New JC virus (JCV) genotypes from Papua New Guinea and Micronesia (Type 8 and Type 2E) and evolutionary analysis of 32 complete JCV genomes

The JC virus (JCV) is a ubiquitous human polyomavirus that frequently resid es in the kidneys of healthy individuals and is excreted in the urine of a large percentage of the population. Geographic-specific JCV variants, isola ted from urine and from brain of progressive multifocal leukoencephalopathy (PML) patients, have been grouped into seven distinct genotypes based on w hole genome analysis and by individual polymorphic nucleotides (typing site s) in the VP I coding region. Mutations in the archetypal regulatory region , sometimes consisting of deletions and/or duplications, are also useful ta xonomic characters for further characterizing and subdividing genotypes. In vestigation of JCV variation in Papua New Guinea (PNG) revealed three disti nct variants called PNG-1, PNG-2, and PNG-3. These variants exhibited consi stent coding region and regulatory region mutations. Evolutionary analysis of 32 complete JCV genomes including six new viral genomes from the western Pacific suggests that the new PNG JCV variants are closely associated with the broad group of Type 2 strains of JCV found throughout Asia, forming a monophyletic group with the Northeast Asian strains (Type 2A). Within the T ype 2 clade, however, the PNG JCV variants cluster as two distinct groups a nd are therefore described here as new JCV genotypes designated Type 2E and Type 8.