title: Evolution of endogenous retroviruses in the Suidae: evidence for different viral subpopulations in African and Eurasian host species.
abstract: BACKGROUND
  Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig (Sus scrofa) genome. Although they are usually inactive, the capacity of γ1 ERVs to infect human cells in vitro has raised concerns about xenotransplantation because the viruses could cross the species barrier to humans. Here we have analyzed the evolution of γ1 ERVs in ten species of Suidae (suids, pigs and hogs) from Eurasia and Africa using DNA sequences for their coding domains (gag, pro/pol and env genes). For comparison with γ1 PERVs, we have also analysed γ2 ERVs which in domestic pigs are known to be inactive and do not pose a risk to xenotransplantation.
  
  
  RESULTS
  Phylogenetic analysis using Bayesian inference showed that γ1 and γ2 ERVs have distinctive evolutionary histories. Firstly, two different viral lineages of γ1 ERVs were found and a coevolutionary analysis demonstrated that they correspond broadly to their host phylogeny, one of Eurasian and another of African species, and show no evidence of horizontal transmission. γ2 ERVs, however, show a bush-like evolution, suggesting a rapid viral radiation from a single common ancestor with no correspondence between host and viral evolutionary trees. Furthermore, though γ1 ERV env genes do not possess frequent stop codons, γ2 env genes do. To understand whether γ1 suid ERVs may be still replicating, we have also evaluated their likely mechanism of proliferation by statistically testing internal to terminal branches using nonsynonymous versus synonymous substitution ratios. Our results suggest that γ1 ERVs are increasing in copy number by reinfection, which requires the translocation of the virus from one cell to another.
  
  
  CONCLUSIONS
  Evidence of at least two viral subpopulations was observed in γ1 ERVs from Eurasian and African host species. These results should be taken into account in xenotransplantation since γ1 ERVs appear to be codiverging with their host and maintaining ongoing capacity to infect somatic and germ cells.
authors: Faculty of Veterinary Science, The University of Sydney, NSW 2006, Australia.
authors: Fabrícia F
authors: FF
authors: Nascimento
authors: Jaime
authors: J
authors: Gongora
authors: Michael
authors: M
authors: Charleston
authors: Michael
authors: M
authors: Tristem
authors: Stewart
authors: S
authors: Lowden
authors: Chris
authors: C
authors: Moran
references: J Mol Evol. 1985;22(2):160-74
references: 3934395
references: Bioinformatics. 2000 Jun;16(6):562-3
references: 10980155
references: Mol Phylogenet Evol. 2003 Jan;26(1):1-7
references: 12470932
references: Science. 1977 Oct 7;198(4312):13-21
references: 331477
references: Virus Genes. 2003 May;26(3):291-315
references: 12876457
references: Genetics. 2007 Jun;176(2):1035-47
references: 17409078
references: Syst Biol. 2004 Feb;53(1):47-67
references: 14965900
references: BMC Evol Biol. 2008 Oct 08;8:276
references: 18842133
references: Mol Biol Evol. 1989 Sep;6(5):526-38
references: 2677599
references: J Mol Evol. 1992 Feb;34(2):126-9
references: 1556748
references: Ann Med. 2004;36(7):504-17
references: 15513301
references: Mol Phylogenet Evol. 2008 Nov;49(2):618-28
references: 18801446
references: J Virol. 1998 Jul;72(7):5955-66
references: 9621058
references: Mol Biol Evol. 1992 Jan;9(1):138-51
references: 1552836
references: J Mol Evol. 1980 Dec;16(2):111-20
references: 7463489
references: Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13757-62
references: 11717435
