Molecular evolution of peste des petits ruminants virus

Emerging Infectious Diseases

Volumn 20, Issue 12, 2014, Pages 2023-2033

  Muniraju, Murali ^a   Munir, Muhammad ^a   Parthiban, Aravindhbabu R ^b   Banyard, Ashley C ^c   Bao, Jingyue ^d   Wang, Zhiliang ^d   Ayebazibwe, Chrisostom ^e   Ayelet, Gelagay ^f   El Harrak, Mehdi ^g   Mahapatra, Mana ^a   Libeau, Geneviève ^h   Batten, Carrie ^a   Parida, Satya ^a,b  

^a INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

^b UNIVERSITY OF HYDERABAD   (India)

^c VETERINARY LABORATORIES AGENCY   (United Kingdom)

^d China Animal Health and Epidemiology Center   (China)

^e National Animal Disease Diagnostics and Epidemiology Centre   (Uganda)

^f NATIONAL VETERINARY INSTITUTE   (Ethiopia)

^g Société de Productions Biologiques et Pharmaceutiques Vétérinaires   (Morocco)

^h CIRAD   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; CONTROLLED STUDY; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PESTE-DES-PETITS-RUMINANTS VIRUS; PHYLOGENETIC TREE; SCORING SYSTEM; SEQUENCE ANALYSIS; AFRICA; ANIMAL; BIOLOGY; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIATION; GENETICS; OPEN READING FRAME; PESTE-DES-PETITS-RUMINANTS; PHYLOGENY; PHYLOGEOGRAPHY; VIROLOGY; VIRUS GENOME;

AFRICA; ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; OPEN READING FRAMES; PESTE-DES-PETITS-RUMINANTS; PESTE-DES-PETITS-RUMINANTS VIRUS; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA;

EID: 84922417166     PISSN: 10806040     EISSN: 10806059     Source Type: Journal    
DOI: 10.3201/eid2012.140684     Document Type: Article

References (40)

