 1/3 of the gene, then that new piece jumped over to a 1991 template provided by a coinfection and that template was used for the next 1/3, and then the remainder of the gene used the original 2002 sequence, resulting in a new recombinanat gene which has the first and last 1/3 from 2002 and the middle 1/3 from 1991, which would have likely come from a pig that had a an H3N2 human HA gene that had been introduced into pigs (in Korea) a decade earlier.

GSGS is looking for something else, which he didn't find because his program only detects one crossover and doesn't allow the original 2002 sequence to be used for the last third of the new recombinant sequence (which is obviously what happened based on the actual sequence data), so he is posting something that comes closest, but has nothing to do with the Korean sequences at Genbank, which have the structure 2002-1991-2002.

The 1991 origin is identified in a few seconds, by just using the middle third of the gene and blasting it against the genbank database.

http://www.flutrackers.com/forum/showpost.php?p=144573&postcount=92
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

my 1-breakpoint program still finds the Korean recombination,
i.e. by comparing partial sequences where HA2 is not available.
It makes the p-value less significant, though.

I keep updating the pictures, so keep checking
http://www.setbb.com/fluwiki2/viewtopic.php?p=842&mforum=fluwiki2

We should check for possible accumulation of non-synonymous mutations
typically concentrated in certain areas of HA1,
remember the recent H5N1 in Egypt.

How do you explain the Denmark picture ?

I improved my recombination-program, (thanks to Dann Corbid from sci.math.num.analysis),
it's 5 times faster now, so maybe I'll rerun everything with two breakpoints later.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

"The swine data supports high fidelity over decades, which may signal RNA repair"

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

now, look at this :

Code: 
>A/Daejeon/258/02(H3N2) 
>A/Cheonnam/338/02(H3N2) 
--------------------------------------------------------.... 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
.............................................c.............. 
............................................................ 
...........c................................................ 
....o........o.....o.....o................................o. 
................................................c........... 
..................................o......................... 
................o........................................... 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
.............................-------------- 


>A/Daejeon/258/02(H3N2) 
>A/Denmark/18-2/03(H3N2) 
--------------------------------------------------------.... 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
............................................................ 
..............................co.c........c..c.........o...c 
.......o.........................................o.........c 
.........c.c.oc....o.......................................c 
....o........o.....o.....o................................o. 
......................o...................co....c........... 
....o..........................o..o......................... 
.......o........o.................o.......................o. 
...............................o...........o................ 
............................................................ 
............................................................ 
.........................o.................................. 
............................................................ 
............................................................ 
............................................................ 
...................................................c........ 
............................................................ 
............................................................ 
............................................................ 
.............................--------------


recombination comes in degrees and slowly increases in two steps in
exactly the same region ?????
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

As mentioned earlier, all 6 recombinants have a 1991 center, and 3 have contemporary sequences in the. middle of 1991
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

the Denmark/2003 virus had acquired 176 mutations in HA since 1972
(5.68 per year in average) from Udorn/1972, the ancestor of all human H3N2.
54 of these (1.74 per year) are in the central region of HA.
This is similar to most other H3N2 viruses from that time.

But the Daejeon/258/2002 virus has only 146 differences from
Udorn/72 in HA and only 29 of these in the central region.
So it is "30 years old" in the outer regions but only 17 years
old in the center - corresponding to viruses from 1989 in the
center.

The Cheonnam/338/2002 virus is between these two with
152 differences from Udorn, 35 of these in the center.
Dating the center back to about 1992.

So, if this was recombination, then we would need an unknown
virus which survived about 10 years without mutation, then
recombined with a contemporary 2002 virus, contributing its central
region in HA to the child. Such viruses without mutation in the
central region (and presumably in the other regions too)
for 10 years are very rare. Long recombinations in human H3N2
are also very rare. Unlikely that two such rare events have combined.

In addition we have the Cheonnam viruses, which would have
to come from another, different recombination event, since the
additional mutations can hardly have emerged within less than a year.

So, how else can this have happened ?
The Daejeon virus was mixed with an Udorn-like virus
during amplification and the mutations happened
during amplification ? Maybe they did several PCRs for several
regions and then joined the result ?
I don't know whether this is possible. Maybe someone with experience
in PCR can comment. (Mingus ? Monotreme ?)

There is also an irregularity in
A/Gyeongbuk/2/2002(H3N1) in the first half of HA, which makes
the correctness of those Korean 2002-HAs doubtful.
 
Does not compute.

Does not compute.

Ecology of H3 avian influenza viruses in Korea and assessment of their pathogenic potentials. J Gen Virol 89 (2008), 949-957.

