Quasispecies composition and phylogenetic analysis of feline coronaviruses (FCoVs) in naturally infected cats

FEMS Immunology and Medical Microbiology

Volumn 39, Issue 2, 2003, Pages 141-147

  Battilani, Mara ^a   Coradin, Tiziana ^a   Scagliarini, Alessandra ^a   Ciulli, Sara ^a   Ostanello, Fabio ^a   Prosperi, Santino ^a   Morganti, Luigi ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Feline coronavirus; Phylogenetic analysis; Quasispecies

Indexed keywords

AMINO TERMINAL SEQUENCE; AMPLICON; ARTICLE; CAT DISEASE; CONTROLLED STUDY; CORONAVIRUS; CORRELATION ANALYSIS; DISEASE SEVERITY; GENETIC HETEROGENEITY; GENOMICS; GEOGRAPHICAL VARIATION (SPECIES); MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE STRAND CONFORMATION POLYMORPHISM; VIRUS GENOME; VIRUS INFECTION; VIRUS VIRULENCE;

EID: 0242475197     PISSN: 09288244     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0928-8244(03)00237-2     Document Type: Article

References (31)

1. De Vries A.A.F., Horzinek M.C., Rottier P.J.M., de Groot R.J. The genome organization of the Nidovirales: similarities and differences between Arteri-, Toro-, and Coronaviruses. Semin. Virol. 8:1997;33-47.
2. Pedersen N.C., Boyle J.F., Floyd K. Infection studies in kittens using feline infectious peritonitis virus propagated in cell culture. Am. J. Vet. Res. 42:1981;363-367.
3. Horzinek, M.C. and Lutz H. (2001) An update of feline infectious peritonitis. Vet. Sci. Tomorrow, 1, http://www.vetscite.org/cgi-bin/pw.exe/vst/reviews/index_1_0800.htm.
4. Vennema H., Poland A., Foley J., Pedersen N.C. Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses. Virology. 243:1998;150-157.
5. Herrewegh A.A.P.M., Mähler M., Hedrich H.J., Haagmans B.L., Egberink H.F., Horzinek M.C., Rottier P.J.M., de Groot R.J. Persistence and evolution of feline coronavirus in a closed cat breeding colony. Virology. 234:1997;349-363.
6. Eigen M. Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften. 58:1971;465-523.
7. Pedersen N.C. Virologic and immunologic aspects of feline infectious peritonitis virus infection. Adv. Exp. Med. Biol. 218:1987;529-550.
8. Horzinek M.C., Herrewegh A.A.P.M., de Groot R.J. Perspectives on feline coronavirus evolution. Feline Pract. 23:(3):1995;34-39.
9. Domingo E., Escarmis C., Sevilla N., Moya A., Elena S.F., Quer J., Novella I.S., Holland J.J. Basic concepts in RNA virus evolution. FASEB J. 10:1996;859-864.
10. Orita M., Iwahana H., Kanazawa H., Hayashi K., Sekiya T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA. 86:1989;2766-2770.
11. Orita M., Suzuki Y., Sekiya T., Hayashi K. Rapid and sensitive detection of point mutations and DNA polymorphims using the polymerase chain reaction. Genomics. 5:1989;874-879.
12. Gut M., Leutenegger C.M., Huder J.B., Pedersen N.C., Lutz H. One-tube fluorogenic reverse transcription-polymerase chain reaction for the quantitation of feline coronaviruses. J. Virol. Methods. 77:1999;37-46.
13. Kiss I., Kecskeméti S., Tanyi J., Klingeborn B., Belák S. Preliminary studies of feline coronavirus distribution in naturally and experimentally infected cats. Res. Vet. Sci. 68:2000;237-242.
14. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
15. Xia X., Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92:2001;371-373.
16. Nicholas K.B., Nicholas H.B. Jr., Deerfield D.W. GeneDoc: analysis and visualization of genetic variation. Embnew. News. 4:1997;14.
17. Swofford, D.L. (2001) PAUP* Phylogenetic Analysis Using Parsimony (*and other methods) 4.0b10. Sinauer Associates, Sunderland, MA.
18. Felsenstein J. Distance methods for inferring phylogenies: A justification. Evolution. 38:1984;16-24.
19. Hasegawa M., Kishino H., Yano T.-A. Dating of the human-ape splitting by a molecular clock of michondrial DNA. J. Mol. Evol. 22:1985;160-174.
20. 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. 10:1993;512-526.
21. Felsenstein, J. (2001) PHYLIP: Phylogenetic Inference Package 3.6 (alpha3). Distributed by the author, Department of Genetics, University of Washington, Seattle, WA.
22. Strimmer K., von Haeseler A. Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:1996;964-969.
23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:1985;783-791.
24. Page R.D. TreeView: an application to display phylogenetic trees on personal computers. Mol. Biol. Evol. 4:1996;406-425.
25. Strimmer K., von Haeseler A. Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. USA. 94:1997;6815-6819.
26. Eigen, E. and Biebricher, C. (1988) Sequence space and quasispecies distribution. In: RNA Genetics, Vol. 3 (Domingo, E., Holland, J.J. and Ahlquist, P., Eds.), pp. 211-245. CRC Press, Boca Raton, FL.
27. Domingo E., Holland J.J. RNA virus mutations and fitness for survival. Annu. Rev. Microbiol. 51:1997;151-178.
28. Makino S., Keck J.G., Stohlman S.A., Lai M.M.C. High-frequency RNA recombination of murine coronaviruses. J. Virol. 57:1986;729-739.
29. Gunn-Moore D.A., Gunn-Moore F.J., Gruffydd-Jones T.J., Harbour D.A. Detection of FCoV quasispecies using denaturing gel electrophoresis. Vet. Microbiol. 69:1999;127-130.
30. Domingo E. Quasispecies and the implication for virus persistence and escape. Clin. Diagn. Virol. 10:1998;97-101.
31. Herrewegh A.A.P.M., Vennema H., Horzinek M.C., Rottier P.J.M., de Groot R.J. The molecular genetics of feline coronaviruses: comparative sequence analysis of the ORF 7a/7b transcription unit of different biotypes. Virology. 212:1995;622-631.