Guidelines for identifying homologous recombination events in influenza A virus.
The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses.
Boni
Maciej F
MF
Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. mboni@oucru.org
de Jong
Menno D
MD
van Doorn
H Rogier
HR
Holmes
Edward C
EC
D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D030541:Databases, Genetic; D005821:Genetic Techniques / Q000592:standards*; D009980:Influenza A virus / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny; D011995:Recombination, Genetic
Syst Biol. 2008 Oct;57(5):758-71
18853362
J Gen Virol. 1996 Apr;77 ( Pt 4):661-71
8627254
Science. 2002 Apr 12;296(5566):211 discussion 211
11951002
PLoS Pathog. 2008 May 30;4(5):e1000076
18516303
Science. 2001 Sep 7;293(5536):1842-5
11546876
Mol Biol Evol. 2009 Jan;26(1):177-87
18931384
J Virol. 2008 Sep;82(17):8947-50
18579605
Nature. 2005 Oct 20;437(7062):1162-6
16208317
J Virol. 2008 May;82(10):4807-11
18353939
Antivir Ther. 2007;12(4 Pt B):603-16
17944268
Virology. 1994 Oct;204(1):462-5
8091680
Nature. 2009 Jun 25;459(7250):1122-5
19516283
J Virol. 1983 Oct;48(1):52-60
6193288
Virology. 2009 Jan 5;383(1):156-61
19000628
Mol Biol Evol. 1997 Mar;14(3):239-47
9066792
J Gen Virol. 2003 Oct;84(Pt 10):2691-2703
13679603
Science. 2004 Jul 16;305(5682):371-6
15218094
Virology. 2008 Oct 10;380(1):12-20
18721995
Vaccine. 2008 Jul 18;26 Suppl 3:C8-14
18773534
J Med Virol. 2007 Oct;79(10):1577-86
17705169
Emerg Infect Dis. 2004 Apr;10(4):693-9
15200862
Mol Biol Evol. 1999 Nov;16(11):1457-65
10555276
J Virol. 1999 Jan;73(1):152-60
9847317
PLoS Pathog. 2008 Feb 29;4(2):e1000012
18463694
Genetics. 2007 Jun;176(2):1035-47
17409078
J Virol. 2009 Jun;83(11):5485-94
19297491
Science. 2009 Jul 10;325(5937):197-201
19465683
Emerg Infect Dis. 2007 May;13(5):713-8
17553249
Mol Biol Evol. 2007 Aug;24(8):1811-20
17522084
N Engl J Med. 2009 Jul 9;361(2):115-9
19474418
Bioinformatics. 1998;14(9):817-8
9918953
Genome Biol. 2003;4(5):R33
12734013
Science. 2008 Jan 25;319(5862):473-6
18218900
J Infect Dis. 2007 Jul 15;196(2):249-57
17570112
Virol J. 2008 May 27;5:65
18505573
PLoS Biol. 2005 Sep;3(9):e300
16026181
Microbiol Rev. 1992 Mar;56(1):152-79
1579108
J Virol. 2009 Sep;83(17):8832-41
19553313
Bioinformatics. 2006 Nov 1;22(21):2688-90
16928733
J Virol. 2008 Apr;82(7):3769-74
18234791
Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):17123-7
17942693
Nature. 1989 Jul 13;340(6229):156-7
2544809
Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7712-8
9223253
Annu Rev Genet. 1998;32:123-62
9928477
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
15034147