Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments

Journal of General Virology

Volumn 85, Issue 5, 2004, Pages 1095-1100

  Haydon, Daniel T ^a,d   Bastos, Armanda D S ^b   Awadalla, Philip ^c  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF PRETORIA   (South Africa)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ARTICLE; CONTROLLED STUDY; FOOT AND MOUTH DISEASE VIRUS; GENE LINKAGE DISEQUILIBRIUM; GENEALOGY; GENETIC DISTANCE; GENETIC HETEROGENEITY; HOMOPLASY; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEROTYPE; SIMULATION; VIRUS RECOMBINATION;

CAPSID PROTEINS; FOOT-AND-MOUTH DISEASE VIRUS; GENES, VIRAL; LINKAGE DISEQUILIBRIUM; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, RNA;

FOOT-AND-MOUTH DISEASE VIRUS;

EID: 2442692750     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/vir.0.19588-0     Document Type: Article

References (39)

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.
2. Awadalla, P. (2003). The evolutionary genomics of pathogen recombination. Nat Rev Genet 4, 50-60.
3. Awadalla, P. & Charlesworth, D. (1999). Recombination and selection at Brassica self-incompatibility loci. Genetics 152, 413-425.
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.
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.
7. Brown, A. H. (1975). Sample sizes required to detect linkage disequilibrium between two or three loci. Theor Popul Biol 8, 184-201.
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.
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.
10. Felsenstein, J. (1993). PHYLIP: Phylogeny Inference Package, version 3.5c. Department of Genetics, University of Washington, Seattle, WA, USA.
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.
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.
13. Hey, J. & Wakeley, J. (1997). A coalescent estimator of the population recombination rate. Genetics 145, 833-846.
14. Hill, W. G. & Robertson, A. (1968). Linkage disequilibrium in finite populations. Theor Appl Genet 38, 226-231.
15. Holmes, E. C., Worobey, M. & Rambaut, A. (1999). Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol 16, 405-409.
16. Hudson, R. R. (1987). Estimating the recombination parameter of a finite population model without selection. Genet Res 50, 245-250.
17. Hudson, R. R. (2001). Two-locus sampling distributions and their application. Genetics 159, 1805-1817.
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.
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.
20. Krebs, O. & Marquardt O. (11992). Identification and characterization of foot-and-mouth disease virus O1 Burgwedel/1987 as an intertypic recombinant. J Gen Virol 73, 613-619.
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.
22. Lewontin, R. C. (1988). On measures of gametic disequilibrium. Genetics 120, 841-847.
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.
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.
25. Maynard Smith, J. (1992). Analysing the mosaic structure of genes. J Mol Evol 34, 126-129.
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.
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.
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, 13757-0762.
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.
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.
31. Schierup, M. H. & Hein, J. (2000). Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879-891.
32. Smith, J. S. (2002). Molecular epidemiology. In Rabies, pp. 79-111. Edited by A. C. Jackson & W. H. Wunner. New York: Academic Press.
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.
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.
35. Wall, J. D. (2000). A comparison of estimators of the population recombination rate. Mol Biol Evol 17, 156-163.
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.
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.
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.
39. Yang, Z. (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 15, 555-556.