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

Saruwatari, Lei; Zheng, Haiyan; Ikegaya, Hiroshi; Takasaka, Tomokazu; Guo, Jing; Kitamura, Tadaichi; Yogo, Yoshiaki; Ohno, Nobutada

doi:10.1537/ase.050629

Cited by 3 publications

(6 citation statements)

References 37 publications

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“…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.…”

Section: Resultsmentioning

confidence: 99%

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

Ikegaya

Zhong

Shimizu

et al. 2008

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Recent studies have identified a Pacific lineage (2E) of JC polyomavirus (also designated as JC virus or JCV) that occurs in both Island Southeast Asia and Oceania, but not in mainland Asia. It has been postulated that this lineage traveled with Austronesian-speaking people who are now spread throughout Island Southeast Asia and Oceania (excluding Australia and inland and southern New Guinea). However, to date, the 2E lineage has been identified in Southeast Asia only in populations of the Philippine islands. Here we report that a high incidence of the 2E lineage was detected in the people of Sumba Island, eastern Indonesia.

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Section: Resultsmentioning

confidence: 99%

“…These lineages have been detected not only in ISEA but also in continental Asia Saruwatari et al, 2006); therefore it is likely that they were transmitted to Sumba in association with relatively recent migrations of Asians from the continent. Miranda et al (2004).…”

Section: Discussionmentioning

confidence: 99%

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

Ikegaya

Zhong

Shimizu

et al. 2008

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“…The resultant complete JCV DNA clones were prepared using a QIAGEN Plasmid Mini kit (QIAGEN GmbH, Hilden, Germany). Cloned complete JCV genomes were subjected to a cycle sequencing reaction using the BigDYE Terminator Cycle Sequencing kit v. 3.1 (Applied Biosystems, Foster City, CA) and primers described previously (Saruwatari et al, 2006). Sequencing was carried out with an automated DNA sequencer (3130 Genetic Analyzer, Applied Biosystems).…”

Section: Dna Analysismentioning

confidence: 99%

“…JCV strains around the world can be classified into more than ten major genotypes, with each genotype occupying a unique geographical domain (Sugimoto et al, 1997;Cui et al, 2004). Hence, JCV genotyping has provided new insights into the origins of various ethnic groups throughout the world (Miranda et al, 2004;Yogo et al, 2004;Zheng et al, 2004Zheng et al, , 2005aIkegaya et al, 2005;Saruwatari et al, 2006;Takasaka et al, 2006a, b).…”

Section: Introductionmentioning

confidence: 99%

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

Zheng

Takasaka

Ohno

et al. 2007

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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.

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Comparison of the distribution patterns of BK polyomavirus lineages among China, Korea and Japan: Implications for human migrations in northeast Asia

Zhong

Jeong

Ikegaya

et al. 2009

Microbiology and Immunology

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BKV is widespread among humans, infecting children asymptomatically and then persisting in renal tissue. Based on the serological or phylogenetic method, BKV isolates worldwide are classified into four subtypes (I-IV), with subtypes I and IV further divided into several genetically-distinct subgroups. Since, similarly to JCV, a close relationship exists between BKV lineages and human populations, BKV should be useful as a marker to trace human migrations. To elucidate ancient human migrations in northeast Asia, urine samples were collected from immunocompetent elderly patients in Shanghai, China; Anyang, South Korea; and various locations in Japan. Partial and complete BKV genomes from these samples were amplified and sequenced using PCR, and the determined sequences were classified into subtypes and subgroups by phylogenetic and SNP analyses. In addition, based on an SNP analysis, the major subtype I subgroup (I/c) was classified into two subdivisions, I/c/Ch and I/c/KJ. The distribution patterns of BKV subgroups and subdivisions among the three regions were compared. Some aspects of the subgroup and subdivision distribution were more similar between Korea and Japan, but others were more similar between China and Korea or between China and Japan. Based on these findings, we inferred various northeast Asian migrations. Most of the JCV-based inferences of northeastern Asian migrations were consistent with those based on BKV, but the previously suggested migration route from the Asian continent to the Japanese archipelago seemed to need revision.

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

Cited by 3 publications

References 37 publications

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

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

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

Comparison of the distribution patterns of BK polyomavirus lineages among China, Korea and Japan: Implications for human migrations in northeast Asia

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