Evolution of Human Polyomavirus JC: Implications for the Population History of Humans

Abstract

The polyomavirus JC virus (JCV), the etiological agent of progressive multifocal leukoencephalopathy, is ubiquitous in the human population, infecting children asymptomatically, then persisting in the kidney. The main mode of transmission of JCV is from parents to children through long-term cohabitation. Twelve JCV subtypes that occupy unique domains in Europe, Africa, and Asia have been identified. Here, we attempted to elucidate the evolutionary relationships among JCV strains worldwide using the whole-genome approach with which a highly reliable phylogeny of JCV strains can be reconstructed. Sixty-five complete JCV DNA sequences, derived from various geographical regions and belonging to 11 of the 12 known subtypes, were subjected to phylogenetic analysis using three independent methods: the neighbor-joining, maximum parsimony, and maximum likelihood methods. The trees obtained with these methods consistently indicated that ancestral JCVs were divided into three superclusters, designated as Types A, B, and C. A split in Type A generated two subtypes, EU-a and -b, mainly containing European and Mediterranean strains. The first split in Type B generated Af2 (the major African subtype). Subsequent splits in Type B generated B1-c (a minor European subtype) and all seven Asian subtypes (B1-a, -b, -d, B2, MY, CY, and SC). Type C generated a single subtype (Af1), consisting of strains derived from western Africa. While the present findings provided a basis on which to classify JCV into types or subtypes, they have several implications for the divergence and migration of human populations.

The Pacific lineage (2E) of JC polyomavirus is prevalent in Sumba Island, Eastern Indonesia

“…All amplified IG fragments were sequenced and an NJ phylogenetic tree was constructed from the sequences, together with reference IG sequences detected in East and South Asia and Oceania. The reference sequences were extracted from complete genome sequences whose lineages have been unambiguously identified (Agostini et al, 1998;Kato et al, 2000;Jobes et al, 2001;Sugimoto et al, 2002;Yanagihara et al, 2002;Saruwatari et al, 2002;Takasaka et al, 2004;Zheng et al, 2004b;Saruwatari et al, 2006;Takasaka et al, 2006;Zheng et al, 2007). According to the resultant tree (Figure 1), most sequences from SBW (SBW-1 to -4, -6 to -12) and SBK (SBK-1, -3, -6, -7, -10 to -16, -18 to -23) were found in a cluster corresponding to the 2E lineage.…”

Dispersal of southeastern Asians based on a global phylogenetic analysis of JC polyomavirus isolates of genotype SC

“…The phylogenetic tree was visualized using the TREEVIEW program. The tree was rooted using isolate CY as the outgroup, since this is a distinct genotype that is closely related to SC (Sugimoto et al, 2002). The symbols for sequences are shown in Table 1.…”

Genotypes of JC virus in Southeast Asia and the western Pacific: implications for human migrations from Asia to the Pacific

“…We constructed an NJ phylogenetic tree from 138 complete sequences, the 30 complete JCV DNA sequences determined in this study plus the 108 complete sequences reported previously. The latter included isolates representing eleven genotypes of JCV worldwide (Kato et al, 2000;Sugimoto et al 2002a), various intra-SC isolates in Myanmar and other Asian countries (Saruwatari et al, 2002a), and various isolates in the western Pacific Yanagihara et al, 2002); the origins of JCV isolates that were used in the phylogenetic analysis are shown in Table 2 and elsewhere . On the resultant tree (Figure 1), we confirmed the first split of the ancestral JCV into three superclusters, Type-A, -B, and -C .…”

“…the Philippines), and the western Pacific. Complete DNA sequences of many JCV isolates in the Philippines were determined in this study and used in the phylogenetic analysis that included previously reported complete JCV DNA sequences of various Asian isolates (Kato et al, 2000;Saruwatari et al, 2002a;Sugimoto et al, 2002a) (some additional Asian isolates were sequenced in this study) and western Pacific isolates Yanagihara et al, 2002). The results obtained were discussed in the context of human dispersals in the western Pacific.…”