To determine the genetic origins of novel H3 avian influenza viruses of chickens and ducks in Korea, genetic characterization of H3 avian influenza viruses isolated from live poultry markets and migratory aquatic birds in South Korea during 2004?2006 was conducted. Phylogenetic analysis revealed that at least four novel genotypes of H3N2 and two genotypes of H3N6 avian influenza viruses were co-circulating in backyard poultry of Korea. The viruses were reassortants between H9N2 viruses of Korean chickens and unknown influenza viruses of migratory birds. Genetic comparison of H3 viruses from live bird markets with those from wild bird isolates revealed that certain gene segments of wild bird isolates are related closely to those of Korean group H9N2 viruses isolated from live poultry markets in 2003.

Your analysis is flawed. You can't conclude A--->B if the database is both incomplete and your algorithm ignores external inputs into specific subtype sequence populations (meaning, genes/fragments are introduced into a local pool by ressortment / recombination between subtypes across numerous species boundaries and distances via migration, not just within subtypes at a fixed geographical locale).

The influenza viral gene databases feature incomplete genomes, partial gene sequences, selective inclusion of sequenced genomes, and is missing a great deal of data, period - due to the haphazard method of field sample DNA acquisition, faulty sampling technique, and missing deposition of known samples into international databases for various reasons (problems mentioned numerous times by Niman in patient conversation here).
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
the Denmark/2003 virus had acquired 176 mutations in HA since 1972
(5.68 per year in average) from Udorn/1972, the ancestor of all human H3N2.
54 of these (1.74 per year) are in the central region of HA.
This is similar to most other H3N2 viruses from that time.

But the Daejeon/258/2002 virus has only 146 differences from
Udorn/72 in HA and only 29 of these in the central region.
So it is "30 years old" in the outer regions but only 17 years
old in the center - corresponding to viruses from 1989 in the
center.

The Cheonnam/338/2002 virus is between these two with
152 differences from Udorn, 35 of these in the center.
Dating the center back to about 1992.

So, if this was recombination, then we would need an unknown
virus which survived about 10 years without mutation, then
recombined with a contemporary 2002 virus, contributing its central
region in HA to the child. Such viruses without mutation in the
central region (and presumably in the other regions too)
for 10 years are very rare. Long recombinations in human H3N2
are also very rare. Unlikely that two such rare events have combined.

In addition we have the Cheonnam viruses, which would have
to come from another, different recombination event, since the
additional mutations can hardly have emerged within less than a year.

So, how else can this have happened ?
The Daejeon virus was mixed with an Udorn-like virus
during amplification and the mutations happened
during amplification ? Maybe they did several PCRs for several
regions and then joined the result ?
I don't know whether this is possible. Maybe someone with experience
in PCR can comment. (Mingus ? Monotreme ?)

There is also an irregularity in
A/Gyeongbuk/2/2002(H3N1) in the first half of HA, which makes
the correctness of those Korean 2002-HAs doubtful.
Click to expand...
The examples of evolutionary stasis are well known. I publushed examples in swine which included 1977 sequences (from Tennessee swine) in 2003/2004 isolates. As you know, there was no Tennessee swine virus in the lab generating those sequences.
 
Re: Does not compute.

Re: Does not compute.

Oracle said:
Ecology of H3 avian influenza viruses in Korea and assessment of their pathogenic potentials. J Gen Virol 89 (2008), 949-957.

To determine the genetic origins of novel H3 avian influenza viruses of chickens and ducks in Korea, genetic characterization of H3 avian influenza viruses isolated from live poultry markets and migratory aquatic birds in South Korea during 2004?2006 was conducted. Phylogenetic analysis revealed that at least four novel genotypes of H3N2 and two genotypes of H3N6 avian influenza viruses were co-circulating in backyard poultry of Korea. The viruses were reassortants between H9N2 viruses of Korean chickens and unknown influenza viruses of migratory birds. Genetic comparison of H3 viruses from live bird markets with those from wild bird isolates revealed that certain gene segments of wild bird isolates are related closely to those of Korean group H9N2 viruses isolated from live poultry markets in 2003.

Your analysis is flawed. You can't conclude A--->B if the database is both incomplete and your algorithm ignores external inputs into specific subtype sequence populations (meaning, genes/fragments are introduced into a local pool by ressortment / recombination between subtypes across numerous species boundaries and distances via migration, not just within subtypes at a fixed geographical locale).

The influenza viral gene databases feature incomplete genomes, partial gene sequences, selective inclusion of sequenced genomes, and is missing a great deal of data, period - due to the haphazard method of field sample DNA acquisition, faulty sampling technique, and missing deposition of known samples into international databases for various reasons (problems mentioned numerous times by Niman in patient conversation here).
Click to expand...
Actually, the data out of south Korea is VERY complex. Earlier publications had obvious examples of recombination (in H9N2) and had clear examples of withheld data (i.e. a partial sequence of a recombinant was released, as well as two more partial partial sequences. The two paprtial partials matched the recombined partial, and the stopped right at the recombination break point).

http://www.recombinomics.com/News/03050501/Chicken_NP_Recombination.html

The internal genes from multiple serotypes were distinct, but had much in common this other Korean sequences, again demonstrating recombination.

