The start of the MMR controversy was born when Wakefield argued that that measles/MMR vaccination was linked to the development of autism in some children, and that there was a persistence of measles virus in autism. Afzal et al have recently published a paper which undermines the virological case for a link between MMR and austism:
The alleged link between measles/MMR vaccination and development of autism in children has been controversial for a number of years. The laboratory studies which reported the persistence of measles virus in autism cases were either carried out by a single study group or through collaborations where all investigators used clinical samples from a single laboratory source.
The findings have not been verified independently by any other study groups using assays reported to detect measles virus in autism cases with gut related complications.
This study was designed to replicate the methodology applied to gut biopsies by Uhlmannet al.  to blood samples of children with confirmed autism diagnosis and MMR vaccination histories.
None of the nucleic acid extracts of leukocytes examined produced measles virus specificDNA fragments either in the realtime QRT-PCR or in conventional RT-PCR-nested PCR amplification procedures.
Translation: measles virus does not persist in autistic children and virology does not support a link between MMR vaccine and autism.