Phylogenetic networks to study the origin and evolution of porcine circovirus type 2 (PCV2) in Cuba

Veterinary Microbiology

Volumn 151, Issue 3-4, 2011, Pages 245-254

  Pérez, Lester J ^a   De Arce, Heidy Díaz ^a   Cortey, Martí ^b   Domínguez, Patricia ^a   Percedo, Maria I ^a   Perera, Carmen L ^a   Tarradas, Joan ^b   Frías, Maria T ^a   Segalés, Joaquim ^b,c   Ganges, Llilianne ^b   Núñez, José I ^b  

^a CENTRO NACIONAL DE SANIDAD AGROPECUARIA CENSA   (Cuba)

^b CENTRE DE RECERCA EN SANITAT ANIMAL CRESA   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Classical phylogenetic trees; Geographic segregation; Phylogenetic networks; Porcine circovirus 2; Selection pressure

Indexed keywords

VIRUS ANTIBODY;

ARTICLE; BAYESIAN INFERENCE; CIRCOVIRUS; CONTROLLED STUDY; CUBA; GENETIC VARIABILITY; HAPLOTYPE; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; PHYLOGENOMICS; PORCINE CIRCOVIRUS TYPE 2; PORCINE CIRCOVIRUS TYPE 2 INFECTION; POSTWEANING MULTISYSTEMIC WASTING SYNDROME; RETROSPECTIVE STUDY; SWINE; SWINE DISEASE; VIRUS GENOME; VIRUS INFECTION; VIRUS STRAIN;

ANIMALS; ANTIBODIES, VIRAL; BAYES THEOREM; CIRCOVIRIDAE INFECTIONS; CIRCOVIRUS; CUBA; HAPLOTYPES; MODELS, GENETIC; ONTARIO; PHYLOGENY; PORCINE POSTWEANING MULTISYSTEMIC WASTING SYNDROME; PRINCIPAL COMPONENT ANALYSIS; QUEBEC; RETROSPECTIVE STUDIES; SEQUENCE ANALYSIS, DNA; SWINE;

PORCINE CIRCOVIRUS 2; RNA VIRUSES; SUIDAE;

EID: 79960157673     PISSN: 03781135     EISSN: 18732542     Source Type: Journal    
DOI: 10.1016/j.vetmic.2011.03.022     Document Type: Article

References (63)

