Time clustered sampling can inflate the inferred substitution rate in foot-and-mouth disease virus analyses

PLoS ONE

Volumn 10, Issue 12, 2015, Pages

  Pedersen, Casper Emil T ^a   Frandsen, Peter ^a   Wekesa, Sabenzia N ^b   Heller, Rasmus ^a   Sangula, Abraham K ^b   Wadsworth, Jemma ^c   Knowles, Nick J ^c   Muwanika, Vincent B ^d   Siegismund, Hans R ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b Wellcome Inst Res Foot and Mouth Dis   (Kenya)

^c INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

^d MAKERERE UNIVERSITY   (Uganda)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; CLADISTICS; CLUSTERED TEMPORAL SAMPLING; EPIDEMIC; FOOT AND MOUTH DISEASE VIRUS; GENE CLUSTER; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; NONHUMAN; PHYLOGENY; RNA SEQUENCE; SAMPLING; SEQUENCE ANALYSIS; SEROTYPE; VIRAL GENETICS; VIRUS EXAMINATION; VIRUS STRAIN; AFRICA; ANIMAL; BIOLOGICAL MODEL; CLASSIFICATION; FOOT-AND-MOUTH DISEASE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETICS; ISOLATION AND PURIFICATION; SEQUENCE ALIGNMENT; SEROTYPING; TIME FACTOR; VETERINARY; VIROLOGY;

VIRUS RNA;

AFRICA; ANIMALS; DISEASE OUTBREAKS; EVOLUTION, MOLECULAR; FOOT-AND-MOUTH DISEASE; FOOT-AND-MOUTH DISEASE VIRUS; MODELS, GENETIC; PHYLOGENY; RECOMBINATION, GENETIC; RNA, VIRAL; SELECTION, GENETIC; SEQUENCE ALIGNMENT; SEROTYPING; TIME FACTORS;

EID: 84955498966     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0143605     Document Type: Article

References (43)

