Thema der Dissertation:
Computational Surveillance and Molecular Analysis of Lassa Virus in Response to Increased Prevalence in Humans and Animals Thema der Disputation:
Genome Assembly of Divergent and Segmented Viruses Using Lassa virus as a Model
Computational Surveillance and Molecular Analysis of Lassa Virus in Response to Increased Prevalence in Humans and Animals Thema der Disputation:
Genome Assembly of Divergent and Segmented Viruses Using Lassa virus as a Model
Abstract: The genome serves as the molecular fingerprint of an organism. In pathogens, genome sequencing can provide critical information about strain identity, evolutionary origin, transmission dynamics, and potential drug resistance. However, sequencing highly divergent pathogens such as Lassa virus presents substantial technical and computational challenges. Lassa virus comprises multiple lineages, with nucleotide divergence exceeding 25% between some strains. This genetic diversity has been shown to affect diagnostic sensitivity when assays developed against one lineage are applied to another. Similar challenges arise in targeted sequencing approaches, where primer mismatch due to lineage divergence may lead to amplification failure, particularly in previously uncharacterized variants. To address these limitations, unbiased metagenomic sequencing is commonly used for Lassa virus. While this approach reduces dependence on lineage-specific primers, it transfers the challenge to genome assembly and downstream bioinformatic analysis. Assembly becomes particularly difficult due to the virus’s high sequence divergence, segmented genome structure, and low abundance within host-derived sequencing data.This presentation will examine genome assembly strategies for divergent RNA viruses through the application of the Broad Institute viral-ngs pipeline. The talk will focus on how metagenomic sequencing, de novo assembly, and reference-guided refinement have been integrated to successfully reconstruct Lassa virus genomes across multiple published studies.
Time & Location
Jun 25, 2026 | 10:00 AM
Seminarraum 046
(Fachbereich Mathematik und Informatik, Takustr. 9, 14195 Berlin)
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WebEx