ArticleNPJ science of food2025
Whole genome sequencing of hepatitis A virus: adapting Illumina protocols for foodborne investigation.
Article in NPJ science of food, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
High-throughput sequencing-based whole-genome sequencing (WGS) is highly effective for identifying viral pathogens in microbial research. However, applying WGS directly to foodborne viruses remains challenging because food matrices contain PCR inhibitors and viral titers are typically much lower than those found in clinical specimens. This study aimed to develop a WGS method for analyzing the hepatitis A virus (HAV) genome in clams using the Illumina MiSeq platform. To enhance the HAV WGS method, we applied four approaches to HAV-positive clam field samples: size-exclusion chromatography for sample preparation, a specialized RNA extraction method, optimized cDNA synthesis, and the selection of DNA polymerase. Nine complete HAV genomes were obtained from clams. The obtained HAV genomes and their genetic characteristics were then compared based on phylogeny. Before optimization, only four clam samples yielded detectable amplification; however, following optimization, two additional samples became amplifiable, resulting in six samples suitable for downstream WGS analysis. The developed WGS method was able to sequence low contamination levels of 2.91-3.61 log
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