Korea is a recombination hotspot, and sequences come flying out of there each season.
View of NA recombination in H9N2 in Korea

http://www.recombinomics.com/phylo/H9N2_NA.html
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

niman said:
The examples of evolutionary stasis are well known. I publushed examples in swine which included 1977 sequences (from Tennessee swine) in 2003/2004 isolates. As you know, there was no Tennessee swine virus in the lab generating those sequences.
Click to expand...

"evolutionary stasis" usually refers to amino-acid mutations. (Webster)
No nucleotide-stasis in human H3N2

h3g1.gif


no two pixels in the same row 10 years apart

BTW. the upper points in 2000 could be an error with some year (?)
BTW.2 , the Fujian-flu 2003 could be re-emergence or recombination
or reassortment or such - you see a jump in 2003
(or maybe this is just because there were two outbreaks in 2003,
Feb.and Dec. in USA, only the year is considered, not months)


for the middle part of HA:
h3g3.gif



partial sequences >1000 BP included
h3g2.gif


you can see how the mutation rate is higher in HA1 than in HA2
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
"evolutionary stasis" usually refers to amino-acid mutations. (Webster)
No nucleotide-stasis in human H3N2

h3g1.gif


no two pixels in the same row 10 years apart

BTW. the upper points in 2000 could be an error with some year (?)
BTW.2 , the Fujian-flu 2003 could be re-emergence or recombination
or reassortment or such - you see a jump in 2003
Click to expand...
The key is the history of a given, position, not the total number. The 2002 Korean sequences clearly have a 1991 central third based on the correspondence with more polymorphisms.

The sequence databases are heavily biased, especially in areas where recombination is most common. Sequences are withheld and partial sequences are submitted.

Averaging changes in a biased database (which is biased further, by eliminating partials) is not very useful.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

I edited my last post, added new pictures
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
I edited my last post, added new pictures
Click to expand...
I think you missed the point. The database itself is biased. Researchers withhold sequences that don't look right. Thus obvious recombinants are not in the database. Short regions are not as obvious, so they get in, but would not appear in the total number of changes in long sequences.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

niman said:
I think you missed the point. The database itself is biased. Researchers withhold sequences that don't look right. Thus obvious recombinants are not in the database. Short regions are not as obvious, so they get in, but would not appear in the total number of changes in long sequences.
Click to expand...


That would require a world-wide conspiracy.
And the recombined viruses mustn't spread, since else
they are detected elsewhere.
But if recombined viruses don't spread - then there is no
danger from them.
We have no clear example of a new strain which was created
by recombination and did spread worldwide. (have we ?)
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
That would require a world-wide conspiracy.
And the recombined viruses mustn't spread, since else
they are detected elsewhere.
But if recombined viruses don't spread - then there is no
danger from them.
We have no clear example of a new strain which was created
by recombination and did spread worldwide. (have we ?)
Click to expand...
Please. No nonsense. The partial sequences are glaring as are the fatally flawed experimental design of searches for recombination.

The vast majority of newly acquired polymorphisms are from homologous recombination, and the spread of this polymorphismsm has been documented in hundreds of travel logs, including G743A in H5N1, which has now spread throughout Europe.
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

I improved my program, it's also much faster now.
I could search the PB2 sequences from genbank
for recombination-candidates with two breakpoints
in 19 hours.
List of candidates here: http://magictour.free.fr/panflu/reco81.l12
Difference-pictures of the most promising candidates (pairs)
for recombination in PB2 of human flu are here :
http://magictour.free.fr/panflu/recs1h

The program is here: http://magictour.free.fr/panflu/recfa.exe
Source code attached to the executable.
It prints all candidates, but needs aligned input, with two lines per virus
and postprocessing to make lists. (to be improved...)
I'd appreciate if someone could run it for other segments,
I can upload the data.
It's running now with randomized sequences (==>no recombinations)
to compare the results.(give me 19 hours...)
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

gsgs said:
I improved my program, it's also much faster now.
I could search the PB2 sequences from genbank
for recombination-candidates with two breakpoints
in 19 hours.
List of candidates here: http://magictour.free.fr/panflu/reco81.l12
Difference-pictures of the most promising candidates (pairs)
for recombination in PB2 of human flu are here :
http://magictour.free.fr/panflu/recs1h

