Evidence of intra-segmental homologous recombination in influenza A virus

[tetano]

Gene. 2011 May 6. [Epub ahead of print]
Evidence of intra-segmental homologous recombination in influenza A virus.
Hao W.
Abstract

The evolution of influenza viruses is remarkably dynamic. Influenza viruses evolve rapidly in sequence and undergo frequent reassortment of different gene segments. Homologous recombination, although commonly seen as an important component of dynamic genome evolution in many other organisms, is believed to be rare in influenza. In this study, 256 gene segments from 32 influenza A genomes were examined for homologous recombination, three recombinant H1N1 strains were detected and they most likely resulted from one recombination event between two closely rated parental sequences. These findings suggest that homologous recombination in influenza viruses tends to take place between strains sharing high sequence similarity. The three recombinant strains were isolated at different time periods and they form a clade, indicating that recombinant strains could circulate. In addition, the simulation results showed that many recombinant sequences might not be detectable by currently existing recombinant detection programs when the parental sequences are of high sequence similarity. Finally, possible ways were discussed to improve the accuracy of the detection for recombinant sequences in influenza.

Copyright ? 2011 Elsevier B.V. All rights reserved.

PMID:
21571048
[PubMed - as supplied by publisher]

http://www.ncbi.nlm.nih.gov/pubmed/21571048

[gsgs]

Re: Evidence of intra-segmental homologous recombination in influenza A virus

not convincing, IMO.
emails with Hao ...

[gsgs]

Re: Evidence of intra-segmental homologous recombination in influenza A virus

http://www.ncbi.nlm.nih.gov/pubmed/22226809

[gsgs]

Re: Evidence of intra-segmental homologous recombination in influenza A virus

another paper :

http://www.ncbi.nlm.nih.gov/pubmed/22381928

> ... falsify the hypothesis that influenza virus do not evolve by homologous recombination.

http://www.sciencedirect.com/science/article/pii/S0042682212000384

A/swine/CDA/1488/99
A/swine/Schwerin/103/89
A/swine/HK/8512/2001
PB1
250 bp width centered on the position plotted, with a step size between
plots of 20 bp. CY022067/A/swine/Tennessee/19/1976, CY022075/A/swine/Iowa/1/1976,
CY022059/A/swine/Tennessee/17/1976 were used as the out-group
and GQ229260A/swine/HK/NS837/2001

GQ229260/A/swine/HK/NS837/2001

------------------------------------------
A/United_Kingdom/1/1933(H1N1) with their two putative parent lineage representatives:
avian (L37795/A/chicken/Brescia/1902(H7N7)) and Human (CY002617/A/New_York/208/2001(H1N1).

segment 7. (A) MP
------------------------------------------

PA
A/swine/Ile_et_Vilaine/1455/99(H1N1) with their two putative parent lineage representatives:
I, GQ161155/A/swine/Greven/IDT2889/2004(H1N1); and II, CY077933/A/swine/Oedenrode/7c/1996(H3N2).
(B)

of 20 bp. EU026115/A/duck/NJ/7717-70/1995(H1N1) and EU026107/A/duck/NY/13152-13/1994(H1N1) w

                                                                             000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111112222222222222222 
                                                                             000001111111222222233333334444444455566666677888899999900001111112222233344566666677778888888888888999990000000001111122 
                                                                             112272235566234456812334460355688803702233706146734448901151256670466923919212567712360124556678899002590056778892668956 
                                                                             297826955612243981847072542835067914194724252001332567081709351799836695867770681728179842232601768279624727032811091068 
-codon-position-------------------------------------------------------------- 1 1    2 2        2  1  1   21 1   1   21          1       1                     2       122 1   2 2                    
---Index---------------------------------------------------------------------TTCTTACAAAAGCAAATTACGGGTGTCCACGGCACAGAGGGTGGTATATATTCACCGTGCAGGCAGTCGCCCTATGTACGCTGGGGCTGAGAATCCCCGTATCCTGGTGGTCGATGACGG 
   1 >A/swine/Germany/2/1981(H1N1)=1578                                      ........................................................................................................................        0      0 ,      0      0       1:>A/swine/Germany/2/1981(H1N1)=1578                                      
   2 >A/swine/Hong Kong/NS837/2001,2001/04/09,H1N1,Hong Kong,Swine,2,.2H-.   .CTC...GGG.AT...C.GA...CA....TA...TG...AACA.CGC.C.CC.GTT.C.T.A..G.C..ATT.G.A.....C...A..AG..G.TTTT.C.....AACAACTAGCAGTTA      121     65 ,    121     65       2:>A/swine/Hong Kong/NS837/2001,2001/04/09,H1N1,Hong Kong,Swine,2,.2H-.   
   3 >A/swine/Schwerin/103/89,1989//,H1N1,Germany,Swine,2,.2G-.              CC.....GGG.A......GA..ACA...G.A........A....CG....C..GTT........G.....TT.G.......C.......G..G..T...C.......C.....G......       48     31 ,     48     31       3:>A/swine/Schwerin/103/89,1989//,H1N1,Germany,Swine,2,.2G-.              
   4 >A/swine/Cotes d'Armor/1488/1999,1999//,H1N1,France,Swine,2,.2G-.       CC..CGA.G.GATGGTCCGAAAACACTAGTAATGTGAGA.ACAACGCGCGCCAGTTACA.GAATGACTATTTCGCACGTATCAAAATCAGATGATTTTACGCTTCA.C.....G.AG..-      111    105 ,    110    104       4:>A/swine/Cotes d'Armor/1488/1999,1999//,H1N1,France,Swine,2,.2G-.       
   5 >A/swine/Hong Kong/8512/2001,2001/02/28,H1N1,Hong Kong,Swine,2,.2E-.    ..TCCGA.GGGATGGTCCGAAAACACTAGTAATGTGAGA.ACAACGCGCGCCAGTTACATGAATGACTATTTCGCACGTATCAAAATCAGATGATTTTACGCTTCAACAACTAGCAGTTA      129    116 ,    129    116       5:>A/swine/Hong Kong/8512/2001,2001/02/28,H1N1,Hong Kong,Swine,2,.2E-.    
                                                                                                                                                                                                      
