Using HSV-1 genome phylogenetics to track past human migrations
Aaron W Kolb1, Cécile Ané, Curtis R Brandt
1Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
Plos One
|October 23, 2013
Summary
Herpes Simplex Virus type 1 (HSV-1) genomic analysis reveals six clades mirroring human migration patterns. This research suggests HSV-1 can serve as a biomarker for studying human population movements.
Area of Science:
- Genomics
- Virology
- Human Evolutionary Studies
Background:
- Herpes Simplex Virus type 1 (HSV-1) is a ubiquitous human pathogen.
- Previous phylogenetic studies suggested a three-clade structure for HSV-1.
- Understanding HSV-1 evolution can provide insights into human history.
Purpose of the Study:
- To investigate the phylogenetic relationships of globally derived HSV-1 genomic sequences.
- To identify evidence of recombination within HSV-1 genomes.
- To correlate HSV-1 genetic diversity with human migration patterns.
Main Methods:
- Comparative analysis of 31 complete/nearly complete HSV-1 genomes.
- Sequence retrieval from NCBI and alignment using Clustal W.
- Phylogenetic tree generation (maximum likelihood) and network analysis.
Main Results:
- A six-clade phylogenetic structure for HSV-1 was identified, correlating with human migration routes.
- East African-derived viruses exhibited the highest genetic diversity, forming four clades.
- East Asian and European/North American viruses formed distinct clades; recombination did not significantly alter the clade structure.
Conclusions:
- The study expands the known HSV-1 phylogenetic structure from three to at least six clades.
- HSV-1 clades reflect global human migration patterns, indicating co-evolution.
- HSV-1 sequencing can be a valuable tool for studying human population structure and migration history.
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