1887

Abstract

We have applied tests for detecting recombination to genes of foot-and-mouth disease virus (FMDV). Our approach estimated summary statistics of linkage disequilibrium (LD), which are sensitive to recombination. Using the genealogical relationships, rate heterogeneity and mutation parameters estimated from individual sets of aligned gene sequences, we simulated matching RNA sequence datasets without recombination. These simulated datasets allowed for recurrent mutations at any site to mimic homoplasy in virus sequence data and allow construction of null distributions for LD parameters expected in the absence of recombination. We tested for recombination in two ways: by comparing LD in observed data with corresponding null distributions obtained from simulated data; and by testing for a negative relationship between observed LD between pairs of polymorphic nucleotide sites and inter-site distance. We applied these tests to six FMDV datasets from four serotypes and found some evidence for recombination in all of them.

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2004-05-01
2024-04-25
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References

  1. Anisimova M., Nielsen R., Yang Z. 2003; Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229–1236
    [Google Scholar]
  2. Awadalla P. 2003; The evolutionary genomics of pathogen recombination. Nat Rev Genet 4:50–60
    [Google Scholar]
  3. Awadalla P., Charlesworth D. 1999; Recombination and selection at Brassica self-incompatibility loci. Genetics 152:413–425
    [Google Scholar]
  4. Bastos A. D. S. 2001; Molecular epidemiology and diagnosis of SAT-type foot-and-mouth disease in southern Africa . PhD thesis University of Pretoria;
  5. Bastos A. D. S., Bertschinger H. J., Cordel C., van Vuuren C. D., Keet D., Bengis R. G., Grobler D. G., Thomson G. R. 1999; Possibility of sexual transmission of foot-and-mouth disease from African buffalo to cattle. Vet Rec 145:77–79
    [Google Scholar]
  6. Bastos A. D. S., Haydon D. T., Forsberg R., Knowles N. J., Anderson E. C., Bengis R. G., Nel L. H., Thomson G. R. 2001; Genetic heterogeneity of SAT-1 type foot-and-mouth disease viruses in southern Africa. Arch Virol 146:1537–1551
    [Google Scholar]
  7. Brown A. H. 1975; Sample sizes required to detect linkage disequilibrium between two or three loci. Theor Popul Biol 8:184–201
    [Google Scholar]
  8. Brown B., Oberste M. S., Maher K., Pallansch M. A. 2003; Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region. J Virol 77:8973–8984
    [Google Scholar]
  9. Conway D. J., Roper C., Oduola A. M., Arnot D. E., Kremsner P. G., Grobusch M. P., Curtis C. F., Greenwood B. M. 1999; High recombination rate in natural populations of Plasmodium falciparum . Proc Natl Acad Sci U S A 96:4506–4511
    [Google Scholar]
  10. Felsenstein J. 1993 phylip: Phylogeny Inference Package, version 3.5c Department of Genetics, University of Washington; Seattle, WA, USA:
    [Google Scholar]
  11. Grassly N. C., Holmes E. C. 1997; A likelihood method for the detection of selection and recombination using sequence data. Mol Biol Evol 14:239–247
    [Google Scholar]
  12. Hasegawa M., Kishino H., Yano T. 1985; Dating of the human–ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 21:160–174
    [Google Scholar]
  13. Hey J., Wakeley J. 1997; A coalescent estimator of the population recombination rate. Genetics 145:833–846
    [Google Scholar]
  14. Hill W. G., Robertson A. 1968; Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231
    [Google Scholar]
  15. Holmes E. C., Worobey M., Rambaut A. 1999; Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol 16:405–409
    [Google Scholar]
  16. Hudson R. R. 1987; Estimating the recombination parameter of a finite population model without selection. Genet Res 50:245–250
    [Google Scholar]