references: Infect Genet Evol. 2011 Apr;11(3):686-93
references: 21256982
references: Nature. 2006 Oct 5;443(7111):521-4
references: 17024082
references: Annu Rev Genet. 2008;42:709-32
references: 18694346
references: BMC Evol Biol. 2009 May 11;9:95
references: 19432984
references: Nat Med. 1997 Mar;3(3):282-6
references: 9055854
references: BMC Evol Biol. 2006 Mar 24;6:29
references: 16563161
references: J Virol. 2005 Jan;79(1):649-54
references: 15596862
references: Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6815-9
references: 9192648
references: Mol Biol Evol. 2002 Oct;19(10):1727-36
references: 12270899
references: PLoS Biol. 2006 Nov;4(11):e352
references: 17105342
references: Virology. 1999 Dec 20;265(2):218-25
references: 10600594
references: Mol Biol Evol. 2007 Aug;24(8):1586-91
references: 17483113
references: Bioinformatics. 2001 Aug;17(8):754-5
references: 11524383
references: Nature. 2000 Sep 7;407(6800):27, 29-30
references: 10993056
references: Bioinformatics. 2002 Mar;18(3):502-4
references: 11934758
references: Methods Mol Biol. 2008;452:331-64
references: 18566772
references: Retrovirology. 2006 Oct 03;3:67
references: 17018135
references: Trends Ecol Evol. 2009 Jun;24(6):332-40
references: 19307040
references: J Virol. 1996 Nov;70(11):8241-6
references: 8892961
references: Mol Phylogenet Evol. 2008 Nov;49(2):669-73
references: 18778782
references: Annu Rev Genomics Hum Genet. 2008;9:217-31
references: 18767964
references: Curr Opin Genet Dev. 1992 Dec;2(6):861-7
references: 1335807
references: Mol Biol Evol. 2004 Oct;21(10):1902-12
references: 15215321
references: Mol Biol Evol. 2005 Apr;22(4):814-7
references: 15659556
references: Rev Sci Tech. 2005 Apr;24(1):335-42
references: 16110900
references: Mol Biol Evol. 1998 May;15(5):568-73
references: 9580986
references: Trends Genet. 2006 Apr;22(4):225-31
references: 16490279
references: Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11678-83
references: 14504385
references: Trends Microbiol. 2005 Oct;13(10):463-8
references: 16109487
references: J Gen Virol. 2001 Aug;82(Pt 8):1829-1834
references: 11457988
references: J Virol. 2001 Mar;75(6):2771-5
references: 11222700
references: J Biomed Inform. 2006 Feb;39(1):51-61
references: 16226061
references: Bioinformatics. 2003 Aug 12;19(12):1572-4
references: 12912839
references: Bioinformatics. 2005 Jan 15;21(2):260-2
references: 15377507
references: Lancet. 1998 Aug 29;352(9129):692-4
references: 9728985
references: J Virol. 2002 Nov;76(22):11738-43
references: 12388734
references: Mol Biol Evol. 2007 Aug;24(8):1596-9
references: 17488738
references: J Virol. 1998 Dec;72(12):9986-91
references: 9811736
references: Nat Med. 1995 Nov;1(11):1100
references: 7584963
references: J Virol. 2009 Oct;83(19):10305-8
references: 19605486
references: Trends Ecol Evol. 2007 May;22(5):258-65
references: 17300853
references: Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):4894-9
references: 15044706
references: J Gen Virol. 2006 Apr;87(Pt 4):977-986
references: 16528048
references: Trends Ecol Evol. 2000 Dec 1;15(12):496-503
references: 11114436
references: Virol J. 2006 Dec 05;3:101
references: 17147829
references: J Virol. 2008 Jan;82(1):582-7
references: 17959664
references: Comput Appl Biosci. 1996 Dec;12(6):543-8
references: 9021275
references: PLoS One. 2009;4(3):e5065
references: 19333384
references: Bioinformatics. 2000 Jul;16(7):573-82
references: 11038328
references: Evolution. 2004 Feb;58(2):404-15
references: 15068356
references: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references: 15034147
references: J Hered. 2001 Jul-Aug;92(4):371-3
references: 11535656