A novel JC virus variant found in the Highlands of Papua New Guinea has a 21-base pair deletion in the agnoprotein gene.
OBJECTIVE
This paper describes a unique JC virus (JCV) variant recovered from the Highlands of Papua New Guinea that contains an inframe 21-bp deletion in the agnoprotein gene. We characterize the mutation and suggest possible roles for the deletion in JCV evolution.


METHODS
JCV DNA was extracted from urine and polymerase chain reaction (PCR) amplified using whole genome primers. PCR products were cloned, 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 alters the predicted secondary structure of the messenger RNA and changes local codon usage at the 3' end of the agnogene. Protein secondary structure predictions suggest the deleted portion of the agnoprotein may be a flexible surface feature.


CONCLUSIONS
We describe the first stable coding region deletion in JCV that presumably signifies a single evolutionary event that led to the split from other Highlands viral groups and occurred well after the human expansions that led to the peopling of the Southwest Pacific.
Jobes
D V
DV
Neurotoxicology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA.
Friedlaender
J S
JS
Mgone
C S
CS
Koki
G
G
Alpers
M P
MP
Ryschkewitsch
C F
CF
Stoner
G L
GL
D001483:Base Sequence; D003062:Codon / Q000235:genetics; D004279:DNA, Viral / Q000652:urine; D004641:Emigration and Immigration; D019143:Evolution, Molecular; D014644:Genetic Variation; D006801:Humans; D007577:JC Virus / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D030361:Papillomavirus Infections / Q000821:virology*; D010219:Papua New Guinea; D016133:Polymerase Chain Reaction; D017433:Protein Structure, Secondary; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D014412:Tumor Virus Infections / Q000821:virology; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics*; D054334:Viral Regulatory and Accessory Proteins; D000086082:Viroporin Proteins
D003062:Codon; D004279:DNA, Viral; D012333:RNA, Messenger; D012367:RNA, Viral; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C042559:agnoprotein, polyomavirus; D000086082:Viroporin Proteins