Intramolecular recombination involves the exchange of nucleic acid sequences between different but usually closely related viruses during viral replication (Fig. 4-1 A) It occurs with all dsDNA viruses, presumably because of staand switching by the viral DNA polymerase Among RNA viruses, intramolecular recombination has been demonstrated for picornaviruses, coronaviruses, and togaviruses. It may be more widespread, because defection has relied on the recovery of viable recombinants, the use of the polymerase chain reaction following reverse transcription may overcome this lack of sensitivity. For some viruses recombination can also occur between viral and cellular RNA, just as it can between viral and cellular DNA.
There is evidence that western equine encephalitis virus arose as a result of intramolecular recombination between a SindbisTike virus and eastern equine encephalitis virus. In experimental situations, intramolecular recombination may also occur between viruses belonging to different families, the best example is between SV40 (a papovavirus) and adenoviruses. Both SV40 and adenovirus DNAs occasionally become integrated into cellular DNA, so it is perhaps not surprising to find that when rhesus monkey cells that harbor a persistent SV40 infection are superinfected with an adenovirus, not only does complementation occur, the SV40 acting as a helper in an otherwise abortive adenovirus infection, but recombination occurs between SV40 DNA and adenovirus DNA to yield hybrid (recombinant) DNA which is packaged into adenovirus capsids. Integration of viral DNA into cellular DNA by intramolecular recombination occurs in cells transformed by adenoviruses, hepad-naviruses, and polyomaviruses, but not always in cells transformed by papillomaviruses or certain herpesviruses, in which transformation may occur although the viral DNA usually remains episom.il (see Chapter 11).
Unlike other RNA viruses, retroviruses have no replicating pool of viral
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