1. Dhar P, Sreenivasa BP, Barrett T, Corteyn M, Singh RP, Bandyopadhyay SK. Recent epidemiology of peste des petits ruminants virus (PPRV). Vet Microbiol. 2002;88:153–9. http://dx.doi.org/10.1016/S0378-1135(02)00102-5
2. Banyard AC, Parida S, Batten C, Oura C, Kwiatek O, Libeau G. Global distribution of peste des petits ruminants virus and prospects for improved diagnosis and control. J Gen Virol. 2010;91:2885–97. http://dx.doi.org/10.1099/vir.0.025841-0
3. Gibbs EP, Taylor WP, Lawman MJ, Bryant J. Classification of peste des petits ruminants virus as the fourth member of the genus Morbillivirus. Intervirology. 1979;11:268–74. http://dx.doi. org/10.1159/000149044
4. de Swart RL, Duprex WP, Osterhaus AD. Rinderpest eradication: lessons for measles eradication? Curr Opin Virol. 2012;2:330–4. http://dx.doi.org/10.1016/j.coviro.2012.02.010
5. Baron MD, Parida S, Oura CA. Peste des petits ruminants: a suitable candidate for eradication? Vet Rec. 2011;169:16–21. http://dx.doi.org/10.1136/vr.d3947
6. Lembo T, Oura C, Parida S, Hoare R, Frost L, Fyumagwa R, et al. Peste des petits ruminants infection among cattle and wildlife in northern Tanzania. Emerg Infect Dis. 2013;19:2037–40. http://dx.doi.org/10.3201/eid1912.130973
7. Balamurugan V, Sen A, Venkatesan G, Bhanot V, Yadav V, Bhanuprakash V, et al. Peste des petits ruminants virus detected in tissues from an Asiatic lion (Panthera leo persica) belongs to Asian lineage IV. J Vet Sci. 2012;13:203–6. http://dx.doi.org/10.4142/jvs.2012.13.2.203
8. Khalafalla AI, Saeed IK, Ali YH, Abdurrahman MB, Kwiatek O, Libeau G, et al. An outbreak of peste des petits ruminants (PPR) in camels in the Sudan. Acta Trop. 2010;116:161–5. http://dx.doi.org/10.1016/j.actatropica.2010.08.002
9. Food and Agriculture Organization of the United Nations. Supporting livelihoods and supporting livelihoods and peste des petits ruminants (ppr) and small ruminant diseases control, 2013 [cited 2014 Sep 2]. http://www.fao.org/docrep/017/aq236e/aq236e00.htm
10. Libeau G, Diallo A, Parida S. Evolutionary genetics underlying the spread of peste des petits ruminants virus. Animal Frontiers. 2014;4:14–20. http://dx.doi.org/10.2527/af.2014-0003
11. Pybus OG, Rambaut A. Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet. 2009;10:540–50. http://dx.doi.org/10.1038/nrg2583
12. Muniraju M, El Harrak M, Bao J, Ramasamy Parthiban AB, Banyard AC, Batten C, et al. Complete genome sequence of a peste des petits ruminants virus recovered from an alpine goat during an outbreak in Morocco in 2008. Genome Announc. 2013;1:e00096–13. http://dx.doi.org/10.1128/genomeA.00096-13
13. Chard LS, Bailey DS, Dash P, Banyard AC, Barrett T. Full genome sequences of two virulent strains of peste-des-petits ruminants virus, the Côte d’Ivoire 1989 and Nigeria 1976 strains. Virus Res. 2008;136:192–7. http://dx.doi.org/10.1016/j.virusres.2008.04.018
14. Diallo A, Barrett T, Barbron M, Meyer G, Lefevre PC. Cloning of the nucleocapsid protein gene of peste-des-petits-ruminants virus: relationship to other morbilliviruses. J Gen Virol. 1994;75:233–7. http://dx.doi.org/10.1099/0022-1317-75-1-233
15. Furley CW, Taylor WP, Obi TU. An outbreak of peste des petits ruminants in a zoological collection. Vet Rec. 1987;121:443–7. http://dx.doi.org/10.1136/vr.121.19.443
16. Taylor WP, al Busaidy S, Barrett T. The epidemiology of peste des petits ruminants in the Sultanate of Oman. Vet Microbiol. 1990;22:341–52. http://dx.doi.org/10.1016/0378-1135(90)90021-M
17. Roeder PL, Abraham G, Kenfe G, Barrett T. Peste des petits ruminants in Ethiopian goats. Trop Anim Health Prod. 1994;26:69–73. http://dx.doi.org/10.1007/BF02239901
18. Bao J, Wang Q, Parida S, Liu C, Zhang L, Zhao W, et al. Complete genome sequence of a peste des petits ruminants virus recovered from wild bharal in Tibet, China. J Virol. 2012;86:10885–6. http://dx.doi.org/10.1128/JVI.01503-12
19. Wang Z, Bao J, Wu X, Liu Y, Li L, Liu C, et al. Peste des petits ruminants virus in Tibet, China. Emerg Infect Dis. 2009;15:299–301. http://dx.doi.org/10.3201/eid1502.080817
20. Bailey D, Banyard A, Dash P, Ozkul A, Barrett T. Full genome sequence of peste des petits ruminants virus, a member of the Morbillivirus genus. Virus Res. 2005;110:119–24. http://dx.doi.org/10.1016/j.virusres.2005.01.013
21. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 1999;41:95–8.
22. Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005;21:676–9. http://dx.doi.org/10.1093/bioinformatics/bti079
23. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–73. http://dx.doi.org/10.1093/molbev/mss075
24. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES science gateway for inference of large phylogenetic trees. Presented at: Proceedings of the Gateway Computing Environments Workshop (GCE); 2010 Nov 14; New Orleans, Louisiana, USA; p. 1–8.
25. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008;25:1253–6. http://dx.doi.org/10.1093/molbev/msn083
26. Kass RE, Raftery AE. Bayes factors. Journal of the American Statistical Association. 1995;90:773–95. http://dx.doi.org/10.1080/01621459.1995.10476572
27. Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots. PLOS Comput Biol. 2009;5:e1000520. http://dx.doi.org/10.1371/journal.pcbi.1000520
28. Radecke F, Spielhofer P, Schneider H, Kaelin K, Huber M, Dotsch C, et al. Rescue of measles viruses from cloned DNA. EMBO J. 1995;14:5773–84.
29. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986;3:418–26.
30. Han GZ, Worobey M. Homologous recombination in negative sense RNA viruses. Viruses. 2011;3:1358–73. http://dx.doi.org/10.3390/v3081358
31. Denison MR, Graham RL, Donaldson EF, Eckerle LD, Baric RS. Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity. RNA Biol. 2011;8:270–9. http://dx.doi.org/10.4161/rna.8.2.15013
32. Pomeroy LW, Bjornstad ON, Holmes EC. The evolutionary and epidemiological dynamics of the paramyxoviridae. J Mol Evol. 2008;66:98–106. http://dx.doi.org/10.1007/s00239-007-9040-x
33. Furuse Y, Suzuki A, Oshitani H. Origin of measles virus: divergence from rinderpest virus between the 11th and 12th centuries. Virol J. 2010;7:52. http://dx.doi.org/10.1186/1743-422X-7-52
34. Wertheim JO, Kosakovsky Pond SL. Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol. 2011;28:3355–65. http://dx.doi.org/10.1093/molbev/msr170
35. Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol. 2002;54:156–65. http://dx.doi.org/10.1007/s00239-001-0064-3
36. Gargadennec L, Lalanne A. Peste des petits ruminants [in French]. Bulletin des Services Zootechniques et des Epizzoties de l’Afrique Occidentale Francaise. 1942;5:16–21.
37. Biek R, Drummond AJ, Poss M. A virus reveals population structure and recent demographic history of its carnivore host. Science. 2006;311:538–41. http://dx.doi.org/10.1126/science.1121360
38. Lemey P, Suchard M, Rambaut A. Reconstructing the initial global spread of a human influenza pandemic: a Bayesian spatialtemporal model for the global spread of H1N1pdm. PLoS Curr. 2009;1:RRN1031. http://dx.doi.org/10.1371/currents.RRN1031
39. Diallo A. Rinderpest and peste des petits ruminants. Constant threats against livestock in many countries [in French]. Impact of Science on Society. 1988;150:191–204.
40. Sen A, Saravanan P, Balamurugan V, Rajak KK, Sudhakar SB, Bhanuprakash V, et al. Vaccines against peste des petits ruminants virus. Expert Rev Vaccines. 2010;9:785–96. http://dx.doi.org/10.1586/erv.10.74