In bacterial sample ,ice crystal formed so damaged it's cell membrane.but in virus sample no cytoplasam ,no other organelles then why freeze thaw cycle affects virus
Depends on the virus. For example, lentivirus is membrane bound (the membrane being the cell membrane as the virus buds off) whereas adeno-associated virus is only enclosed by the protein capsid.
Regardless, freeze-thawing damages proteins (e.g.Article Effect of freezing and thawing rates on denaturation of prot...
) which is why, for example, freeze-thawing antibodies for immunohistochemistry etc. should be avoided
growing ice crystals damage not only cell mebranes, but also, like Simon N Waddington said, proteins and nearly all bio-molecules. They are more or less like growing needles, penetrating everything in their way (inside or outside of a cell or bio particle, like a virus). So it is very likely that growing ice needles penetrate the virus capsule and DNA/RNA.
Another factor to consider is pH changes during the freezing process - ever notice how samples in tissue culture medium change colour at -80? The indicator dye is telling you something... Viruses that use low pH in the endosomal pathway to trigger fusion can have their fusion proteins irreversibly and prematurely flipped into the wrong conformation by this.
Simply buffering your samples with a relatively pH-insensitive buffer (e.g. hepes) can help avoid this.