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

Abstract

JC virus (JCV) is a useful marker for tracing human dispersal. Four genotypes of JCV (CY, SC, B1-b, and MY) are mainly distributed in Asia. The population history of humans carrying CY, SC, or MY has been studied in some detail, but that of humans carrying B1-b remains poorly understood. The objective of this study was to gain insights into the population history of Asians carrying B1-b. A neighbor-joining phylogenetic tree was reconstructed from 26 complete B1-b DNA sequences from various regions of Asia. On the tree, the B1-b DNA sequences diverged into two clades, designated B1-b1 and B1-b2, each clustered with a high bootstrap probability. The split into B1-b1 and B1-b2 was estimated to have occurred about 20000 years ago, based on Ks values (synonymous substitutions per synonymous site) and the suggested rate of synonymous nucleotide substitutions. Comparison of the complete B1-b1 and B1-b2 sequences revealed that two single nucleotide polymorphisms (SNPs) between B1-b1 and B1-b2 occurred in a 610 bp region (the IG region) of the viral genome. Based on these SNPs, 145 B1-b isolates previously identified in the Old World were classified into B1-b1 or B1-b2. B1-b1 was widespread on the Asian continent, spreading from Northeast Siberia to West Asia. In contrast, B1-b2 was localized to part of South Asia, including South India and Sri Lanka. On the basis of the present findings, we inferred the dispersals of Asians carrying B1-b.

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.…”

Molecular epidemiology of JC polyomavirus in HIV-infected patients and healthy individuals from Iran

“…JCPyV is a member of the Polyomaviridae family infecting human in the late childhood without any symptom and then persists in the kidneys, bone marrow, and lymphoid tissues [26,27]. According to the seroepidemiological investigations, approximately 80% of human population is JCPyV seropositive while only 40% of human population excretes JCPyV in their urine [5,6].…”