Nature Biotechnology
14, 491 - 493 (1996)
doi:10.1038/nbt0496-491
Detection of evolving virusesYih Lee1
& John Yin*
1Biotechnology and Biochemical Engineering Program, Thayer School of Engineering, Dartmouth College, Hanover, NH 03755-8000.
*Corresponding author (e-mail: jyin@dartmouth.edu). The spread of viruses on a homogeneous lawn of receptive hosts provides an opportunity to detect the dynamics of their evolution. We have previously found that when repeated virus passages are confined to the expanding perimeter of a growing plaque, the appearance and outgrowth of genetically diverse strains (all descended from the same parent strain) can be traced along different radii of the plaque. As a plaque grows, the random mutation and selection of new fast-growing strains reduce the roundness or circularity of the growing plaque. Here we have quantified such changes in growing plaques of bacteriophage T7 using a digital imaging system. We find that T7 populations not adapted for fast growth exhibit a broader diversity of growth rates than populations adapted for fast growth. These results provide a foundation for understanding how viruses exploit mutation and selection processes to persist in nature.
REFERENCES
- Debyser, Z., De Vreese, K., Knops-Gerrits, P.P., Baekelandt, V., Bhikhabhai, R., Strandberg, B., et al. 1993. Kinetics of different human immunodeficiency virus type 1 reverse transcriptases resistant to human immunodeficiency virus type 1-specific reverse transcriptase inhibitors. Mol. Pharmacol. 43: 521−526. | PubMed | ISI | ChemPort |
- Domingo, E. 1989. RNA virus evolution and the control of viral disease. Prog. Drug Res. 33: 93−133. | PubMed | ChemPort |
- Ecomoto, N., Sato, C., Kurosaki, M., and Marumo, F. 1994. Hepatitis C virus after interferon treatment has the variation in the hypervariable region of envelope 2 gene. J. Hepatol. 20: 252−261. | PubMed |
- el-Farrash, M.A., Kuroda, M.J., Kitazaki, T., Masuda, T., Kato, K., Hatanaka, M., et al. 1994. Generation and characterization of a human immunodeficiency virus type 1 (HIV-1) mutant resistant to an HIV-1 protease inhibitor. J. Virol. 68: 233−239. | PubMed | ChemPort |
- Heinz, B.A., Rueckert, R.R., Shepard, D.A., Dutko, F.J., McKinlay, M.A., Fancher, M., et al. 1989. Genetic and molecular analysis of spontaneous mutants of human rhinovirus 14 that are resistant to an antiviral compound. J. Virol. 63: 2476−2485. | PubMed | ISI | ChemPort |
- Jacobsen, H., Yasargil, K., Winslow, D.L., Craig, J.C., Krohn, A., Duncan, I.B., et al. 1995. Characterization of human immunodeficiency virus type 1 mutants with decreased sensitivity to proteinase inhibitor Ro 31-8959. Virol. 206: 527−534. | ISI | ChemPort |
- Lisziewicz, J., Sun, D., Klotman, M., Agrawal, S., Zamecnik, P., and Gallo, R. 1992. Specific inhibition of human immunodeficiency virus type 1 replication by antisense oligonucleotides: an in vitro model for treatment. Proc. Natl. Acad. Sci. USA 89: 11209−11213. | PubMed | ChemPort |
- Merigan, T.C. and Kundu, S.K. 1994. Human immunodeficiency virus envelope glycoproteins. J. AIDS [7 Suppl.] 1: S14−20.