1. Allan G., Krakowa S., Ellis J. PCV2: ticking the time bomb. Pig Prog. 2002, 18:13-15.
2. Anderson M.J. PCO: A FORTRAN Computer Program for Principal Coordinate Analysis 2003, Department of Statistics, University of Auckland, New Zealand.
3. Carman S., Cai H., DeLay J., Youssef S., McEwen B., Gagnon C., Tremblay D., Hazlett M., Lusis P., Fairles J., Alexander H., van Dreumel T. The emergence of a new strain of porcine circovirus-2 in Ontario and Quebec swine and its association with severe porcine circovirus associated disease-2004-2006. Can. J. Vet. Res. 2008, 72:259-268.
4. Cheung A.K., Lager K.M., Kohutyuk O.I., Vincent A.L., Henry S.C., Baker R.B., Rowland R.R., Dunham A.G. Detection of two porcine circovirus type 2 genotypic groups in United States swine herds. Arch. Virol. 2007, 152:1035-1044.
5. Chiarelli-Neto O., Yotoko K.S., Vidigal P.M., Silva F.M., Castro L.A., Fietto J.L., Silva A., Almeida M.R. Classification and putative origins of Brazilian porcine circovirus 2 inferred through phylogenetic and phylogeographical approaches. Virus Res. 2009, 140:57-63.
6. Clement M., Posada D., Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 2000, 9:1657-1660.
7. Cortey M., Pileri E., Sibila M., Pujols J., Balasch M., Plana J., Segalés J. Genotypic shift of porcine circovirus type 2 from PCV-2a to PCV-2b in Spain from 1985 to 2008. Vet. J. 2010, 10.1016/j.tvjl.2009.12.023.
8. Dupont K., Nielsen E.O., Baekbo P., Larsen L.E. Genomic analysis of PCV2 isolates from Danish archives and a current PMWS case-control study supports a shift in genotypes with time. Vet. Microbiol. 2008, 128:56-64.
9. Firth C., Charleston M.A., Duffy S., Shapiro B., Holmes E.C. Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. J. Virol. 2009, 83(24):12813-12821.
10. Gagnon C.A., Music N., Fontaine G., Tremblay D., Harel J. Emergence of a new type of porcine circovirus in swine (PCV): a type 1 and type 2 PCV recombinant. Vet. Microbiol. 2010, 10.1016/j.vetmic.2009.09.072.
11. Gagnon C.A., Tremblay D., Tijssen P., Venne M.-H., Houde A., Elahi S.M. The emergence of porcine circovirus 2b genotype (PCV-2b) in swine in Canada. Can. Vet. J. 2007, 48:811-819.
12. Grau-Roma L., Segalés J. Detection of porcine reproductive and respiratory syndrome virus, porcine circovirus type 2, swine influenza virus and Aujeszky's disease virus in cases of porcine proliferative and necrotizing pneumonia (PNP) in Spain. Vet. Microbiol. 2007, 119:144-151.
13. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 1999, 41:95-98.
14. Hesse R., Kerrigan M., Rowland R.R. Evidence for recombination between PCV2a and PCV2b in the field. Virus Res. 2008, 132:201-207.
15. Huelsenbeck J.H., Ronquist F., Nielsen R., Bollback J. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 2001, 294:2310-2314.
16. Kim J., Chung H.K., Chae C. Association of porcine circovirus 2 with porcine respiratory disease complex. Vet. J. 2003, 166:251-256.
17. Kishino H., Miyata T., Hasegawa M. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 1990, 30:151-160.
18. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 1989, 29:170-179.
19. Krakowka S., Ellis J.A., McNeilly F., Ringler S., Ring D.M., Allan G. Activation of the immune system is the pivotal event in the production of wasting disease in pigs infected with porcine circovirus-2 (PCV-2). Vet. Pathol. 2001, 38:31-42.
20. Krakowka S., Ellis J.A., Meehan B., Kennedy S., McNeilly F., Allan G. Viral wasting syndrome of swine: experimental reproduction of postweaning multisystemic wasting syndrome in gnotobiotic swine by coinfection with porcine circovirus 2 and porcine parvovirus. Vet. Pathol. 2000, 37:254-263.
21. Kühne M., Brown D.W.G., Jin L. Genetic variability of measles virus in acute and persistent infections. Infect. Genet. Evol. 2006, 6:269-276.
22. Kyriakis S.C., Saoulidis K., Lekkas S., Miliotis Ch C., Papoutsis P.A., Kennedy S. The effects of immuno-modulation on the clinical and pathological expression of postweaning multisystemic wasting syndrome. J. Comp. Pathol. 2002, 126:38-46.
23. Lager K.M., Gauger P.C., Vincent A.L., Opriessnig T., Kehrli M.E., Cheung A.K. Mortality in pigs given porcine circovirus type 2 subgroup 1 and 2 viruses derived from DNA clones. Vet. Rec. 2007, 161:428-429.
24. Larochelle R., Magar R., D'Allaire S. Genetic characterization and phylogenetic analysis of porcine circovirus type 2 (PCV2) strains from cases presenting various clinical conditions. Virus Res. 2002, 90:101-112.
25. Liu J., Chen I., Kwang J. Characterization of a previously unidentified viral protein in porcine circovirus type 2-infected cells and its role in virus induced apoptosis. J. Virol. 2005, 79:8262-8274.
26. Lohse L., Botner A., Hansen A.S.L., Frederiksen T., Dupont K., Christensen C., Bækbo P., Nielsen J. Examination for a viral co-factor in postweaning multisystemic wasting syndrome (PMWS). Vet. Microbiol. 2008, 129:97-107.
27. Lopez-Soria S., Segales J., Rose N., Vinas M.J., Blanchard P., Madec F., Jestin A., Casal J., Domingo M. An exploratory study on risk factors for postweaning multisystemic wasting syndrome (PMWS) in Spain. Prev. Vet. Med. 2005, 69:97-107.
28. Lowings P., Ibata G., Needham J., Paton D. Classical swine fever virus diversity and evolution. J. Gen. Virol. 1996, 77:1311-1321.
29. Ma C.M., Hon C.C., Lam T.Y., Li V.Y., Wong C.K., de Oliveira T., Leung F.C. Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and Mainland China. J. Gen. Virol. 2007, 88:1733-1737.
30. Madec F., Rose N., Grasland B., Cariolet R., Jestin A. Post-weaning multisystemic wasting syndrome and other PCV2-related problems in pigs: a 12-year experience. Transboundary Emerg. Dis. 2008, 55:273-283.
