Published July 20, 2023 | Version v1
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Tracking the public health hazard of foodborne Hepatitis E

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Description

Observed epidemiological dynamics in HEV disease incidence can be explained by genomic variation among predominant HEV subtypes in pigs and clinical human cases. Most of the available sequences are partial but whole genome sequences are preferred for further research, however a good whole genome sequencing procedure was not yet available. In this thesis project, we developed a protocol for optimal sample (pre)processing (enrichment) to do whole genome sequencing of the Hepatitis E virus. We developed a new HEV-probe enrichment set based on probe capture enrichment to sequence all the different HEV strains. With this new probe set we were able to generate whole-genome sequences from samples of Ct values up to 30 from different origins. 

In this project, we set up a HEV analysis method for timed phylogeny of known sequences from the NCBI. This should enable us to later apply this method to the sequences we generated ourselves. As most of the HEV sequences from NL only cover a small (493 nt) region of the viral genome, we have tested to what extent this fragment could be suitable for performing accurate diagnostics or inferring any viral population-scale processes. To do this, we started with a set of viral whole genome sequences that we had sequentially trimmed to various fragment lengths (down to 148 nt) and used each of the fragments to infer the richness and diversity of the viral sequence types, typing accuracy, and phylodynamics. By comparing the results obtained with each of the fragments we could conclude the utility of using particular genomic loci in molecular diagnostics, typing, phylogenetics and phylodynamics of HEV.

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