- Pircher, H., Moskophidis, D., Rohrer, U., Burki, K., Hengartner, H., and Zinkernagel, R.M. 1990. Viral escape by selection of cytotoxic T cell-resistant virus variants in vivo. Nature 346: 629−633. | Article | PubMed | ISI | ChemPort |
- Smerdon, S.J., Jager, J., Wang, J., Kohlstaedt, L.A., Chirino, A.J., Friedman, J.M., et al. 1994. Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1. Proc. Natl. Acad. Sci. USA 91: 3911−3915. | PubMed | ChemPort |
- Buonagurio, D.A., Nakada, S., Parvin, J.D., Krystal, M., Palese, P., and Fitch, W.M. 1986. Evolution of human influenza A viruses over 50 years: rapid, uniform rate of change in NS gene. Science 232: 980−982. | PubMed | ISI | ChemPort |
- Cane, P.A. and Pringle, C.R. 1995. Evolution of subgroup A respiratory syncy-tial virus: evidence for progressive accumulation of amino acid changes in the attachment protein. J. Virol. 69: 2918−2925. | PubMed | ISI | ChemPort |
- Goodenow, M., Huet, T., Saurin, W., Kwok, S., Sninsky, J., and Wain-Hobson, S. 1989. HIV-1 isolates are rapidly evolving quasispecies: evidence for viral mixtures and preferred nucleotide substitutions. J. AIDS 2: 344−352. | ChemPort |
- Linnemann, C.C.J., Biron, K.K., Hoppenjans, W.G., and Solinger, A.M. 1990. Emergence of acyclovir-resistant varicella zoster virus in an AIDS patient on prolonged acyclovir therapy. AIDS 4: 577−579. | PubMed | ISI |
- Buynak, E.B. and Hilleman, M.R. 1966. Live attenuated mumps virus vaccine. 1. Vaccine development. Proc. Soc. Exp. Biol. Med. 123: 768−775. | PubMed | ISI | ChemPort |
- Clarke, D.K., Duarte, E.A., Moya, A., Elena, S.F., Domingo, E., and Holland, J. 1993. Genetic bottlenecks and population passages cause profound fitness differences in RNA viruses. J. Virol. 67: 222−228. | PubMed | ISI | ChemPort |
- Domingo, E., Sabo, D., Taniguchi, T., and Weissmann, C. 1978. Nucleotide sequence heterogeneity of an RNA phage population. Cell 13: 735−744. | Article | PubMed | ISI | ChemPort |
- Kong, D. and Yin, J. 1995. Whole-virus vaccine development by continuous culture on a complementing host. Bio/Technology 13: 583−586. | PubMed | ISI | ChemPort |
- Larder, B.A., Coates, K.E., and Kemp, S.D. 1991. Zidovudine-resistant human immunodeficiency virus selected by passage in cell culture. J. Virol. 65: 5232−5236. | PubMed | ISI | ChemPort |
- Durbin, R., Kane, A., and Stollar, V. 1991. A mutant of Sindbis virus with altered plaque morphology and a decreased ratio of 26 S:49 S RNA synthesis in mosquito cells. Virol. 183: 306−312. | ISI | ChemPort |
- Palca, J. 1992. Errant HIV strain renders test virus stock useless. Science 256: 1387−1388. | PubMed | ISI | ChemPort |
- Tikhonenko, A.T. and Linial, M.L. 1993. Transforming variants of the avian myc-containing retrovirus FH3 arise prior to phenotypic selection. J. Virol. 67: 3635−3638. | PubMed | ISI | ChemPort |
- Bauer, G.J., McCaskill, J.S., and Otten, H. 1989. Traveling waves of in vitroevolving RNA. Proc. Natl. Acad. Sci. USA 86: 7937−7941. | PubMed | ChemPort |
- McCaskill, J.S. and Bauer, G.J. 1993. Images of evolution: origin of spontaneous RNA replication waves. Proc. Natl. Acad. Sci. USA 90: 4191−4195. | PubMed | ChemPort |
- Yin, J. 1993. Evolution of bacteriophage T7 in a growing plaque. J. Bacteriol. 175: 1272−1277. | PubMed | ISI | ChemPort |
- Yin, J. 1991. A quantifiable phenotype of viral propagation. Biochem. Biophys. Res. Comm. 174: 1009−1014. | PubMed | ISI | ChemPort |
- Yin, J. and McCaskill, J.S. 1992. Replication of viruses in a growing plaque: a reaction-diffusion model. Biophys. J. 61: 1540−1549. | PubMed | ISI | ChemPort |
- Adams, M.H. 1959. Bacteriophages. Interscience Publishers, New York.
- Miller, J.H. 1972. Experiments in Molecular Genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
- Studier, F.W. 1969. The genetics and physiology of bacteriophage T7. Virol. 39: 562−574. | Article | ISI | ChemPort |
- Gonzalez, R.C. and Woods, R.E. 1992. Digital Image Processing. Addison-Wesley Publishing Company, Inc., New York.
|