31. Manokaran G., Lin Y.-N., Soh M.-L., Lim, E A.-S., Lim C.-W., Tan B.-H. Detection of porcine circovirus type 2 in pigs imported from Indonesia. Vet. Microbiol. 2008, 132:165-170.
32. Martin D., Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 2000, 16:562-563.
33. Meerts P., Van Gucht S., Cox E., Vandebosch A., Nauwynck H.J. Correlation between type of adaptive immune response against porcine circovirus type 2 and level of virus replication. Viral Immunol. 2005, 18:333-341.
34. Misinzo G., Delputte P.L., Meerts P., Lefebvre D.J., Nauwynck H.J. Porcine circovirus 2 uses heparan sulfate and chondroitin sulfate B glycosaminoglycans as receptors for its attachment to host cells. J. Virol. 2006, 80:3487-3494.
35. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3:418-426.
36. Morrison D.A. Networks in phylogenetic analysis: new tools for population biology. Int. J. Parasitol. 2005, 35:567-582.
37. O'Connor B., Gauvreau H., West K., Bogdan J., Ayroud M., Clark E., Konoby C., Allan G., Ellis J.A. Multiple porcine circovirus 2 associated abortion and reproductive failure in a multiple-site swine production unit. Can. Vet. J. 2001, 42:551-553.
38. Ohlinger V.F., Schmidt U., Pesch S. Studies on pathogenic aspects of the postweaning multisystemic wasting syndrome (PMWS). Proceedings of the 16th International Pig Veterinary Society Congress 2000.
39. Olvera A., Busquets N., Cortey M., de Deus N., Ganges L., Núñez J.I., Peralta B., Toskano J., Dolz R. Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing. Vet. J. 2010, 184:130-137.
40. Olvera A., Cortey M., Segalés J. Molecular evolution of porcine circovirus type 2 genomes: phylogeny and clonality. Virology 2007, 357:175-185.
41. Opriessnig T., McKeown N.E., Zhou E.M., Meng X.J., Halbur P.G. Genetic and experimental comparison of porcine circovirus type 2 (PCV2) isolates from cases with and without PCV2-associated lesions provides evidence for differences in virulence. J. Gen. Virol. 2006, 87:2923-2932.
42. Pérez L.J., Díaz de Arce H., Frías M.T. Genetic characterization and phylogenetic analysis of porcine circovirus type 2 strains present in Cuban swine herds. Res. Vet. Sci. 2010, 10.1016/j.rvsc.2010.03.013.
43. Pérez L.J., Díaz de Arce H., Percedo M.I., Domínguez P., Frías M.T. First report of porcine circovirus type 2 infections in Cuba. Res. Vet. Sci. 2010, 88(3):528-530.
44. Posada D., Crandall K. ModelTest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
45. Ronquist F., Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
46. Rosell C., Segalés J., Ramos-Vara J.A., Folch J.M., Rodriguez-Arrioja G.M., Duran C.O., Balasch M., Plana-Duran J., Domingo M. Identification of porcine circovirus in tissues of pigs with porcine dermatitis and nephropathysyndrome. Vet. Rec. 2000, 146:40-43.
47. Rovira A., Balasch M., Segales J., Garcia L., Plana-Duran J., Rosell C., Ellerbrok H., Mankertz A., Domingo M. Experimental inoculation of conventional pigs with porcine reproductive and respiratory syndrome virus and porcine circovirus 2. J. Virol. 2002, 76:3232-3239.
48. Sandvik T., Grierson S., King D.P., Spencer Y., Banks M., Drew T. Detection and genetic typing of porcine circovirus DNA isolated from archived paraffin embedded pig tissues. Proceedings-ssDNA Viruses of Plants, Birds, Pigs and Primates 2001, (Comp. Virol.).
49. Segalés J., Allan G.M., Domingo M. Porcine circovirus diseases. Anim. Health Res. Rev. 2005, 6:119-142.
50. Segalés J., Olvera A., Grau-Roma L., Charreyre C., Nauwynck H., Larsen L., Dupont K., McCullough K., Ellis J., Krakowka S., Mankertz A., Fredholm M., Fossum C., Timmusk S., Stockhofe-Zurwieden N., Beattie V., Armstrong D., Grassland B., Baekbo P., Allan G. PCV-2 genotype definition and nomenclature. Vet. Rec. 2008, 162:867-868.
51. Shackelton L.A., Holmes E.C. Phylogenetic evidence for the rapid evolution of human B19 erythrovirus. J. Virol. 2006, 80:3666-3669.
52. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
53. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. 2002, Sinauer Associates, Sunderland, Massachusetts.
54. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
55. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993, 10:512-526.
56. Templeton A.R., Crandall K.A., Sing C.F. A cladistic analysis of phenotypic association with haplotypes inferred from restriction endonucleases mapping and DNA sequence data III Cladogram estimation. Genetics 1992, 132:619-633.
57. Timmusk S., Wallgren P., Belák K., Berg M., Fossum C. Genetic analysis of PCV2 capsid protein sequences reveals two main groups of Swedish isolates. International Conference on Animal Circoviruses and Associated Diseases 2005, p. 82.
58. Tomás A., Fernandes L.T., Valero O., Segalés J. A meta-analysis on experimental infections with porcine circovirus type 2 (PCV2). Vet. Microbiol. 2008, 132:260-273.
59. Umemura T., Tanaka Y., Kiyosawa K., Alter H.J., Shih J. Observation of positive selection within hypervariable regions of a newly identified DNA virus (SEN virus). FEBS Lett. 2002, 510(3):171.
60. West K.H., Bystrom J.M., Wojnarowicz C., Shantz N., Jacobson M., Allan G.M., Haines D.M., Clark E.G., Krakowka S., McNeilly F., Konoby C., Martin K., Ellis J.A. Myocarditis and abortion associated with intrauterine infection of sows with porcine circovirus 2. J. Vet. Diagn. Invest. 1999, 11:530-532.
61. Wiederkehr D.D., Sydler T., Buergi E., Haessig M., Zimmermann D., Pospischil A., Brugnera E., Sidler X. A new emerging genotype subgroup within PCV-2b dominates the PMWS epizooty in Switzerland. Vet. Microbiol. 2009, 136:27-35.
62. Xia X., Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 2001, 92(4):371-373.
63. Yang Z. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.