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

Abstract

JC virus (JCV) genotyping is a novel method of tracing human migrations.

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

“…According to the phylogenetic tree (Figure 2), the SC isolates worldwide can be classified into several clusters, previously designated SC-a to -f and SC-x (Saruwatari et al, 2002b;Takasaka et al, 2004), with BPs ranging from 46% to 100%. Although the BP for SC-f was not high (63%), we found that all SC-f isolates examined carried a unique pentanucleotide deletion in the transcriptional control region (Saruwatari et al, 2002b), whereas this deletion was absent in all other subgroups (Table 1).…”

“…Based on this SNP, we subclassified a large number of SC isolates worldwide into SC-f or non-SC-f subgroups (Table 3). The findings shown in Table 3 can be summarized as follows: (1) SC-f isolates predominated in all regions of China, with only the occasional occurrence of non-SC-f; (2) non-SC-f isolates predominated in one region of Thailand and most regions of Myanmar, with the exception of Peinnebeen, where isolates classified as SC-f were mainly detected; (3) SC-f isolates predominated in two regions of Vietnam and in single regions in Malaysia and Indonesia; (4) SC-f isolates predominated in three islands in the Philippines, although non-SC-f isolates occurred at lower but significant rates (P < 0.01 vs. Hanoi and Danang; Fisher's exact test) in two islands (Luzon and Cebu) of the Philippines, these were previously identified as a unique subgroup (SC-x) of the SC genotype (Miranda et al, 2003;Takasaka et al, 2004); (5) only SC-f isolates occurred in regions (e.g. southern Africa and southern Japan) remote from the areas where SC is most common (i.e.…”

“…We determined the complete sequences of 15 clones containing full-length JCPyV genomes obtained in this and a previous study (Guo et al, 1996). The SC sequences thus obtained, those recently reported but left unclassified into subgroups (Cui et al, 2004;Venter et al, 2004), and those subclassified previously (Saruwatari et al, 2002b;Takasaka et al, 2004) were all subjected to a phylogenetic analysis. Furthermore, we performed a single nucleotide polymorphism (SNP) analysis of 275 reported partial SC DNA sequences worldwide.…”

“…Using phylogenetic analysis based on complete viral DNA sequences, Saruwatari et al (2002b) subclassified many SC isolates in Myanmar, together with a few in other countries, into six subgroups, SC-a to -f. Most subgroups (SC-a to -e) contained isolates in Myanmar, but one (SC-f) included isolates in various regions of southeastern Asia and southern China. Using complete viral DNA sequences, Takasaka et al (2004) analyzed phylogenetic relationships among JCPyV isolates in the Philippines and in other geographic regions. While a novel SC subgroup (named SC-x) was identified among modern Filipinos based on this analysis, it was also confirmed that most Filipino isolates belong to the SC-f subgroup.…”

“…To extend the findings of Saruwatari et al (2002b) and Takasaka et al (2004), we performed a profound phylogenetic analysis of many SC isolates recovered at various sites worldwide. We determined the complete sequences of 15 clones containing full-length JCPyV genomes obtained in this and a previous study (Guo et al, 1996).…”