The program is here: http://magictour.free.fr/panflu/recfa.exe
Source code attached to the executable.
It prints all candidates, but needs aligned input, with two lines per virus
and postprocessing to make lists. (to be improved...)
I'd appreciate if someone could run it for other segments,
I can upload the data.
It's running now with randomized sequences (==>no recombinations)
to compare the results.(give me 19 hours...)
Click to expand...
I took your first example which showed that the 1997 isolate, A/Hong Kong/498/97(H3N2) has a 3' half that looked like a sequence from 2 decades earlier. so I did a blast of the 3' half beginning at position 1102 and as expected, the best matches were isolates collected in the 70's, even though the sequence used was from 1997

gb|AF258842.1| Influenza A virus (A/Hong Kong/498/97(H3N2)) R... 2237 0.0
gb|CY002751.1| Influenza A virus (A/Memphis/109/72(H3N2)) seg... 2214 0.0
gb|CY007978.1| Influenza A virus (A/Guandong/243/72(H3N2)) se... 2214 0.0
gb|CY006051.1| Influenza A virus (A/Beijing/39/75(H3N2)) segm... 2214 0.0
gb|CY003535.1| Influenza A virus (A/Hong Kong/11/73(H3N2)) se... 2205 0.0
gb|CY006914.1| Influenza A virus (A/Hong Kong/49/74(H3N2)) se... 2205 0.0
gb|CY002103.1| Influenza A virus (A/Memphis/102/72(H3N2)) seg... 2201 0.0
gb|CY009011.1| Influenza A virus (A/Hong Kong/33/73(H3N2)) se... 2199 0.0
gb|CY021948.1| Influenza A virus (A/Albany/1/1976(H3N2)) segm... 2186 0.0
gb|CY003735.1| Influenza A virus (A/Hong Kong/43/75(H3N2)) se... 2186 0.0
gb|CY008699.1| Influenza A virus (A/Memphis/106/76(H3N2)) seg... 2186 0.0
gb|CY006730.1| Influenza A virus (A/Memphis/137/76(H3N2)) seg... 2186 0.0
gb|CY006842.1| Influenza A virus (A/Memphis/110/76(H3N2)) seg... 2185 0.0
gb|M91712.1|FLAP2A Influenza A virus (A/Udorn/307/1972(H3N2))... 2185 0.0
gb|CY009067.1| Influenza A virus (A/Memphis/105/76(H3N2)) seg... 2181 0.0
gb|CY022316.1| Influenza A virus (A/Memphis/104/1976(H3N2)) s... 2179 0.0
gb|CY003503.1| Influenza A virus (A/Hong Kong/14/74(H3N2)) se... 2177 0.0
gb|CY008707.1| Influenza A virus (A/Memphis/108/76(H3N2)) seg... 2177 0.0
gb|CY006890.1| Influenza A virus (A/Memphis/103/76(H3N2)) seg... 2177 0.0
gb|CY009643.1| Influenza A virus (A/Udorn/72(H3N2)) segment 1... 2176 0.0
gb|CY006106.1| Influenza A virus (A/Hong Kong/45/80(H3N2)) se... 2174 0.0
gb|CY006818.1| Influenza A virus (A/Memphis/3/73(H3N2)) segme... 2172 0.0
gb|CY003495.1| Influenza A virus (A/Hong Kong/46/80(H3N2)) se... 2168 0.0
gb|CY009307.1| Influenza A virus (A/Swine/Colorado/1/77(H3N2)... 2168 0.0
gb|CY008691.1| Influenza A virus (A/Memphis/105/72(H3N2)) seg... 2168 0.0
gb|CY008467.1| Influenza A virus (A/Memphis/103/72(H3N2)) seg... 2168 0.0
