A novel JC virus variant found in the Highlands of Papua New Guinea has a 21-base pair deletion in the agnoprotein gene

Objectives: This paper describes a unique JC virus (JCV) variant recovered from the Highlands of Papua New Guinea that contains an inframe 21-bp delet ion in the agnoprotein gene. We characterize the mutation and suggest possi ble roles for the deletion in JCV evolution. Study Design/Methods: JCV DNA was extracted from urine and polymerase chain reaction (PCR) amplified using whole genome primers. PCR products were clo ned, and multiple clones were sequenced. The JCV agnogene was PCR amplified to verify the presence of the agnogene deletion. Results: This mutation creates a 21-bp deletion near the 3' end, which alte rs the predicted secondary structure of the messenger RNA and changes local codon usage at the 3' end of the agnogene. Protein secondary structure pre dictions suggest the deleted portion of the agnoprotein may be a flexible s urface feature. Conclusions: We describe the first stable coding region deletion in JCV tha t presumably signifies a single evolutionary event that led to the split fr om other Highlands viral groups and occurred well after the human expansion s that led to the peopling of the Southwest Pacific. (C) Lippinott Williams & Wilkins, Inc.