  17. Hudson R. R. 2001; Two-locus sampling distributions and their application. Genetics 159:1805–1817
    [Google Scholar]
  18. King A. M. Q. 1988; Preferred sites of recombination in poliovirus RNA: analysis of 40 intertypic cross-over sequences. Nucleic Acids Res 6:11705–11723
    [Google Scholar]
  19. King A. M. Q., McCahon D., Saunders K., Newman J. W., Slade W. R. 1985; Multiple sites of recombination within the RNA genome of foot-and-mouth disease virus. Virus Res 3:373–384
    [Google Scholar]
  20. Krebs O., Marquardt O. 1992; Identification and characterization of foot-and-mouth disease virus O1 Burgwedel/1987 as an intertypic recombinant. J Gen Virol 73:613–619
    [Google Scholar]
  21. Kuiken C., Thakallapalli R., Eskild A., de Ronde A. 2000; Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus. Am J Epidemiol 152:814–822
    [Google Scholar]
  22. Lewontin R. C. 1988; On measures of gametic disequilibrium. Genetics 120:841–847
    [Google Scholar]
  23. Liu H. M., Zheng D. P., Zhang L. B., Oberste M. S., Kew O. M., Pallansch M. A. 2003; Serial recombination during circulation of type 1 wild-vaccine recombinant polioviruses in China. J Virol 77:10994–11005
    [Google Scholar]
  24. Manly B. F. J. 1986; Randomization and regression methods for testing for associations with geographical, environmental and biological distances between populations. Res Popul Ecol 28:201–218
    [Google Scholar]
  25. Maynard Smith J. 1992; Analysing the mosaic structure of genes. J Mol Evol 34:126–129
    [Google Scholar]
  26. McVean G. A. T., Awadalla P., Fearnhead P. 2002; A coalescent based method for detecting and estimating recombination from gene sequences. Genetics 160:1231–1241
    [Google Scholar]
  27. Plikat U., NieseltStruwe K., Meyerhans A. 1997; Genetic drift can dominate short-term human immunodeficiency virus type 1 nef quasispecies evolution in vivo. J Virol 71:4233–4240
    [Google Scholar]
  28. Posada D., Crandall K. A. 2001; Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98:13757–13762
    [Google Scholar]
  29. Samuel A. R., Knowles N. J. 2001; Foot-and-mouth disease type 0 viruses exhibit genetically and geographically distinct lineages (topotypes). J Gen Virol 82:609–621
    [Google Scholar]
  30. Schaeffer S. W., Miller E. L. 1993; Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura . Genetics 135:541–552
    [Google Scholar]
  31. Schierup M. H., Hein J. 2000; Consequences of recombination on traditional phylogenetic analysis. Genetics 156:879–891
    [Google Scholar]
  32. Smith J. S. 2002; Molecular epidemiology. In Rabies pp  79–111 Edited by Jackson A. C., Wunner W. H. New York: Academic Press;
    [Google Scholar]
  33. Tosh C., Hemadri D., Sanyal A. 2002; Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus. J Gen Virol 83:2455–2460
    [Google Scholar]
  34. van Rensburg H., Haydon D., Fourie Joubert F., Bastos A. D. S., Heath L., Nel L. 2002; Genetic heterogeneity in the foot-and-mouth disease virus leader and 3C proteinase genes. Gene 289:19–29
    [Google Scholar]
  35. Wall J. D. 2000; A comparison of estimators of the population recombination rate. Mol Biol Evol 17:156–163
    [Google Scholar]
  36. Wise C. A., Srmal M., Easteal S. 1998; Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees. Genetics 148:409–421
    [Google Scholar]
  37. Worobey M. 2001; A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Mol Biol Evol 18:1425–1434
    [Google Scholar]
  38. Yang C. F., Naguib T., Yang S. J. 10 other authors 2003; Circulation of endemic type 2 vaccine-derived poliovirus in Egypt from 1983 to 1993. J Virol 77:8366–8377
    [Google Scholar]
  39. Yang Z. 1997; paml: a program package for phylogenetic analysis by maximum likelihood. CABIOS 15:555–556
    [Google Scholar]
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