Five complete genomes of JC virus Type 3 from Africans and African Americans

• Published in: Archives of virology Vol. 142; no. 4; pp. 637 - 655
• Main Authors: Agostini, H. T, Ryschkewitsch, C. F, Brubaker, G. R, Shao, J, Stoner, G. L
• Format: Journal Article
• Language: English
• Published: Wien Springer-Verlag 01.01.1997; New York, NY Springer; Springer Nature B.V
• Subjects: African Americans; Africans; Amino Acid Sequence; antigens; Base Sequence; Biological and medical sciences; Black or African American; Black People; consensus sequence; DNA, Viral; Fundamental and applied biological sciences. Psychology; Genes; Genetics; genome; Genome, Viral; Genomes; genotype; Humans; JC polyomavirus; JC Virus - genetics; JC Virus - isolation & purification; Male; Microbiology; Molecular Sequence Data; patients; polymerase chain reaction; Regulatory Sequences, Nucleic Acid; Replication Origin - genetics; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Species Specificity; Tanzania; United States; urine; Viral Proteins - chemistry; Viral Proteins - genetics; Virology; zinc finger motif; Tanzania; East Africa; Africa; United States; Human; Nervous system diseases; Genome organization; Genetic variability; Nucleotide sequence; Polyomavirus; Papovaviridae; Cerebral disorder; Inflammatory disease; Progressive multifocal leukoencephalopathy; Infection; Virus; JC virus; Viral disease; DNA; Central nervous system disease; Molecular epidemiology; Genome; Clinical isolate; Structural analysis; Slow virus
• ISSN: 0304-8608; 1432-8798
• DOI: 10.1007/s007050050108

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.