gb|CY006059.1| Influenza A virus (A/Hong Kong/1/82(H3N2)) seg... 2165 0.0
gb|CY021836.1| Influenza A virus (A/Albany/15/1976(H3N2)) seg... 2163 0.0
gb|CY006826.1| Influenza A virus (A/Memphis/102/74(H3N2)) seg... 2163 0.0
gb|CY021084.1| Influenza A virus (A/Albany/42/1975(H3N2)) seg... 2159 0.0
gb|CY002503.1| Influenza A virus (A/Memphis/1/71(H3N2)) segme... 2159 0.0
gb|CY006722.1| Influenza A virus (A/Memphis/101/74(H3N2)) seg... 2159 0.0
gb|DQ508926.1| Influenza A virus (A/Udorn/307/1972(H3N2)) pol... 2158 0.0
gb|CY021604.1| Influenza A virus (A/Memphis/3/1971(H3N2)) seg... 2154 0.0
gb|CY021100.1| Influenza A virus (A/Albany/20/1974(H3N2)) seg... 2154 0.0
gb|CY009355.1| Influenza A virus (A/Port Chalmers/73(H3N2)) s... 2154 0.0
gb|CY006834.1| Influenza A virus (A/Memphis/103/74(H3N2)) seg... 2154 0.0
gb|AF251394.1|AF251394 Influenza A virus (A/Swine/Colorado/1/... 2152 0.0
gb|CY009363.1| Influenza A virus (A/England/72(H3N2)) segment... 2150 0.0
gb|CY003559.1| Influenza A virus (A/Hong Kong/6/72(H3N2)) seg... 2150 0.0
gb|AY210150.1| Influenza A virus (A/Tokyo/31/72(H3N2)) PB2 po... 2149 0.0
gb|CY003527.1| Influenza A virus (A/Hong Kong/24/85(H3N2)) se... 2147 0.0
gb|M38277.1|FLAPB2L Influenza A virus (A/Kiev/59/1979(H1N1)) ... 2147 0.0
gb|CY008683.1| Influenza A virus (A/Memphis/101/72(H3N2)) seg... 2145 0.0
gb|CY020228.1| Influenza A virus (A/Albany/14/1978(H3N2)) seg... 2141 0.0
gb|EU273802.1| Influenza A virus (A/swine/Heilongjiang/1/05(H... 2134 0.0
gb|CY021724.1| Influenza A virus (A/California/10/1978(H1N1))... 2132 0.0
gb|CY003543.1| Influenza A virus (A/Hong Kong/7/85(H3N2)) seg... 2132 0.0
gb|AY210149.1| Influenza A virus (A/England/42/72(H3N2)) PB2 ... 2131 0.0
gb|CY028731.1| Influenza A virus (A/California/45/1978(H1N1))... 2129 0.0
gb|M73517.1|FLAH3N2P2 Influenza A virus (A/Memphis/8/1988(H3N... 2129 0.0
gb|CY006850.1| Influenza A virus (A/Memphis/5/77(H3N2)) segme... 2127 0.0
gb|CY008130.1| Influenza A virus (A/Memphis/4/77(H3N2)) segme... 2127 0.0
gb|CY008122.1| Influenza A virus (A/Memphis/2/77(H3N2)) segme... 2127 0.0
gb|CY007618.1| Influenza A virus (A/Memphis/19/78(H3N2)) segm... 2127 0.0
gb|CY006746.1| Influenza A virus (A/Memphis/3/77(H3N2)) segme... 2127 0.0
gb|CY006738.1| Influenza A virus (A/Memphis/1/77(H3N2)) segme... 2127 0.0
gb|CY006762.1| Influenza A virus (A/Nanjing/2/82(H3N2)) segme... 2127 0.0
gb|CY026418.1| Influenza A virus (A/Albany/8/1979(H1N1)) segm... 2123 0.0
gb|CY002095.1| Influenza A virus (A/Memphis/66/86(H3N2)) segm... 2123 0.0
gb|CY006858.1| Influenza A virus (A/Nanjing/36/83(H3N2)) segm... 2123 0.0
gb|CY006226.1| Influenza A virus (A/Memphis/2/71(H3N2)) segme... 2123 0.0
gb|U62543.1|IAU62543 Influenza A virus (A/LosAngeles/2/1987(H... 2123 0.0
