Asian domains of four major genotypes of JC virus, Af2, B1-b, CY and SC

Abstract

JC virus (JCV) strains worldwide can be classified into various genotypes based on DNA sequence variations. To define the domains of the four major JCV genotypes in Asia, we collected urine samples at six unstudied sites: three in southeastern Asia, two in the central highlands and one in central Asia. DNA was extracted from urine samples, and used to amplify a 610-bp region of the viral genome. For each geographical site, we determined 16 to 31 sequences, from which a phylogenetic tree was constructed to unambiguously classify detected JCV isolates into distinct genotypes. From JCV genotype profiles at the sites studied here and elsewhere, the following conclusions were drawn. Although Af2 is the major genotype in Africa, this genotype also occurs in western and central Asia. B1-b mainly occurs in western and central Asia, including the central highlands. CY occurs in northeastern Asia with the southern boundary between China and southeast Asian countries. Although SC predominates in southeastern Asia, it also occurs in northern and central Asia at lower frequencies. In addition, a few minor JCV genotypes (B1-a, B2 and B3) occur at many sites. We discuss here the anthropological and medical significance of the present findings.

Peopling of Myanmar as Demonstrated by Genotyping of Urinary JC Virus DNA.

“…JCV isolates in the world were classified into more than 10 groups (designated as subtypes) according to the results of phylogenetic analysis of a 610-bp region (IG region) of the viral genome Guo et al, 1998). Each JCV subtype occupies a unique domain in the Old World Guo et al, 1998;Saruwatari et al, 2002). The evolutionary relationships among JCV sub typeswere recently examined using the whole-genome ap proachwith which a highly reliable phylogeny of JCV isolates can be reconstructed (Jobes et al, 1998;Hatwell and Sharp, 2000).…”

Human dispersals based on a global phylogenetic analysis of JC virus isolates of genotype B1-b

“…The populations carrying B1-b1 or B1-b2 would have intermixed with populations carrying distinct genotypes of JCV (the latter populations might have already colonized there or migrated there afterwards). For example, populations carrying B1-b1 intermixed with those carrying CY in northeast Asia and the Central highlands (Sugimoto, 1999;Guo et al, 2001;Saruwatari et al, 2002a), with those carrying various subgroups of SC in Myanmar (Saruwatari et al, 2002a, b), and with those carrying Af2 in Uzbekistan (Saruwatari et al, 2002a, b). DNA sequences.…”

“…4 (1) references for isolates, (2) references for complete JCV DNA clones, (3) references for sequences. A, Sugimoto et al, 2002b;B, Sugimoto, 1999;C, Guo et al, 1998;D, Cui et al, 2004;E, Saruwatari et al, 2002a;F, Saruwatari et al, 2002b;G, Sugimoto et al, 1997;; -, this study; na, not applicable.…”

“…Using a PCR that amplifies the IG region (see Materials and Methods), we detected JCV DNA from 17 (34%), 16 (40%), and 11 (31%) urine samples collected at Laigu, Rakhine, and Peradeniya, respectively. The amplified IG regions were sequenced and the resultant sequences were used to reconstruct an NJ phylogenetic tree as described previously (Saruwatari et al, 2002a). According to the tree (not shown), JCV isolates in urine samples were classified as belonging to distinct genotypes (Table 2).…”

JC virus genotype profile in the Mamanwa, a Philippine Negrito tribe, and implications for its population history

“…Port Louis, Mauritius UZ-13 Tashkent, Uzbekistan #233 New Britain #234 Guam #801 to #804 Papua New Guinea G1 Illertissen, Germany a Kunitake et al (1995), Kitamura et al (1997), Sugimoto et al (1997), Chang et al (1999), Jobes et al (2001), Saruwatari et al (2002a), and Miranda et al (2003). Figure 1.…”