viral metagenomics study of vaccine sample

Metagenomics and microarray technologies were used to examine eight live attenuated viral vaccines. Viral nucleic acids in trivalent oral poliovirus (OPV), rubella (Meruvax), measles (Attenuvax), yellow fever (YF Vax), human herpes 3 (Varivax), rotavirus (Rotarix and Rotateq) and multivalent Measles/Mumps/Rubella(MMR-II) live vaccines were randomly amplified and then pyrosequenced. Over half a million pyrosequence reads were generated covering from 20 to 99% of the attenuated viral genomes at a depth of up to 8000 reads per nucleotides. Mutations and minority variants were detected relative to previously reported vaccine strains in OPV, mumps virus, and varicella-zoster virus. The anticipated detection of endogeneous retroviral sequences from the producer avian or primate cells was confirmed. Avian leucosis virus (ALV), previously shown to be non-infectious for humans, was present as RNA in viral particles while simian retrovirus (SRV) was present as genetically defective DNA. An orally administered vaccine contained porcine circovirus-1, a highly prevalent pig virus, which has not been shown to be infectious in human. Hybridization of vaccine nucleic acids to a pan microbial microarray confirmed the presence of endogenous retroviral and PCV1 nucleic acids. Deep sequencing and microarrays can therefore detect attenuated virus sequence changes, minority variants, and adventitious viruses and help maintain the current safety record of live attenuated viral vaccines.