gb|CY003727.1| Influenza A virus (A/Hong Kong/26/83(H3N2)) se... 2122 0.0
gb|M91713.1|FLAP2B Influenza A virus (A/Great Lakes/0389/1965... 2122 0.0
gb|CY003551.1| Influenza A virus (A/Hong Kong/7/87(H3N2)) seg... 2120 0.0
gb|CY020332.1| Influenza A virus (A/Memphis/16/1978(H3N2)) se... 2118 0.0
gb|DQ508822.1| Influenza A virus (A/Bangkok/01/1979(H3N2)) po... 2116 0.0
gb|CY009075.1| Influenza A virus (A/Memphis/2/85(H3N2)) segme... 2114 0.0
gb|CY006714.1| Influenza A virus (A/Memphis/18/78(H3N2)) segm... 2114 0.0
gb|CY006706.1| Influenza A virus (A/Memphis/12/78(H3N2)) segm... 2114 0.0
gb|CY006698.1| Influenza A virus (A/Memphis/2/78(H3N2)) segme... 2114 0.0
gb|CY019746.1| Influenza A virus (A/Memphis/1/1979(H1N1)) seg... 2113 0.0
gb|CY002759.1| Influenza A virus (A/Memphis/1/86(H3N2)) segme... 2113 0.0
gb|CY021108.1| Influenza A virus (A/Albany/4/1977(H3N2)) segm... 2109 0.0
gb|CY009059.1| Influenza A virus (A/Memphis/33/83(H3N2)) segm... 2109 0.0
gb|CY008667.1| Influenza A virus (A/Memphis/1/80(H3N2)) segme... 2109 0.0
gb|CY008475.1| Influenza A virus (A/Memphis/3/80(H3N2)) segme... 2109 0.0
gb|CY008459.1| Influenza A virus (A/Memphis/5/85(H3N2)) segme... 2109 0.0
gb|CY006898.1| Influenza A virus (A/Memphis/9/80(H3N2)) segme... 2109 0.0
gb|CY007634.1| Influenza A virus (A/Memphis/1/81(H3N2)) segme... 2109 0.0
gb|CY021916.1| Influenza A virus (A/USSR/46/1979(H1N1)) segme... 2107 0.0
gb|AY210145.1| Influenza A virus (A/Queensland/7/70(H3N2)) PB... 2107 0.0
gb|AY210144.1| Influenza A virus (A/Taiwan/2/70(H3N2)) PB2 po... 2107 0.0
gb|CY003743.1| Influenza A virus (A/Hong Kong/5/83(H3N2)) seg... 2105 0.0
gb|CY009315.1| Influenza A virus (A/Swine/Wisconsin/194/80(H3... 2105 0.0
gb|CY007626.1| Influenza A virus (A/Memphis/4/80(H3N2)) segme... 2105 0.0
gb|CY006314.1| Influenza A virus (A/Hong Kong/50/72(H3N2)) se... 2105 0.0
gb|CY006322.1| Influenza A virus (A/Hong Kong/14/83(H3N2)) se... 2105 0.0
gb|CY006210.1| Influenza A virus (A/Nanjing/13/80(H3N2)) segm... 2104 0.0
gb|CY008179.1| Influenza A virus (A/Nanjing/28/84(H3N2)) segm... 2100 0.0
gb|CY006330.1| Influenza A virus (A/Hong Kong/4/84(H3N2)) seg... 2100 0.0
gb|CY003519.1| Influenza A virus (A/Hong Kong/2/88(H3N2)) seg... 2096 0.0
gb|AY210148.1| Influenza A virus (A/Chiba/5/71(H3N2)) PB2 pol... 2095 0.0
gb|AY210147.1| Influenza A virus (A/Caracas/1/71(H3N2)) PB2 p... 2095 0.0
gb|CY003751.1| Influenza A virus (A/Hong Kong/7/84(H3N2)) seg... 2093 0.0
gb|CY020340.1| Influenza A virus (A/Memphis/3/1986(H3N2)) seg... 2091 0.0
gb|CY016067.1| Influenza A virus (A/Memphis/2/1986(H3N2)) seg... 2091 0.0
gb|CY011479.1| Influenza A virus (A/Memphis/12/1985(H3N2)) se... 2091 0.0
gb|CY011295.1| Influenza A virus (A/Memphis/5/1986(H3N2)) seg... 2091 0.0
<!--/#descriptions-->
 
Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

A blast of the first half of the gene (to position 1101) yields matches with sequences from the late 90's as expected:

gb|AF258842.1| Influenza A virus (A/Hong Kong/498/97(H3N2)) R... 1986 0.0
gb|AF258841.1| Influenza A virus (A/Hong Kong/497/97(H3N2)) R... 1941 0.0
gb|CY001983.1| Influenza A virus (A/New York/324/1999(H3N2)) ... 1925 0.0
gb|CY003631.1| Influenza A virus (A/New York/458/1999(H3N2)) ... 1916 0.0
gb|CY003615.1| Influenza A virus (A/New York/456/1999(H3N2)) ... 1916 0.0
gb|CY006067.1| Influenza A virus (A/New York/452/1999(H3N2)) ... 1907 0.0
gb|CY003591.1| Influenza A virus (A/New York/451/1999(H3N2)) ... 1907 0.0
gb|CY002311.1| Influenza A virus (A/New York/398/1999(H3N2)) ... 1907 0.0
gb|CY001903.1| Influenza A virus (A/New York/333/1999(H3N2)) ... 1907 0.0
gb|CY003639.1| Influenza A virus (A/New York/459/1999(H3N2)) ... 1905 0.0
gb|CY003623.1| Influenza A virus (A/New York/457/1999(H3N2)) ... 1905 0.0
gb|CY003247.1| Influenza A virus (A/New York/431/2000(H3N2)) ... 1905 0.0
gb|CY002391.1| Influenza A virus (A/New York/330/1998(H3N2)) ... 1905 0.0
gb|CY002303.1| Influenza A virus (A/New York/347/1999(H3N2)) ... 1905 0.0
gb|CY001831.1| Influenza A virus (A/New York/314/1999(H3N2)) ... 1905 0.0
gb|CY003832.1| Influenza A virus (A/New York/440/2000(H3N2)) ... 1903 0.0
gb|CY003271.1| Influenza A virus (A/New York/436/2000(H3N2)) ... 1903 0.0
gb|CY002383.1| Influenza A virus (A/New York/328/1998(H3N2)) ... 1903 0.0
gb|CY001943.1| Influenza A virus (A/New York/340/1999(H3N2)) ... 1903 0.0
gb|CY006642.1| Influenza A virus (A/New York/548/1998(H3N2)) ... 1903 0.0
gb|CY006514.1| Influenza A virus (A/New York/522/1997(H3N2)) ... 1903 0.0
gb|CY006586.1| Influenza A virus (A/New York/539/1998(H3N2)) ... 1903 0.0
gb|CY006242.1| Influenza A virus (A/New York/505/1997(H3N2)) ... 1903 0.0
gb|DQ486029.1| Influenza A virus (A/Moscow/10/99(H3N2)) polym... 1902 0.0
gb|CY003816.1| Influenza A virus (A/New York/429/2000(H3N2)) ... 1902 0.0
gb|CY001999.1| Influenza A virus (A/New York/332/1999(H3N2)) ... 1902 0.0
gb|CY001695.1| Influenza A virus (A/New York/248/1999(H3N2)) ... 1902 0.0
gb|CY001879.1| Influenza A virus (A/New York/323/1999(H3N2)) ... 1902 0.0
gb|CY001991.1| Influenza A virus (A/New York/331/1999(H3N2)) ... 1900 0.0
gb|CY001895.1| Influenza A virus (A/New York/329/1999(H3N2)) ... 1900 0.0
gb|CY001847.1| Influenza A virus (A/New York/317/1999(H3N2)) ... 1900 0.0
gb|CY006626.1| Influenza A virus (A/New York/546/1998(H3N2)) ... 1900 0.0
gb|DQ487334.1| Influenza A virus (A/Panama/2007/1999(H3N2)) s... 1898 0.0
gb|CY003599.1| Influenza A virus (A/New York/453/1999(H3N2)) ... 1898 0.0
gb|CY003583.1| Influenza A virus (A/New York/450/1999(H3N2)) ... 1898 0.0
gb|CY000704.1| Influenza A virus (A/New York/174/2000(H3N2)) ... 1898 0.0
gb|CY000624.1| Influenza A virus (A/New York/161/1999(H3N2)) ... 1898 0.0
gb|CY006794.1| Influenza A virus (A/New York/506/1998(H3N2)) ... 1898 0.0
gb|CY006290.1| Influenza A virus (A/New York/517/1998(H3N2)) ... 1898 0.0
gb|CY002375.1| Influenza A virus (A/New York/325/1999(H3N2)) ... 1896 0.0
gb|CY001919.1| Influenza A virus (A/New York/336/1999(H3N2)) ... 1896 0.0
gb|CY001775.1| Influenza A virus (A/New York/282/1999(H3N2)) ... 1896 0.0
gb|CY008955.1| Influenza A virus (A/New York/529/1998(H3N2)) ... 1894 0.0
gb|CY001935.1| Influenza A virus (A/New York/338/1999(H3N2)) ... 1894 0.0
gb|CY000720.1| Influenza A virus (A/New York/176/2000(H3N2)) ... 1894 0.0
gb|CY006810.1| Influenza A virus (A/New York/538/1998(H3N2)) ... 1894 0.0
gb|CY006538.1| Influenza A virus (A/New York/525/1998(H3N2)) ... 1894 0.0
gb|CY006618.1| Influenza A virus (A/New York/545/1997(H3N2)) ... 1894 0.0
gb|CY006546.1| Influenza A virus (A/New York/528/1998(H3N2)) ... 1894 0.0
