If you interested in the pathogenesis of the virus you could apply immunological techniques (i.e. antibody-based detection methods) for analysis of various proteins. Howevr, this would require either the availability of monoclonal antibodies to various proteins of the virus and / or the production of monospecific anti-sera by inoculating rabbits or mice with recombinant proteins or synthetic peptides of the proteins of interest and appying the anti-sera in your studies. Producing the recombinant proteins or synthetic peptides would require knowledge of the viral genome to determine the genes encoding for the antigens of interest. Laser scanning confocal microscopy or fluorescent microscopy would be required for the analysis of fluorescently labelled secondary antibodies. I hope this might be useful. 

In addition to what has been suggested by Sean, you may go for PCR detection of viral genes - specially the coat protein ones -I find that to be quite easy.

ELISA is the simple and confirmatory studies for virus diagnosis in absence of  Transmission Electron Microscopy. Even though you dont have TEM facility, you can send the sample to the National Institutes and get the electron micrograph pictures. Also you can check for amplification of coat protein of different primers available or try with Universal primers. Transmission studies on Nicotiana benthamiana and also members of same family of crops can also be carried out. Rolling Circle Amplification studies for gemini virus may also help you out.

Dear Chetan, your question is quite vast... Viruses are really fun and you can do so many things with them!! Of course there are all the biological assays (host range, virulence analyzes, characterization of virus cycle, subcellular localization during infection...) but what I understood is that you are more interested in in vitro analyzes.. So then, you can work on protein structures (cristallography, RMN,..), enzymology, characterization of the interactions between viral proteins and host factors (Ka and Kd measurements, interaction domains,..) etc... You can even use viruses in nanotechnologies as a biophysical support for enzymatic cascade... Have fun!