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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
Published on: March 11, 2020
Genetic diversity of Usutu virus
Simone Peletto1, Alessandra Lo Presti, Paola Modesto
1Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'osta, Turin, Italy.
The New Microbiologica
|June 19, 2012
Summary
Usutu virus, a mosquito-borne pathogen, shows higher genetic diversity in Europe than anticipated. Phylogenetic analysis suggests multiple introductions and distinct viral lineages circulating across the continent.
Area of Science:
- Virology
- Molecular Biology
- Epidemiology
Background:
- Usutu virus (USUV) is a mosquito-borne flavivirus first identified in South Africa.
- The virus has recently emerged in Europe, with initial detection outside Africa in Austria.
- Understanding the genetic diversity and evolutionary dynamics of circulating USUV strains in Europe is crucial for public health surveillance.
Purpose of the Study:
- To conduct a comprehensive phylogenetic analysis of Usutu virus strains circulating in Europe.
- To investigate the genetic diversity and evolutionary patterns of Usutu virus based on E and NS5 gene sequences.
- To identify potential sources of Usutu virus introduction and spread within Europe.
Main Methods:
- Phylogenetic analysis was performed on Usutu virus strains.
- Target genes for analysis included the E (Envelope) and NS5 (Non-structural protein 5) genes.
- Selective pressure analysis was conducted on the E and NS5 proteins.
Main Results:
- Phylogenetic analysis of the NS5 gene revealed two major clades, with Italian sequences belonging to one clade.
- The E gene tree showed all sequences within a single main clade, but Austrian sequences formed two distinct clusters.
- Analysis identified sites under negative selective pressure in both E and NS5 proteins, indicating conserved regions.
Conclusions:
- Usutu virus circulating in Europe exhibits greater genetic diversity than previously assumed.
- The findings suggest that Usutu virus introductions into Europe may have occurred from multiple independent sources.
- The observed genetic structure implies complex transmission dynamics and the presence of distinct viral lineages across European regions.
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