1. Alexandersen S, Mowat N. Foot-and-mouth disease: host range and pathogenesis. Curr Top Microbiol Immunol. 2005; 288: 9-42. doi: 10.1007/b138628 PMID: 15648173
2. Bittle J, Houghten R, Alexander H. Protection against foot-and-mouth disease by immunization with a chemically synthesized peptide predicted from the viral nucleotide sequence. Nature. 1982; 298: 30-33. doi: 10.1038/298030a0 PMID: 7045684
3. Sangula AK, Belsham GJ, Muwanika VB, Heller R, Balinda SN, Siegismund HR. Co-circulation of two extremely divergent serotype SAT 2 lineages in Kenya highlights challenges to foot-and-mouth disease control. Arch Virol. 2010; 155: 1625-30. doi: 10.1007/s00705-010-0742-9 PMID: 20614146
4. Hall MD, Knowles NJ, Wadsworth J, Rambaut A, Woolhouse MEJ. Reconstructing geographical movements and host species transitions of foot-and-mouth disease virus serotype SAT 2. MBio. 2013; 4: e00591-13. doi: 10.1128/mBio.00591-13 PMID: 24149511
5. Wekesa SN, Sangula AK, Belsham GJ, Muwanika VB, Heller R, Balinda SN, et al. Genetic diversity of serotype A foot-and-mouth disease viruses in Kenya from 1964 to 2013; implications for control strategies in eastern Africa. Infect Genet Evol. 2013; 21: 408-417. doi: 10.1016/j.meegid.2013.12.006 PMID: 24368254
6. Bari FD, Parida S, Tekleghiorghis T, Dekker A, Sangula A, Reeve R, et al. Genetic and antigenic characterisation of serotype A FMD viruses from East Africa to select new vaccine strains. Vaccine. Elsevier Ltd; 2014; 32: 5794-5800. doi: 10.1016/j.vaccine.2014.08.033 PMID: 25171846
7. Di Nardo A, Knowles NJ, Wadsworth J, Haydon DT, King DP. Phylodynamic reconstruction of O CATHAY topotype foot-and-mouth disease virus epidemics in the Philippines. Vet Res. 2014; 45:90: 1-12. doi: 10.1186/s13567-014-0090-y PMID: 25209700
8. Grubman M, Baxt B. Foot-and-mouth disease. Clin Microbiol Rev. 2004; 17: 465-493. doi: 10.1128/ CMR.17.2.465-493.2004 PMID: 15084510
9. Knowles N, Samuel A. Molecular epidemiology of foot-and-mouth disease virus. Virus Res. 2003; 91: 65-80. http://dx.doi.org/10.1016/S0168-1702(02)00260-5 PMID: 12527438
10. Vosloo W, Bastos AD, Sangare O, Hargreaves SK, Thomsom GR. Review of the status and control of foot and mouth disease in sub-Saharan Africa. Rev Sci Tech. 2002; 21: 437-449. Available: http:// bvs1.panaftosa.org.br/local/file/textoc/Vosloo.pdf PMID: 12523685
11. Valdazo-González B, Knowles N, Hammond J, King DP. Genome sequences of SAT 2 foot-and-mouth disease viruses from Egypt and Palestinian Autonomous Territories (Gaza strip). J Virol. 2012; 86: 8901-8902. doi: 10.1128/JVI.01231-12 PMID: 22843860
12. Roeder P, Knowles N. Foot-and-mouth disease virus type C situation: the first target for eradication. Glob Control FMD - Tools, Ideas Ideals. 2009; Available: http://scholar.google.com/scholar?hl= en&btnG=Search&q=intitle:Foot-and-mouth+diseases+virus+type+C+:+the+first+target+for +eradication+?#5
13. Sangula AK, Siegismund HR, Belsham GJ, Balinda SN, Masembe C, Muwanika VB. Low diversity of foot-and-mouth disease serotype C virus in Kenya: evidence for probable vaccine strain re-introductions in the field. Epidemiol Infect. 2011; 139: 189-96. doi: 10.1017/S0950268810000580 PMID: 20334728
14. Vosloo W, Bastos AD, Kirkbride E, Esterhuysen JJ, van Rensburg DJ, Bengis RG, et al. Persistent infection of African buffalo (Syncerus caffer) with SAT-type foot-and-mouth disease viruses: rate of fixation of mutations, antigenic change and interspecies. J Gen Virol. 1996; 77: 1457-1467. Available: http://vir.sgmjournals.org/content/77/7/1457.short PMID: 8757987
15. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiol Rev. 1992; 56: 152-179. PMID: 1579108
16. Duchêne S, Holmes EC, Ho SYW. Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proc B R Soc. 2014; 281: 20140732. doi: 10.1098/rspb.2014. 0732
17. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, et al. Time-dependent rates of molecular evolution. Molecular Ecology. 2011. pp. 3087-3101. doi: 10.1111/j.1365-294X.2011.05178. x PMID: 21740474
18. Duffy S, Shackelton L a, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet. 2008; 9: 267-76. doi: 10.1038/nrg2323 PMID: 18319742
19. Cottam EM, Haydon DT, Paton DJ, Gloster J, Wilesmith JW, Ferris NP, et al. Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001. J Virol. 2006; 80: 11274-82. doi: 10.1128/JVI.01236-06 PMID: 16971422
20. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012; 29: 1969-1973. doi: 10.1093/molbev/mss075 PMID: 22367748
21. Binder H. Terrestrial Animal Health Code 2004 (OIE). Schweiz Arch Tierheilkd. 2005; 147: 0143-0143. doi: 10.1024/0036-7281.147.3.143a
22. Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, et al. ClustalW and ClustalX version 2. Bioinformatics. 2007; 23: 2947-2948. doi: 10.1093/bioinformatics/btm404 PMID: 17846036
23. Darriba D, Taboada G, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012; 9: 772-772. doi: 10.1038/nmeth.2109 PMID: 22847109
24. Rodriguez F, Oliver J, Marin A, Medina J. The general stochastic model of nucleotide substitution. J Theor Biol. 1990; 142: 485-501. doi: 10.1016/S0022-5193(05)80104-3 PMID: 2338834
25. Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985; 22: 160-174. doi: 10.1007/BF02101694 PMID: 3934395
26. Drummond A, Rambaut A. Tracer v1. 1. Available from http//beast.bio.ed.ac.uk/Tracer. 2007; Accessed 30 Okt. 2014. Available: http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle: Tracer+V1.5#1
27. Ramsden C, Holmes EC, Charleston M a. Hantavirus evolution in relation to its rodent and insectivore hosts: No evidence for codivergence. Mol Biol Evol. 2009; 26: 143-153. doi: 10.1093/molbev/msn234 PMID: 18922760
28. Firth C, Kitchen a., Shapiro B, Suchard M a., Holmes EC, Rambaut a. Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses. Mol Biol Evol. 2010; 27: 2038-2051. doi: 10.1093/molbev/msq088 PMID: 20363828
29. Pond S, Frost S. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 2005; 22: 1208-1222. doi: 10.1093/molbev/msi105 PMID: 15703242
30. Pond S, Posada D, Gravenor M. Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol. 2006; 23: 1891-1901. doi: 10.1093/molbev/msl051 PMID: 16818476
31. Martin D, Lemey P, Lott M, Moulton V. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics. 2010; 26: 2462-2463. doi: 10.1093/bioinformatics/btq467 PMID: 20798170
32. Posada D, Crandall K. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci. 2001; 98: 13757-13762. doi: 10.1073/pnas.241370698 PMID: 11717435
33. Padidam M, Sawyer S, Fauquet C. Possible emergence of new geminiviruses by frequent recombination. Virology. 1999; 265: 218-225. doi: 10.1006/viro.1999.0056 PMID: 10600594
34. Smith J. Analyzing the mosaic structure of genes. J Mol Evol. 1992; 34: 126-129. doi: 10.1007/ BF00182389 PMID: 1556748
35. Schierup MH, Hein J. Consequences of recombination on traditional phylogenetic analysis. Genetics. 2000; 156: 879-891. PMID: 11014833
36. Jackson A, O'neill H. Mosaic structure of foot-and-mouth disease virus genomes. J Gen Virol. 2007; 88: 487-492. doi: 10.1099/vir.0.82555-0 PMID: 17251567
37. Ho SYW, Phillips MJ, Cooper A, Drummond AJ. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 2005; 22: 1561-8. doi: 10.1093/ molbev/msi145 PMID: 15814826
38. Murray GGR, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, et al. The effect of genetic structure on molecular dating and tests for temporal signal. Methods Ecol Evol. 2015; n/a-n/a.
39. Duchêne S, Duchêne D, Holmes EC, Ho SYW. The performance of the date-randomisation test in phylogenetic analyses of time-structured virus data. Mol Biol Evol. 2015; msv056. doi: 10.1093/molbev/ msv056 PMID: 25771196
40. Ho SYW, Kolokotronis S-O, Allaby RG. Elevated substitution rates estimated from ancient DNA sequences. Biol Lett. 2007; 3: 702-705. doi: 10.1098/rsbl.2007.0377 PMID: 17785261
41. Samuel AR, Knowles NJ. Foot-and-mouth disease type O viruses exhibit genetically and geographically distinct evolutionary lineages (topotypes). J Gen Virol. 2001; 82: 609-21. Available: http://www. ncbi.nlm.nih.gov/pubmed/11172103 PMID: 11172103
42. Bastos AD, Haydon DT, Forsberg R, Knowles NJ, Anderson EC, Bengis RG, et al. Genetic heterogeneity of SAT-1 type foot-and-mouth disease viruses in southern Africa. Arch Virol. 2001; 146: 1537-51. Available: http://www.ncbi.nlm.nih.gov/pubmed/11676416 PMID: 11676416
43. Heller R, Chikhi L, Siegismund HR. The confounding effect of population structure on Bayesian skyline plot inferences of demographic history. PLoS One. 2013; 8. doi: 10.1371/journal.pone.0062992 PMID: 23667558