---Index---------------------------------------------------------------------TTCTTACAAAAGCAAATTACGGGTGTCCACGGCACAGAGGGTGGTATATATTCACCGTGCAGGCAGTCGCCCTATGTACGCTGGGGCTGAGAATCCCCGTATCCTGGTGGTCGATGACGG 
-codon-position-------------------------------------------------------------- 1 1    2 2        2  1  1   21 1   1   21          1       1                     2       122 1   2 2                    
                                                                             000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111112222222222222222 
                                                                             000001111111222222233333334444444455566666677888899999900001111112222233344566666677778888888888888999990000000001111122 
                                                                             112272235566234456812334460355688803702233706146734448901151256670466923919212567712360124556678899002590056778892668956 
                                                                             297826955612243981847072542835067914194724252001332567081709351799836695867770681728179842232601768279624727032811091068

                         0000000000000000000000000000000000000000000000000000000000000000000000000000000 
                         0001111122222223333333333333344444444444444444455555555555666666666777778888999 
                         1471158957889990001334456678800022334445556788900224458899001235599022342359123 
                         0351403220281470295393570151728903281470698169214280352514033731439009579815903 
-codon-position----------11              2    1   1     1                            1      1    112112  
---Index-----------------TGGCTAACTACATAGCGTGGAGATCGCTCGGATATGACACAGTCCGAAAAGAGGAGGAAGGTAACCTACAGATCCGAAG 
A/BM/1/1918,H1N1         ...............................................................................        0      0 ,      0      0       1:>A/BM/1/1918,H1N1         
A/Ck/Brescia/1902,H7N7   C..ACGGTAGTCCGA.AAAAG.GCTAACTAA.AGAAGTCTGACA.AGCCGAG..GAAGGA..GGATCC.GAGCT.TGCA
A/Ck/Brescia/1902,H7N7   CC.ACGGTAGTCCGA.AAAAG.GCTAACTAA.AGAAGTCTGACA.AGCCGAG..GAAGGA..GGATCC.GAGCT.TGCA

A/Ck/Brescia/1902,H7N7   CA.ACGGTAGTCCGA.AAAAG.GCTAACTAA.AGAAGTCTGACA.AGCCGAGA.GAAGGA..GGATCC.GAGCT.TGCA parent
A/UK/1/1933(H1N1)        C.A........T...T.....A..T......G..........C.T......TAA......AC...T.CT.AG..TA..A child
A/NY/208/2001,H1N1       CAA..G.........T.....A..T...A..GC..T......C.T......T.A..A.T.ACG..TCCT.....TA.GA parent
                         ...x                                                             x.............
positions supp.rec.       x                                                  x                 xx

                                 0000000000000000000000000000000000000111111111111111111111111111111111111111111111111222 
                                 0011122222222233334444466677889999999000000011112222222334444445555666666777888889999001 
                                 1534801144799912491578912309790267899002268936660005679592234771368244568199045690455460 
                                 8727070606314657261610823522013712469280923641280894329322870033161057750314062692106349 
-codon-position------------------             2          22      1          1  11 2             11   1 1      11          
---Index-------------------------AGTGACGGAAGCGATGAAGAACGACGCGACGAAAGCCCAGACGCATACGCACTACCCCCCCGCATCTCCCGCGTGACAAACGCCCCAC 
Index2                           GAC..TAAGG.TA..AG..GTT..A.TA.T.G....TTG....T..GT.TGT.....T....GG.T.T..T.AC.G.T.GT.T..TTT
Index1                           ........................................................................................
A/Sw/Germany/2/1981              .....T.......G......TT....TA.............T......TTGT...............T...TT..C.T......T..T
                                    x                                                                                x    breakpoint
A/Sw/Oedenrode/7c/1996,1996//    GAC..TAAGG.TA..AG..GTT.GA.T..TAG..A.TT...T....GT.TGT.....T....GG.T.T.TT.AC.G.T.GT.T..TTT  parent
A/Sw/Ille et Vilaine/1455/1999   .ACTGTAAGGATA.CAGGA.TTAGAATAGTAGCGAA.TGAT.ATGCGT.TGGCGTTTTATTAGGCTCTATT.AAAGTTGG.ATT.TTT  child
A/Sw/Greven/IDT2889/2004         ..CTGTAAG.ATAGCAGGA.TTAGAATAGT.GCGAATTGAT.ATGCGTTTGGCGTTTTATTAGGCTCTATTTAAAGTTGG.ATTTTT.  parent

mutations to support recomb.      x                                                                                  x  x

I do not see much evidence here for spreading,surviving recombined sequences.
And there are better examples anyway. No "falsification" , as they claim