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Evolution of human Polyomavirus JC: implications for the population history of humans
Chie Sugimoto1, Masami Hasegawa, Atsushi Kato
1Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
Insights
JC virus (JCV) subtypes show distinct evolutionary paths, forming three main superclusters (A, B, C) with specific geographical distributions. This whole-genome analysis clarifies JCV evolution and human population migration patterns.
Area of Science:
- Virology
- Human Genetics
- Evolutionary Biology
Background:
- JC virus (JCV) is a ubiquitous human polyomavirus, causing progressive multifocal leukoencephalopathy.
- JCV is transmitted from parents to children and persists in the kidney, with 12 known subtypes occupying distinct geographical domains.
- Understanding JCV evolutionary relationships is crucial for tracing human migration and population dynamics.
Purpose of the Study:
- To elucidate the evolutionary relationships among global JC virus (JCV) strains.
- To reconstruct a reliable phylogeny of JCV strains using a whole-genome approach.
- To investigate the implications of JCV evolution for human population divergence and migration.
Main Methods:
- Phylogenetic analysis of 65 complete JCV DNA sequences from diverse geographical regions and 11 subtypes.
- Utilized three independent phylogenetic methods: neighbor-joining, maximum parsimony, and maximum likelihood.
- Whole-genome sequencing and analysis for robust evolutionary reconstruction.
Main Results:
- Ancestral JCVs consistently divided into three superclusters: Types A, B, and C.
- Type A split into EU-a and EU-b subtypes (European/Mediterranean).
- Type B diversified into African (Af2) and seven Asian subtypes, plus a minor European subtype (B1-c). Type C yielded the African subtype Af1.
Conclusions:
- The study provides a robust classification framework for JCV types and subtypes based on evolutionary relationships.
- Findings offer insights into the historical divergence and migration patterns of human populations.
- The whole-genome phylogenetic analysis confirms distinct evolutionary trajectories for JCV subtypes across different continents.
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.