gb|CY006498.1| Influenza A virus (A/New York/520/1998(H3N2)) ... 1894 0.0
gb|CY016554.1| Influenza A virus (A/New South Wales/16/1999(H... 1893 0.0
gb|CY016075.1| Influenza A virus (A/New South Wales/13/1999(H... 1889 0.0
gb|CY003808.1| Influenza A virus (A/New York/428/1999(H3N2)) ... 1889 0.0
gb|CY003567.1| Influenza A virus (A/New York/448/1998(H3N2)) ... 1889 0.0
gb|CY003463.1| Influenza A virus (A/New York/439/2000(H3N2)) ... 1889 0.0
gb|CY003455.1| Influenza A virus (A/New York/430/2000(H3N2)) ... 1889 0.0
gb|CY008987.1| Influenza A virus (A/New York/550/1998(H3N2)) ... 1889 0.0
gb|CY008931.1| Influenza A virus (A/New York/504/1998(H3N2)) ... 1889 0.0
gb|CY008939.1| Influenza A virus (A/New York/507/1997(H3N2)) ... 1889 0.0
gb|CY008947.1| Influenza A virus (A/New York/514/1998(H3N2)) ... 1889 0.0
gb|CY008963.1| Influenza A virus (A/New York/530/1998(H3N2)) ... 1889 0.0
gb|CY008971.1| Influenza A virus (A/New York/540/1998(H3N2)) ... 1889 0.0
gb|CY000808.1| Influenza A virus (A/New York/141/1999(H3N2)) ... 1889 0.0
gb|CY006266.1| Influenza A virus (A/New York/511/1997(H3N2)) ... 1889 0.0
gb|CY006906.1| Influenza A virus (A/New York/460/1999(H3N2)) ... 1889 0.0
gb|CY006802.1| Influenza A virus (A/New York/527/1998(H3N2)) ... 1889 0.0
gb|CY006778.1| Influenza A virus (A/New York/535/1998(H3N2)) ... 1889 0.0
gb|CY006634.1| Influenza A virus (A/New York/547/1997(H3N2)) ... 1889 0.0
gb|CY006570.1| Influenza A virus (A/New York/533/1998(H3N2)) ... 1889 0.0
gb|CY006562.1| Influenza A virus (A/New York/532/1998(H3N2)) ... 1889 0.0
gb|CY006554.1| Influenza A virus (A/New York/531/1998(H3N2)) ... 1889 0.0
gb|CY006530.1| Influenza A virus (A/New York/524/1997(H3N2)) ... 1889 0.0
gb|CY006450.1| Influenza A virus (A/New York/501/1997(H3N2)) ... 1889 0.0
gb|CY006466.1| Influenza A virus (A/New York/512/1998(H3N2)) ... 1889 0.0
gb|CY006282.1| Influenza A virus (A/New York/515/1997(H3N2)) ... 1889 0.0
gb|CY006250.1| Influenza A virus (A/New York/508/1997(H3N2)) ... 1889 0.0
gb|CY006234.1| Influenza A virus (A/New York/503/1997(H3N2)) ... 1889 0.0
gb|CY003824.1| Influenza A virus (A/New York/432/2000(H3N2)) ... 1887 0.0
gb|CY003287.1| Influenza A virus (A/New York/438/2000(H3N2)) ... 1887 0.0
gb|CY003263.1| Influenza A virus (A/New York/434/2000(H3N2)) ... 1887 0.0
gb|CY020204.1| Influenza A virus (A/New South Wales/7/1999(H3... 1885 0.0
gb|CY011431.1| Influenza A virus (A/New York/577/1996(H3N2)) ... 1885 0.0
gb|CY011271.1| Influenza A virus (A/New York/559/1996(H3N2)) ... 1885 0.0
gb|CY011263.1| Influenza A virus (A/New York/557/1996(H3N2)) ... 1885 0.0
gb|CY011143.1| Influenza A virus (A/New York/602/1996(H3N2)) ... 1885 0.0
gb|CY010611.1| Influenza A virus (A/New York/561/1996(H3N2)) ... 1885 0.0
gb|CY010035.1| Influenza A virus (A/New York/591/1996(H3N2)) ... 1885 0.0
gb|CY010011.1| Influenza A virus (A/New York/563/1996(H3N2)) ... 1885 0.0
gb|CY009995.1| Influenza A virus (A/New York/536/1998(H3N2)) ... 1885 0.0
gb|CY009755.1| Influenza A virus (A/New York/597/1997(H3N2)) ... 1885 0.0
gb|CY009739.1| Influenza A virus (A/New York/589/1996(H3N2)) ... 1885 0.0
gb|CY009667.1| Influenza A virus (A/New York/568/1996(H3N2)) ... 1885 0.0
gb|CY009131.1| Influenza A virus (A/Nelson Marlborough/1/2000... 1885 0.0
gb|CY008979.1| Influenza A virus (A/New York/549/1998(H3N2)) ... 1885 0.0
gb|CY008539.1| Influenza A virus (A/New York/544/1998(H3N2)) ... 1885 0.0
gb|CY008187.1| Influenza A virus (A/New York/502/1998(H3N2)) ... 1885 0.0
gb|CY006610.1| Influenza A virus (A/New York/543/1998(H3N2)) ... 1885 0.0
gb|CY006522.1| Influenza A virus (A/New York/523/1998(H3N2)) ... 1885 0.0
gb|CY006578.1| Influenza A virus (A/New York/534/1998(H3N2)) ... 1885 0.0
gb|CY006490.1| Influenza A virus (A/New York/519/1998(H3N2)) ... 1885 0.0
 
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