does someone knows why the counterparts of virus A infectious clone swapped by same region of virus B cDNA fragments, virus A plasmid changed to low-copy?
Some viral cDNA fragment affects plasmid or E coli survival. Some viral fragment even is regarded as non-clonable, especially in high copy number plasmid. These fragments includes special second RNA structure or membrane proteins.
E coli will choose the low copy ones so that E coli can survive.