title: Five complete genomes of JC virus type 3 from Africans and African Americans.
abstract: The central demyelinating disease progressive multifocal leukoencephalopathy (PML) is caused by the human polyomavirus JC virus (JCV). JCV evolved as geographically based genotypes of which Type 3 is an African variant first characterized in HIV-1 positive patients from Tanzania. This study reports the complete sequence of five JCV Type 3 strains. The entire JCV genome was PCR amplified from urine specimens of three African and two African-American individuals. The African consensus sequence was compared to the Type 1 and Type 2 prototype strains, JCV (Mad-1) and JCV(GS/B), respectively. Type 3 differed in 2.2% of its coding region genome from JCV (Mad-1) and in 1.3% from JCV(GS/B). Within the coding region the sequence variation among the three types was higher in the capsid protein VP1 and in the regulatory protein large T antigen than in the agnoprotein or in VP2/3. Notable Type 3-specific changes were located at sites adjacent to the zinc finger motif and near the major donor and acceptor splice junctions of large T antigen. Four of the five urinary Type 3 strains had an unrearranged, archetypal regulatory region. African strain #309 showed a 10-bp deletion at a location similar to that previously described for #307 from Tanzania. The African-American Type 3 strain #312 was closely related to the African consensus sequence. The complete genome of a urinary JCV strain from another African-American male, previously reported as a possible Type 5, showed a sequence difference of only 0.52% from the Tanzanian consensus and has been reclassified as a subtype of Type 3.
authors.affiliation: Laboratory of Experimental Neuropathology, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA.
authors.forename: H T
authors.initials: HT
authors.lastname: Agostini
authors.forename: C F
authors.initials: CF
authors.lastname: Ryschkewitsch
authors.forename: G R
authors.initials: GR
authors.lastname: Brubaker
authors.forename: J
authors.initials: J
authors.lastname: Shao
authors.forename: G I
authors.initials: GI
authors.lastname: Stoner
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D044383:Black People; D004279:DNA, Viral; D016679:Genome, Viral; D006801:Humans; D007577:JC Virus / Q000235:genetics* / Q000302:isolation & purification; D008297:Male; D008969:Molecular Sequence Data; D012045:Regulatory Sequences, Nucleic Acid; D018741:Replication Origin / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013636:Tanzania; D014481:United States; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics; D001741:Black or African American
chemical_list: D004279:DNA, Viral; D014764:Viral Proteins